Resonance Assignment/Abacus: Difference between revisions

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<div style="margin: 12pt 0cm 3pt;">'''<font size="6">&nbsp;</font>'''</div>
#[[Introduction to ABACUS]]
'''&lt;span style="font-size: 16pt;" /&gt;'''
#[[FMCGUI objects]]  
<div style="margin: 12pt 0cm 3pt;">'''<font size="6"><span><font size="5">INTRODUCTION TO ABACUS</font></span></font>'''</div><div align="left" style="line-height: 12pt;">&nbsp;</div><div style="text-indent: 36pt;"><span style="font-size: 11pt; color: black;">ABACUS (''A''pplied ''BACUS'') is a novel approach for protein structure determination that has been applied successfully for more than 20 NESG targets. ABACUS is characterized by use of BACUS, a procedure for automated probabilistic interpretation of NOESY spectra in terms of unassigned proton chemical shifts based on the known information on "connectivity" between proton resonances. BACUS is used in both the resonance assignment and structure calculation steps. The</span><span style="font-size: 11pt;"> ABACUS<span style="color: black;"> is distinguished from conventional approaches to NMR structure determination mostly by its resonance assignment strategy (see Fig.1.1A). </span></span></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div>
#[[FMCGUI commands]]  
{| width="666" cellspacing="0" cellpadding="0" border="0" style="width: 499.75pt; border-collapse: collapse;" class="FCK__ShowTableBorders"
#FMCGUI Data Formats
|- style="height: 269.1pt;"
#*[[Protein Sequence format]]  
| width="395" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 296.55pt; height: 269.1pt; background-color: transparent;" | <div>&lt;span /&gt;</div>
#*[[Peak Lists format]]  
| width="271" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 203.2pt; height: 269.1pt; background-color: transparent;" | <div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;</span></div><div>'''&nbsp;'''</div><div>'''<span style="font-size: 11pt;">Figure &nbsp;1.1. </span>'''<span><span style="font-size: 11pt;">'''A'''.(''on the left'') Flowchart of resonance assignmnent by ABACUS''.''</span></span></div><div>'''<span style="font-size: 11pt;">B</span>'''<span>''<span style="font-size: 11pt;">. (on the &nbsp;top)</span>''</span><span><span style="font-size: 11pt;">Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span></span></span></div>
#*[[Spin systems format]]  
|}
#FMCGUI HOW-TOs  
<div>'''<sup><span style="font-size: 11pt;">1)</span></sup>'''<span style="font-size: 11pt;">Lemak A., Steren, C., Arrowsmith, C.H. and Llinás, M. (2008) ''J. Biomol. NMR'', 41, 29-41.''' <sup>2)</sup> '''Grishaev, A., Steren, C.A., Wu, B., Pineda-Lucena, A., Arrowsmith, C. and Llinás, M. (2005) ''Proteins'', 61,36-43.''' &nbsp;<sup>3)</sup>'''Grishaev, A. and Llinás, M. (2004) ''J. Biomol. NMR'', 28, 1-10</span><span style="font-size: 10pt;">.</span></div><div>&nbsp;</div><div>&nbsp;</div><div><span style="font-size: 11pt;">Some features /advantages of the ABACUS protocol:</span></div><div style="margin: 0cm 0cm 0pt 18pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">It does not rely on sequential connectivities from less sensitive experiments such as HNCACB indispensable for most traditional sequential assignment procedures</span><span style="font-size: 11pt;">;</span></div><div style="margin: 0cm 0cm 0pt 18pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">Inter-residue sequential connectivities are established mainly from NOE data, which saves time at a later stage in “troubleshooting” NOE and resonance assignments.;</span></div><div style="margin: 0cm 0cm 0pt 18pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">Probabilistic nature of the ABACUS procedure provides measure of reliability of assignments, and therefore one</span><span style="font-size: 11pt;"> can obtain a partial, yet highly reliable assignment (even when the NMR data are sub-optimal) with the knowledge of</span><span style="font-size: 11pt;"> where to focus manual intervention</span>;</div><div style="margin: 0cm 0cm 0pt 18pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">It can make use of&nbsp;partial spin-systems; </span></div><div style="margin: 0cm 0cm 0pt 18pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">It can efficiently identify manual errors in the input peak lists;</span></div><div>&nbsp;</div><div>&nbsp;</div>
#*[[Spin systems identification]]  
<font size="4"><span>NMR spectra required for ABACUS</span></font>
#*[[Sequence specific assignment of PB fragments]]  
 
#*[[Structure calculation setup and analysis]]  
&nbsp;
#*[[Water refinement setup and analysis]]
<div><span style="font-size: 11pt;">The spectra typically needed for ABACUS approach are most conveniently separated into 3 groups: NH-rooted, the CH-rooted and the aromatic (also CH-rooted). &nbsp;Table 1 shows the optimal set of NMR spectra. This, of course, is neither an exclusive or exhaustive list. For example, a simultaneous CN-NOESY could be recorded instead of three different ones listed in the table. In case there are very few aromatic residues in a protein, to collect only one aromatic spectrum, namely aromatic NOESY, could be enough for assignment of aromatic resonances. </span></div><div>&nbsp;</div><div>'''Table 1.''' ABACUS optimal set of experiments </div><div>&nbsp;</div>
{| cellspacing="0" cellpadding="0" border="0" style="border-collapse: collapse;" class="FCK__ShowTableBorders"
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| width="197" valign="top" style="border-style: none none solid; border-color: rgb(212, 208, 200) rgb(212, 208, 200) windowtext; border-width: medium medium 1pt; padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>'''NH-rooted'''</div>
| width="197" valign="top" style="border-style: none none solid; border-color: rgb(212, 208, 200) rgb(212, 208, 200) windowtext; border-width: medium medium 1pt; padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>'''CH-rooted'''</div>
| width="197" valign="top" style="border-style: none none solid; border-color: rgb(212, 208, 200) rgb(212, 208, 200) windowtext; border-width: medium medium 1pt; padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>'''Aromatic'''</div>
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| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div><sup>15</sup>N-HSQC</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div><sup>13</sup>C-CT-HSQC</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div><sup>13</sup>C-HSQC-aro</div>
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| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>HNCO</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div><sup>13</sup>C-HSQC</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>H(C)CH-TOCSY-aro</div>
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| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>HNCA</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>H(C)CH-TOCSY</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>(H)CCH-TOCSY-aro</div>
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| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>CBCA(CO)NH</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>(H)CCH-TOCSY</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div><sup>13</sup>C-NOESY-HSQC-aro</div>
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| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>HBHA(CO)NH</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div><sup>13</sup>C-NOESY-HSQC</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>&nbsp;</div>
|-
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div><sup>15</sup>N-NOESY-HSQC</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>&nbsp;</div>
| width="197" valign="top" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 147.6pt; background-color: transparent;" | <div>&nbsp;</div>
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| width="590" valign="top" colspan="3" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 442.8pt; background-color: transparent;" | <div>''CCCONH-TOCSY (optional)''</div>
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| width="590" valign="top" colspan="3" style="border: medium none rgb(212, 208, 200); padding: 0cm 5.4pt; width: 442.8pt; background-color: transparent;" | <div>''H(CCCO)NH-TOCSY (optional)''</div>
|}
<div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'<font size="4">Spin-system identification strategy</font></div><div>'''''&nbsp;'''''</div><div><span style="font-size: 11pt; color: black;">The resonance assignment procedure starts from grouping resonances in spin systems (PB-, or peptide bond, fragments) comprising correlated resonances from the side chain of residue i and the NH resonances of residue i+1 (see Figure1.1B). The uncompleted HN-rooted PB spin-systems, which include resonances of&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;atoms only, are called bPB-fragments in this manual.</span></div><div><span style="font-size: 11pt; color: black;">Spin-system identification in ABACUS approach consists of 3 main steps.</span></div><div><span style="font-size: 11pt; color: black;">1. On the first step, bPB-fragments are collected from high sensitivity NMR correlation experiments (such as HNCO, CBCA(CO)NH, and HBHA(CO)NH) that transfer magnetization via the intervening peptide bond (see Figure 1.2A)</span></div><div>&nbsp;</div><div><span style="font-size: 11pt; color: black;">2. On the second step, completion of bPB-fragments with side-chain aliphatic resonances as well as identification of additional spin-systems (lacking HN resonances) is performed using HCCH-TOCSY and 13C-NOESY spectra (see Figure 1.2B) &nbsp;</span></div><div>&nbsp;</div><div><span style="font-size: 11pt; color: black;">3. Finally, spin-system validation and correction is performed. </span><span style="font-size: 11pt;">This step allows one to find mistakes made during spectra peak-picking and to correct the mistakes by going back to the spectra. </span></div><div><span style="font-size: 11pt;">For each spin-system, 20 scores S(T) were calculated during the validation (see Figure 1.3). Here T corresponds to amino acid type, and T=A,R,D,…, and V, respectively. The score evaluate goodness-of-fit of the spin-system resonances to those observed in BMRB data base.&nbsp;If the best score , where ,&nbsp;is too low, it means that either the spin-system has very unusual chemical shifts or the spin-system does not make sense and need to be corrected.''''' '''''</span></div><div>'''''&nbsp;'''''</div><div>'''''&nbsp;'''''</div><div style="margin: 12pt 0cm 3pt;"><font size="4">Fragments assignment by FMC</font></div><div>'''''&nbsp;'''''</div><div><span style="font-size: 11pt; color: black;">Sequence-specific assignment of PB-fragments is achieved using a Fragment Monte Carlo (FMC) stochastic search procedure. The scoring function used in the FMC procedure is based on both fragment amino acid typing (matching the spin system to amino acid types) and fragment contact map (reflecting which residue is next to which) derived from HNCA data and the analysis of NOEs interpreted by BACUS (see Figure 1.4).</span></div><div>'''''&nbsp;'''''</div><div>'''''&nbsp;'''''</div><br><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment </span><span style="font-size: 11pt;">probabilities are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations. &nbsp;Here, &nbsp;is a </span><span style="font-size: 11pt;">probability of fragment ''k'' to occupy position ''s;''</span>''<span style="font-size: 11pt;">k = 1,….,N<sub>f.&nbsp;; </sub></span>''<span style="font-size: 11pt;">and ''<sub>&nbsp;</sub>s''</span><span style="font-size: 11pt;"> = 1,….,N<sub>s</sub>+1.&nbsp;Sequence-specific assignment of PB-fragments is achieved by analyzing probabilities </span><span style="font-size: 11pt;">(see Figure 1.5) as well as sub-optimal fragment’s mapping that are provided by MC simulations.</span></div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="4"><span>''FMCGUI''</span></font>'''</div><div>&nbsp;</div><div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. </div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="6"><span><font size="5">FMCGUI_2.2 COMMANDS</font></span></font>'''</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="4"><span>''0. FMCGUI objects.''</span></font>'''</div><div>&nbsp;</div><div><span style="font-size: 11pt;">Most of FMCGUI commands operate mainly with the following three objects that are located in computer memory:&nbsp;protein sequence, peak list, and PB-fragments. </span></div><div>&nbsp;</div><div>'''<span style="font-size: 11pt;">Protein sequence</span>'''<span style="font-size: 11pt;">. This object can be created in memory using [<span style="color: rgb(153, 51, 102);">Data&gt;Protein sequence&gt;load</span>] or [<span style="color: rgb(153, 51, 102);">Project&gt;load</span>] commands.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;The position ID of the first residue in the sequence should be specified by user upon loading sequence file (in the case it is not specified in the input file). Some commands in FMCGUI implies that the first residue of the protein sequence has position ID of 1. Therefore, if there is HIS-tag in the loaded sequence, it should be numbered accordingly starting with a negative position ID of the first residue.</span></div><div>&nbsp;</div><div>'''<span style="font-size: 11pt;">Peak Lists.</span>'''<span style="font-size: 11pt;"> Different peak lists objects can be created in memory using ['''<span style="color: rgb(153, 51, 102);">Data&gt;</span>'''”<span style="color: blue;">Peak list name</span>'''<span style="color: rgb(153, 51, 102);">”&gt;load</span>'''] or ['''<span style="color: rgb(153, 51, 102);">Project&gt;load</span>'''] commands. For some peak-lists, peaks in the list could be referenced by spin-system (fragment) user ID.</span></div><div><span style="font-size: 11pt;">The following table shows what peak lists are required referencing (+), peak lists </span></div><div><span style="font-size: 11pt;">that are optionally referenced (+/-), and peak lists for which referencing is not used </span></div><div><span style="font-size: 11pt;">even if present&nbsp;in the input file (-):</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div>
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| width="176" valign="top" style="border: 1pt solid windowtext; padding: 0cm 5.4pt; width: 132.05pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">N15 NOESY&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div>
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| width="88" valign="top" style="border-style: none solid solid none; border-color: rgb(212, 208, 200) windowtext windowtext rgb(212, 208, 200); border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 65.95pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">-</span></div>
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| width="176" valign="top" style="border-style: none solid solid; border-color: rgb(212, 208, 200) windowtext windowtext; border-width: medium 1pt 1pt; padding: 0cm 5.4pt; width: 132.05pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">Arom NOESY&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div>
| width="88" valign="top" style="border-style: none solid solid none; border-color: rgb(212, 208, 200) windowtext windowtext rgb(212, 208, 200); border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 65.95pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">-</span></div>
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| width="176" valign="top" style="border-style: none solid solid; border-color: rgb(212, 208, 200) windowtext windowtext; border-width: medium 1pt 1pt; padding: 0cm 5.4pt; width: 132.05pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">N15 HSQC</span></div>
| width="88" valign="top" style="border-style: none solid solid none; border-color: rgb(212, 208, 200) windowtext windowtext rgb(212, 208, 200); border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 65.95pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">+</span></div>
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| width="88" valign="top" style="border-style: none solid solid none; border-color: rgb(212, 208, 200) windowtext windowtext rgb(212, 208, 200); border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 65.95pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">+</span></div>
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| width="176" valign="top" style="border-style: none solid solid; border-color: rgb(212, 208, 200) windowtext windowtext; border-width: medium 1pt 1pt; padding: 0cm 5.4pt; width: 132.05pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">HNCA</span></div>
| width="88" valign="top" style="border-style: none solid solid none; border-color: rgb(212, 208, 200) windowtext windowtext rgb(212, 208, 200); border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 65.95pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">+/-</span></div>
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| width="176" valign="top" style="border-style: none solid solid; border-color: rgb(212, 208, 200) windowtext windowtext; border-width: medium 1pt 1pt; padding: 0cm 5.4pt; width: 132.05pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">HNCO</span></div>
| width="88" valign="top" style="border-style: none solid solid none; border-color: rgb(212, 208, 200) windowtext windowtext rgb(212, 208, 200); border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 65.95pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">-</span></div>
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| width="88" valign="top" style="border-style: none solid solid none; border-color: rgb(212, 208, 200) windowtext windowtext rgb(212, 208, 200); border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 65.95pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">+/-</span></div>
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| width="88" valign="top" style="border-style: none solid solid none; border-color: rgb(212, 208, 200) windowtext windowtext rgb(212, 208, 200); border-width: medium 1pt 1pt medium; padding: 0cm 5.4pt; width: 65.95pt; background-color: transparent;" | <div align="center"><span style="font-size: 11pt;">+</span></div>
|}
<div align="center"><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div>&nbsp;</div><div>'''<span style="font-size: 11pt;">List of Fragments</span>'''<span style="font-size: 11pt;">. This object can be created in memory using ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Load</span>'''], ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Create</span>'''], or ['''<span style="color: rgb(153, 51, 102);">Project&gt;load</span>'''] commands. Each fragment in the list has the following main properties:</span></div><div><span style="font-size: 11pt;">- Fragment ID assigned by user, ''U_id'';</span></div><div>''<span style="font-size: 11pt;">U_id</span>''<span style="font-size: 11pt;"> can’t be changed within FMCGUI.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">- Assignment ID, ''A_id'', that indicate the sequence position ID to which the fragment is assigned; ( ''A_id'' = -99 if&nbsp;the fragment is not assigned to any position in the sequence)</span></div><div>''<span style="font-size: 11pt;">A_id</span>''<span style="font-size: 11pt;"> could be set up or modified by the commands: ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Fix Assignment&gt;Manually</span>'''], ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Fix Assignment&gt;Using probability Map</span>'''], and ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Fix Assignment&gt;Reset all</span>'''].</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">- Typing probabilities &nbsp;&nbsp;, where&nbsp;''t ''correspond to one of 20 AA residue types.</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp; &nbsp;could be calculated or modified by the commands: </span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Type&gt;Calculate</span>'''] and ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Type&gt;Fix</span>'''].</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">- &nbsp;Three Fragment contact maps&nbsp;, &nbsp;, and , respetively.&nbsp;Each contact map scores the possibility for any fragment ''f'' to be next to fragment ''U_id'' in the protein sequence; were ''f''&nbsp;and ''U_id'' stand for&nbsp;fragment user ID. </span></div><div><span style="font-size: 11pt;">is calculated from HNCA spectrum by the command&nbsp;&nbsp; ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Contact&gt;HNCA</span>''']</span></div><div><span style="font-size: 11pt;">&nbsp;Fragment&nbsp;&nbsp; contact maps &nbsp;and , calculated from NOESY spectra with and without using BACUS procedure, respectively;</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp; &nbsp;can be calculated by the commands&nbsp;&nbsp; ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Contact&gt;NOE&gt;fawn</span>''']&nbsp;&nbsp;&nbsp; and ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Contact&gt;NOE&gt;abacus</span>'''], while &nbsp;is calculated by ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Contact&gt;NOE&gt;abacus</span>'''].</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">- Fragment assignment probabilities &nbsp;and &nbsp;are calculated using SA and REM Monte Carlo simulations, respectively. Here ''s'' stands for protein sequence position ID. </span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;is calculated&nbsp;by command ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Calculate probabilities&gt;SA</span>'''] or it can be loaded in memory using command ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Load probabilities</span>'''];</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;is calculated&nbsp;by command ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Calculate probabilities&gt;REM</span>'''] or it can be loaded in memory using command ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Load probabilities</span>'''];</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">The current values of all these properties for a particular fragment could be observed in the “Fragment Graph “window which is opened by command ['''<span style="color: rgb(153, 51, 102);">View&gt;Fragment</span>''']</span></div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="4"><span>''&nbsp; ''</span></font>'''<font size="4">''1. Main window''</font></div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div>''<span style="font-size: 11pt;">The main frame of FMC Graphical Interface consist of 4 sections (see Figure )</span>''</div><div>''<span style="font-size: 11pt;">&nbsp;- the title bar displays the name of the current project and the directory where the project is located;</span>''</div><div>''<span style="font-size: 11pt;">&nbsp;- the bar with six menu: Project, Data, Fragment, Assignment, Structure, and View, respectively;</span>''</div><div>''<span style="font-size: 11pt;">- the main message window, where message from the last executed command is displayed&nbsp;;</span>''</div><div>''<span style="font-size: 11pt;">- the log window,&nbsp;where the history of executed commands is shown.</span>''</div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div style="margin: 12pt 0cm 3pt;"><font size="4"><span>''2. PROJECT menu''</span>&lt;/font&lt;/div&gt;</font><div><font size="4">'''&nbsp;'''</font></div><div><span style="font-size: 11pt;"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Project&gt;New</span>''']&nbsp;:&nbsp;'''To start a new project.</font></span></div><div><font size="4">&nbsp;</font></div><div><span style="font-size: 11pt;"><font size="4">User have to provide a name of the project PROJECTNAME,and to select a directory that will host the project. The project root directory with the same name&nbsp;PROJECTNAME is created.''' '''</font></span></div><div><span style="font-size: 11pt;"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''</font></span></div><div><span style="font-size: 11pt;"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Project&gt;Load</span>''']&nbsp;: To continue to work on previously saved project.'''</font></span></div><div><font size="4">'''&nbsp;'''</font></div><div><span style="font-size: 11pt;"><font size="4">'''User have to select file PROJECTNAME.prj in the directory PROJECTNAME, where PROJECTNAME is the name of the root directory of the project.'''</font></span></div><div><font size="4">'''&nbsp;'''</font></div><div><span style="font-size: 11pt;"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Project&gt;Save</span>''']&nbsp;: To save the&nbsp;current state of the project.'''</font></span></div><div><font size="4">'''&nbsp;'''</font></div><div><span style="font-size: 11pt;"><font size="4">'''What is currently in the computer memory is saved in the file PROJECTNAME.prj located in the root directory of the project. '''</font></span></div><div><font size="4">'''&nbsp;'''</font></div><div><span style="font-size: 11pt;"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Poject&gt;Quit</span>''']&nbsp;: To save the current state of the project and to quit.'''</font></span></div><div><font size="4">'''&nbsp;'''</font></div><div><font size="4">'''&nbsp;'''</font></div><div style="margin: 12pt 0cm 3pt;"><font size="4"><font size="4"><span>''3. DATA menu''</span>&lt;/font&lt;/div&gt;</font></font><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''The DATA section serves to load&amp;save the data (such as protein sequence and peak lists). Since there are different formats of data-files that could be loaded in memory or saved on disk, one can use this section as format converter as well.'''</font></font></span></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;Protein Sequence&gt;Load</span>''']&nbsp;: To load a protein sequence into memory.'''</font></font></span></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><font size="4"><font size="4">'''''<span style="font-size: 11pt;">The input formats</span>''<span style="font-size: 11pt;">: </span>'''</font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;&nbsp; 1-letter code (fasta format); '''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;- &nbsp;&nbsp;3-letter code (standard format).'''</font></font></span></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''User have to select the file with sequence and to specify the first residue ID, in the case when the ID is not specified in the input file. It is recommended, that if there is His-tag in the sequence file, than the first residue ID should be set to a negative number so that the first&nbsp;residue of a protein has ID of 1. '''</font></font></span></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;Protein Sequence&gt;Save as</span>''']&nbsp;: To save protein sequence in the file on disk.'''</font></font></span></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><font size="4"><font size="4">'''''<span style="font-size: 11pt;">The output formats</span>''<span style="font-size: 11pt;">:</span>'''</font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - &nbsp;1-letter code (fasta format);'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;- &nbsp;3-letter code ("standard" format, for cyana)'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - &nbsp;&nbsp;3-letter code (for AutoStructure);'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;&nbsp;3-letter code (for RCI);'''</font></font></span></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''There are separate buttons for different peak lists. '''</font></font></span></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;N15 NOESY&gt;load/Save as</span>''']'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;C13 NOESY&gt;load/Save as</span>''']'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;Arom NOESY&gt;load/Save as</span>''']'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;N15 HSQC&gt;load/Save as</span>''']'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;C13 HSQC&gt;load/Save as</span>''']'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;HNCA&gt;load/Save as</span>''']'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;HNCO&gt;load/Save as</span>''']'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;CBCACONHN&gt;load/Save as</span>''']'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;HBHACONH&gt;load/Save as</span>''']&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;:&nbsp;&nbsp; To load or save a peak list.'''</font></font></span></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Input and output formats</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - Sparky;'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;Xeasy;'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;Standard;'''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; '''</font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Data&gt;Tolerances</span>''']&nbsp;: To set tolerances for chemical shift matching in different spectral dimensions.'''</font></font></span></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div><font size="4"><font size="4">'''&nbsp;'''</font></font></div><div style="margin: 12pt 0cm 3pt;"><font size="4"><font size="4"><font size="4"><span>''4. FRAGMENT menu''</span>&lt;/font&lt;/div&gt;</font></font></font><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Load&gt;assigned</span>''']&nbsp;: To load assigned chemical shifts (spin-systems) in the memory.&nbsp;'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Prerequisites:</span>'''''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - </span>''<span style="font-size: 11pt;">Loaded sequence</span>'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Input formats</span>''<span style="font-size: 11pt;">: </span>'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - assigned AA-fragments in standard format;'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;CYANA chemical shift file (prot-file);'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Load&gt;PB fragments</span>''']&nbsp;: To load unassigned spin-systems in the memory.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Input format</span>''<span style="font-size: 11pt;">&nbsp;:</span>'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PB-fragments in standard format.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Save&gt;PB fragments</span>''']&nbsp;: To save PB-fragments in a file on disk.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Output format</span>''<span style="font-size: 11pt;">: </span>'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; PB-fragments in standard format. '''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''The name of the saved file and it’s location are specified by user. '''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''There are 3 options to save PB-fragments in the file:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp; -&nbsp;in order of fragments index, that is in the order by which fragments are stored in memory;'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp; -&nbsp;in order of fragments user ID, ''U_id'';'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp; -&nbsp;in order of fragments assignment ID, ''A_id''.&nbsp;In this case 2 files are saved. One file, with user&nbsp;&nbsp;&nbsp; specified name 'user_name', contains only fragments assigned to protein sequence positions, that is to positions with residue ID of&nbsp;&gt;= 1. The second file, with the name 'user_name_na', contains all not assigned fragments (that is fragments with ''A_id'' = -99). '''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Save&gt;cyana</span>''']&nbsp;: To save assigned chemical shifts (that is fragments with ''A_id'' &gt;0 ) in CYANA format.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Save&gt;bmrb</span>''']&nbsp;: To save assigned chemical shifts in the format suitable for BMRB deposition (star2.1)'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Save&gt;talos</span>''']&nbsp;: To save assigned chemical shifts in the format suitable for TALOS/CS-Rosetta;'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Save&gt;abacus</span>''']&nbsp;:To save unassigned PB-fragments&nbsp;in the format suitable for BACUS;'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''</font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4">Fragment&gt;Create&gt;fawn</font></font></font></span><font size="4"><font size="4"><font size="4">'''<span style="font-size: 11pt;">]&nbsp;: To create/evaluate ''b''PB-fragments.</span>'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- loaded in memory <u>referenced</u> peak lists of CBCA(CO)HN, HBHA(CO)HN, N15HSQC, and HNCA spectra;'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- Specified tolerances.'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''There are two steps in executing this command.'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''On the first step, a fake C13HSQC peak list is created and shown in the popped up window “fake C13HSQC”.&nbsp;'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''User can use the information shown in the main FMCGUI window and check /edit the list in the entry section of “fake C13HSQC” window. &nbsp;Pressing OK will result in loading the peak list from the entry window into memory as C13HSQC peak list.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''On the second step, a number of ''b''PB-fragments corresponding to 20 different AA types are generated from user-identified spin-systems. Each generated ''b''PB-fragment is evaluated by a score SpS that measure how good the spin-system chemical shifts match corresponding statistical chemical shifts derived from BMRB database. The ''b''PB-fragment with highest score is selected to form a list of bPB-fragments. '''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''In the result, a new window ‘Create Fragment’ pops up and warning messages of the ‘sps_create’ script are shown in the main FMCGUI window. '''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''The window consists of three sections. The left sections contains suggested bPB-fragments,&nbsp;while the other sections contains two reports of fragments scoring with&nbsp;both C and H resonances and with only C&nbsp;resonances, respectively. Following the warning messages &nbsp;shown in the main FMCGUI window, user can accept/modify generated ''b''PB-fragments. Alternatively, when&nbsp;‘poor’ ''b''PB-fragments are present, user can go back to spectra, fix the pick lists accordingly, and repeat the fragment generation again.'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''U'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''ser-approved'''</font></font></font></span><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">b</span>''<span style="font-size: 11pt;">PB-fragments will be loaded in the memory by pressing OK button.</span>'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Results:</span>'''''</font></font></font></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''C13HSQC peak list loaded in memory'''</font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''bPB-fragments are loaded in memory'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''</font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4">Fragment&gt;Create&gt;abacus</font></font></font></span><font size="4"><font size="4"><font size="4">'''<span style="font-size: 11pt;">] </span>''':'''&nbsp;To create/evaluate PB-fragments.'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- loaded in memory <u>referenced</u> C13HSQC, N15HSQC, and HNCA peak lists and &nbsp;<u>not referenced</u> CBCA(CO)HN peak list; ( as an option, HNCA peak list could be not referenced as well)'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- Specified tolerances.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''On the second step, a number of PB-fragments corresponding to 20 different AA types are generated from user-identified spin-systems. Each generated PB-fragment is evaluated by a score SpS that measure how good the spin-system chemical shifts match corresponding statistical chemical shifts derived from BMRB database. The PB-fragment with highest score is selected to form a list of bPB-fragments.'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''Spin-system which have all SpS scores less than 10-4 are reported in the main FMCGUI window.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''Following these warnings user can accept&nbsp;or to modify generated PB-fragments in the left section of “Create Fragment’ window. Alternatively, user can go back to spectra, fix the pick lists accordingly, and repeat the fragment generation again.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''U'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''ser-approved'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">''' bPB-fragments will be loaded in the memory by pressing OK button'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Results:</span>'''''</font></font></font></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''PB-fragments are loaded in memory'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''</font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4">Fragment&gt;Type&gt;Calculate&gt;fawn/abacus</font></font></font></span><font size="4"><font size="4"><font size="4">'''<span style="font-size: 11pt;">] </span>''':'''&nbsp;Probabilistic typing of bPB-fragments (fawn) or PB-fragments (abacus)&nbsp;.'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- loaded in memory protein sequence'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- loaded in memory PB-fragments'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- specified tolerances.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Results:</span>'''''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''-&nbsp;Fragment typing probabilities are calculated and loaded in memory.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''The main FMCGUI window displays:'''</font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''the summary table that shows how many fragments of each AA-residue type are expected and how many fragments were actually recognized by the typing script;'''</font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''warning messages that suggest user to check and possibly modify typing manually of some fragments manually'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''</font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4">Fragment&gt;Type&gt;fix</font></font></font></span><font size="4"><font size="4"><font size="4">'''<span style="font-size: 11pt;">] </span>''':'''To modify typing probabilities .'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- loaded in memory protein sequence'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- loaded in memory PB-fragmen'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''New window "Fragment Property Modification" (FPM) window is opened.'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''This window has 3 sections.&nbsp;'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''In the top section of FPM window user can select fragment user ID, ''U_id''. Then typing probabilities '''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;for all AA types ''t'' will be shown on the graph. The chemical shifts of the fragments and its assignment status (''A_id'') are shown as well. User can&nbsp;modify typing probabilities of the selected fragment by selecting&nbsp;AA types by clicking right mouse button and pressing ‘Update’ button. In the result only propapbilities corresponding to the selected AA types will be set to the same non-zero values.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''In the top section of FPM window user can select&nbsp;AA residue type ''t1.''Then the graph will show typing probabilities &nbsp;'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''that correspond to the selected residue type ''t1'' for all available fragments IDs ''f'' . Selecting a particular fragment ''U_id'' by clicking right mouse button (the color of U_id&nbsp;is changed to red) and pressing “Update” button will set the probability '''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;to 1 while &nbsp;for all other f will be set to 0.&nbsp;'''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''Selecting a particular fragment ''U_id'' by clicking left mouse button (the color of U_id&nbsp;is changed to blue) and pressing “Update” button will set the probability '''</font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;to 0.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;&nbsp; '''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''</font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4">Fragment&gt;Expected Peaks&gt;”spectra name”</font></font></font></span><font size="4"><font size="4"><font size="4">'''<span style="font-size: 11pt;">] </span>''':'''To generate different&nbsp;peak lists expected from covalent structure of fragments.'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- protein sequence is loaded in memory'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- PB-fragments are loaded in memory'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''['''</font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4">Fragment&gt;Modify assigned</font></font></font></span><font size="4"><font size="4"><font size="4">'''<span style="font-size: 11pt;">] </span>''': '''To correct assigned fragments.'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- loaded in memory protein sequence'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- loaded in memory PB-fragments '''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- loaded&nbsp;HNCO, CBCACONH, and HNCA peak lists.'''</font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''- specified tolerances.'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4">'''In the result &nbsp;CO chemical shifts are added and chemical shift names are corrected for PB-fragments which are assigned (that is which has A_id &gt; -99 )'''</font></font></font></span></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div><font size="4"><font size="4"><font size="4">'''&nbsp;'''</font></font></font></div><div style="margin: 12pt 0cm 3pt;"><font size="4"><font size="4"><font size="4"><font size="5"><span>''5. Assignment menu''</span>&lt;/font&lt;/div&gt;</font></font></font></font><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''['''</font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5">Assignment&gt;Contacts&gt;HNCA</font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To calculate&nbsp;&nbsp;fragments contact map.'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- PB-fragments are loaded in memory&nbsp;;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- typing probabilities are calculated; '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- HNCA peak list (recommended to be referenced) is loaded in memory.'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- tolerances are specified.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''In the result, the contact map &nbsp;is calculated and loaded in the memory.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''['''</font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5">Assignment&gt;Contacts&gt;NOE&gt;fawn</font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To calculate &nbsp;fragments contact map.'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- PB-fragments are loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- typing probabilities are calculated; '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;N15_NOESY peak list is loaded in memory.'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- tolerances are specified.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''In the result, the contact map is calculated using N15 NOESY peak list and loaded in memory.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''['''</font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5">Assignment&gt;Contacts&gt;NOE&gt;abacus</font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To calculate&nbsp;both &nbsp;and fragments contact maps.'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- PB-fragments are loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;typing probabilities are calculated; '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;N15_NOESY and C13_NOESY peak lists are loaded in memory.'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- tolerances are specified.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''In the result, the contact map is calculated using only N15_NOESY peak list while&nbsp;&nbsp;contact map is calculated using both N15_NOESY and C13_NOESY peak lists that are interpreted by BACUS procedure. Both calculate maps are loaded in memory.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''['''</font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5">Assignment&gt;Calculate Probabilities&gt;SA</font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To calculate assignment probabilities.'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;PB-fragments are loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;typing probabilities are calculated; '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;fragments contact map is calculated;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- at least one of &nbsp;and fragments contact maps is calculated;'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''Probabilistic mapping of PB-fragments onto protein sequence is performed using Simulated Annealing Monte Carlo simulations. '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''A new window “Calculate SA” is open were user can specify different parameters in the control file of the SA simulations.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''The main parameters to consider are:'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“Name of the SA run”. Normally the name is sa_run#. A new directory under this name will be created within PROJECTNAME/assign directory.&nbsp;SA calculations will be curried out and the results will be stored in this directory.'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;“Size of the pool for unassigned fragments”. The number of positions that are appended to the protein sequence and&nbsp;discarded (unassigned) fragments, if there are any,&nbsp;will be located there. It is safe to over-estimate this number. (If this number is under-estimated, this will force the mapping of spurious spin-systems onto protein sequence);'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“Number of SA trajectories”. The time needed for calculations is proportional to this number. On the other hand, having more SA trajectories the assignment probabilities could be calculated more accurately. In the case of good data, when all SA trajectories converge to assignments with the same energy, 10-15 trajectories should be enough. In the case of poor data, it is better to calculate 40-50 SA trajectories.'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“NOE bbcmap type”. User should specify which one NOE contact map, &nbsp;(abacus) or &nbsp;(fawn) should be used in the calculations;'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“Fixing position flag”.&nbsp;If the flag is set to 1, sequence position of all fragments which has assignment ID &gt; -99 &nbsp;will be fixed during the simulation.'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“Final temperature”. Setting the optimal final temperature will provide all SA trajectories converge to optimal or sub-optimal assignments (the assignments that are in the vicinity of the global energy minimum). The optimal final temperature could be find by running one or a few SA runs with 3-4 trajectories and by analysing convergence of the trajectories from the report shown in the main FMCGUI window after each run.'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 18pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 18pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div style="margin: 0cm 0cm 0pt 18pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''.&nbsp;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''In the result of the SA calculations assignment probability map &nbsp;is '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''calculated and loaded in memory. The map is also saved in the file 'sa.probmap' located into PROJECTNAME/assignment/sa_run# directory.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''['''</font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5">Assignment&gt;Calculate Probabilities&gt;REM</font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To calculate assignment probabilities.'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;PB-fragments are loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;typing probabilities are calculated; '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;fragments contact map is calculated;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- at least one of &nbsp;and fragments contact maps is calculated;'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''Probabilistic mapping of PB-fragments onto protein sequence is performed using Replica Exchange Method Monte Carlo simulations. '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''A new window “Calculate REM” is open were user can specify different parameters in the control file of the REM simulations.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;&nbsp;&nbsp; '''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''The main parameters to consider are:'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“Name of the REM run”. Normally the name is rem_run#. A new directory under this name will be created within PROJECTNAME/assign directory. REM calculations will be curried out and the results will be stored in this directory.'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;“Size of the pool for unassigned fragments”. The number of positions that are appended to the protein sequence and discarded (unassigned) fragments, if there are any,&nbsp;will be located there. It is safe to over-estimate this number. (If this number is under-estimated, this will force the mapping of spurious spin-systems onto protein sequence);'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“Number of REM steps”. The time needed for calculations is proportional to this number. On the other hand, with more REM steps more extensive sampling of assignment space wil be achieved, which in turn results in more accurate assignment probabilities. This number should be increased for large proteins.'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;“NOE bbcmap type”. User should specify which one NOE contact map, &nbsp;(abacus) or &nbsp;(fawn) should be used in the calculations;'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“Fixing position flag”.&nbsp;If the flag is set to 1, sequence position of all fragments which has assignment ID &gt; -99&nbsp;will be fixed during the simulation.'''</font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“Low temperature”. The optimal low temperature will provide extensive sampling of should sub-optimal assignments during REM simulation. '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''User can check a correct setting of the low temperature as well as the number of REM steps by analysing a report shown in the main FMCGUI window after the calculations are done.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''In the result, the 50 lowest energy assignments are used to calculate assignment probabilities . The probabilities are loaded in memory and saved in the file ‘rem.prbmap’ located into PROJECTNAME/assign/rem_run# directory. '''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''['''</font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5">Assignment&gt;Fix Assignment&gt;Using Probability map</font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To perform sequence specific assignment of PB-fragments using results of SA or REM calculations.'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;PB-fragments loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;at least one SA or REM calculations of assignment probabilities was done'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''Calculation of assignment probabilities with FMCGUI could be repeated a few times using different methods and parameters. Results of each calculation are stored in a separate directory with the user-specified name. Therefore, there could be a few different directories (for example, sa_run1, sa_run2, rem_run0, rem_run1, rem_run2) located within PROJECTNAME/assign/ directory that contain different assignment probability maps. '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''User will be asked to select the calculation directory (sa_run# or rem_run#) and &nbsp;to specify the value of acceptance probability P_a. Normally,&nbsp;P_a =0.9 is appropriate. &nbsp;A fragment is considered to be assigned to a sequence position if the corresponding assignment probability (taken from the selected directory) is &gt;= P_a. '''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''In the result, part of the PB-fragments will be assigned, namely, their assignment IDs A_id will be specified. The assignment report will be shown in the main FMCGUI window as well as saved in the corresponding simulation directory (‘sa.fix ‘or ‘rema.fix’ files). &nbsp;For each sequence position, the IDs of both unambiguously and ambiguously assigned fragments are shown in the report. The list of discarded fragments is also presented.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;&nbsp; '''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''['''</font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5">Assignment&gt;Fix Assignment&gt;Manually</font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To perform sequence specific assignment of PB-fragments manually.'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;PB-fragments are loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''This command allows user to fix sequence position of individual fragments.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''“Fragment Property Modification” window&nbsp;will be open. User can select a fragment in the bottom section of the window and the ingormation regarding&nbsp;the fragment assignemts will be displayed in this section. Namely, the graph shows assignment probabilities (&nbsp;or ) that are currently loaded in memory and the text part shows the chemical shifts making up the fragment and it’s assignment ID (A_id). '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''To modify the current &nbsp;fragment assignment &nbsp;user have to select sequence position on the graph (by clicking on it by mouse) and then to press ‘Update’ button. '''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;&nbsp;&nbsp; '''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''In the result, Assignment ID of the selected fragment will be set to the selected sequence position.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''There are two special positions “U” and “B”&nbsp;shown on the graph at the end of the protein sequence.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''Selecting “U” and pressing “Update” button results in changing assignment status of the fragments to Unassigned, that is A_id is set to -99. '''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''Selecting “B” and pressing “Update” button results in fixing fragment position in the pool of discarded fragments.'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''['''</font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5">Assignment&gt;Fix Assignment&gt;Reset all</font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To change assignment status of all fragments to “Unassigned”.'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;PB-fragments are loaded in memory;'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''In the result, for all fragments&nbsp;A_id is set to -99. '''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''['''</font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5">Assignment&gt;Load Probabilities</font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To load assignment probabilities in memory.'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''- &nbsp;PB-fragments are loaded in memory;'''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''-&nbsp;&nbsp; SA / REM calculations of assignment probabilities was done'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''User have to select a directory where SA or REM calculations were done (sa_run# or rem_run#). '''</font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5">'''The assignment probabilities from the selected directory will be loaded in memory.'''</font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5">'''&nbsp;'''</font></font></font></font></div><div style="margin: 12pt 0cm 3pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5"><span>''6. Structure menu''</span>&lt;/font&lt;/div&gt;</font></font></font></font></font><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;Constraints&gt;Talos&gt;calculate</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To generate dihedral angle constraints.'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''- &nbsp;assigned shemical shifts are loaded in memory;'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''Backbone dihedral angles are predicted&nbsp;using TALOS and then transformed to dihedral angle contraints. '''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''In the result, the constraints are saved in two formats: files &nbsp;'belok.aco' and 'prot_dihe.tbl'&nbsp;for CYANA&nbsp;and CNS calculations, respectively. Both files are saved in the root project directory PROJECTNAME.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;Constraints&gt;Talos&gt;load</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To load dihedral angle constraints in CYANA format (aco-file).'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;Constraints&gt;H-bonds&gt;Specify</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To prepare H-bond distance constraints manually.'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''A new window “O/HN Pairs” is opened. '''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''For each H-bond constraint, user have to specify&nbsp;O-HN pair by typing in the ID of residues corresponding to O and HN atoms.&nbsp;Pressing “OK” will save H-Bond constraints in two formats:&nbsp;files &nbsp;'hbond.upl' and 'prot_hbond.tbl'&nbsp;for CYANA&nbsp;and CNS calculations, respectively. Both files are saved in the root project directory PROJECTNAME.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;Constraints&gt;H-Bonds&gt;load</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To load HBond distance&nbsp;constraints in CYANA format (upl-file).'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;Calculate&gt;Cyana</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To set up a new structure calculation run with CAYANA.'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''''<span style="font-size: 11pt;">&nbsp;Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''- &nbsp;assigned chemical shifts are loaded in memory;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;N15_NOESY, C13_NOESY, and Aron_NOESY peak lists are loaded in memory'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''- &nbsp;Specified tolerances.'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;dihedral angle constraints are created ( file “belok.aco” is present in the root project directory PROJECTNAME)'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''''<span style="font-size: 11pt;">&nbsp;Optional:</span>'''''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;- Hbond distance constraints (file “hbond.upl” is present in the root project directory PROJECTNAME)'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;- file that contains ZN ion ligands (file “zn_ligands” is present in the root project directory PROJECTNAME)'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''A new directory under the name that is specified by user (normally “crun#”) will be created inside project root directory PROJECTNAME. This directory contains all files required to start automatic structure calculations with CYANA.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;Calculate&gt;Cyana</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To set up ABACUS structure calculations.(Under construction)'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;RPF&gt;RP</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To perform Recall/Precision analysis of structural ensemble.'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;''Prerequisites'':&nbsp;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''- &nbsp;assigned shemical shifts are loaded in memory;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;N15_NOESY, C13_NOESY, and Arom_NOESY peak lists are loaded in memory'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''- &nbsp;Specified tolerances.'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;coordinates of structural ensemble in CYANA format (final.pdb) or in CNS format (prot_ref_al.pdb). pdb '''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''The parameters to set up:'''</font></font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''“RP directory name”. Normally the name is rp#. A new directory under this name will be created within PROJECTNAME/assign directory. The&nbsp;results of the RPFanalysis will be stored in this directory.'''</font></font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''“sequence gap”. &nbsp;Residue pairs separated by less than the value of sequence gap will be excluded from generating expected peak lists.'''</font></font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''“cutting distance for recall”. Distance threshold for evaluating matching of an experimental peak to&nbsp;a structural ensemble (Recall score)'''</font></font></font></font></font></span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''</font></font></font></font></font></span><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''“cutting distance for precition”. Distance threshold for generating expected peak from structural ensemble (Precision score)'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''The results of the RPF analysis will be saved in a new directory (the name of which is specified by user) that is located in the project root directory PROJECTNAME. The results include peak lists in the SPARKY format of both false negative and false positive peaks for different NOESY spectra in a separate files.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;RPF&gt;DP</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To set up calculations of DP score with AutoStructure.'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;protein sequence is loaded in memory;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''- &nbsp;assigned shemical shifts are loaded in memory;'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;N15_NOESY, C13_NOESY, and Aron_NOESY peak lists are loaded in memory'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''- &nbsp;Specified tolerances.'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;coordinates of structural ensemble in CYANA format (final.pdb) or in CNS format (prot_ref_al.pdb). pdb '''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;Water refinement&gt;calculate</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To set up water refinement of structural ensemble obtained with CYANA.'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;structure calculation with CYANA should be done'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''''<span style="font-size: 11pt;">Optional:</span>'''''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;- RDC data in PALES format.'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;- file that contains ZN ion ligands (file “zn_ligands” )'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''User will be asked to specify the name of directory for water refinement calculations WATDIR and to select a number of files with coordinates and constraints. In addition to this user have to indicate cisProline residues (if there are any) and to specify protonation state of HIS residues which is double protonated by default.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''In the result, a new directory WATDIR will be created inside PROJECTNAME directory that contains all files and scripts required to carry out water refinement calculations with CNS. It is recommended to start calculations on linux cluster.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;Water refinement&gt;summary</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To create a summary.'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''''<span style="font-size: 11pt;">Prerequisites</span>''<span style="font-size: 11pt;">:&nbsp;</span>'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''-&nbsp;water refinement with CNS should be done.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''User will be asked to specify residues used for structure superposition and to select the water refinement directory WATDIR.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; '''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''The refined structural models will be superimpose and combined in one file. The created summary&nbsp;reports values of different energy&nbsp;components and&nbsp;constraint violation statistic for each structural model. A new directory WATDIR_results will be created. The directory contains final superimposed coordinates, distance and dihedral angle constrains in a format suitable for PDB deposition, summary and constraint violations report.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;Add ZN ligands</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To create zn_ligands file.'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''User have to tipe in IDs of residues that ligate zinc ion into the popped up entry window “ZN ligands”. If there are a few zinc ions, information for each ion should be provided in a separate row.'''</font></font></font></font></font></span></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''The file “zn_ligands” will be created inside the project root directory PROJECTNAME by pressing “OK” button.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''['''</font></font></font></font></font></span><span style="font-size: 12pt; color: rgb(153, 51, 102);"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">Structure&gt;RCI</font></font></font></font></font></span><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''<span style="font-size: 11pt;">] </span>''':'''To calculate Random Coil Index.'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><span style="font-size: 11pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''Random Coil Index &nbsp;is calculated using rci_v_1c.py script. New directory &nbsp;PROJECTNAME/rci that contains the results of calculations is created.'''</font></font></font></font></font></span></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div><font size="4"><font size="4"><font size="4"><font size="5"><font size="5">'''&nbsp;'''</font></font></font></font></font></div><div style="margin: 12pt 0cm 3pt;"><font size="4"><font size="4"><font size="4"><font size="5"><font size="5"><font size="5"><span>''7. View menu''</span>&lt;/font&lt;/div&gt;<div>'''&nbsp;'''</div><div><span style="font-size: 11pt;">'''This section provides means to visualize data and calculation results.'''</span></div><div>'''&nbsp;'''</div><div><span style="font-size: 11pt;">'''['''</span><span style="font-size: 12pt; color: rgb(153, 51, 102);">View&gt;Fragment</span>'''<span style="font-size: 11pt;">] </span>''':'''To display current fragment properties.'''</div><div>'''&nbsp;'''</div><div><span style="font-size: 11pt;">'''&nbsp;This command opens “Fragment Graph” (FG) &nbsp;window were all properties of a selected fragment that currently are loaded in memory will be displayed. '''</span></div><div>'''&nbsp;'''</div><div><span style="font-size: 11pt;">'''The chemical shifts making up the fragment are shown in the middle part of the window.&nbsp;The heading line (for example line “Fragment #21 rem_run1 L108” shown on Figure ) shows fragment ID (#21), the name of directory that contains assignment probabilities used to assign the fragment (rem_run1) and sequence position to which the fragment is assigned (L108). &nbsp;All other fragment properties are shown in the form of graphs. Typing probabilities&nbsp;the top section of the window one can see typing probabilities &nbsp;and both assignment probabilities &nbsp;and &nbsp;&nbsp;are shown on three graph on the top part of the&nbsp;FG window.&nbsp;It is also indicated the name of the directories from which the displayed assignment probabilities were loaded.&nbsp;Two graphs on the bottom part of the FG window shows a column (or&nbsp;)&nbsp;and a row (or&nbsp;)&nbsp;of a contact map calculated from NOESY data, respectively. Here ''U_id'' is selected fragment ID, while ''f'' is any fragment ID for which the corresponding score is &gt; 0.&nbsp;What contact map, or),&nbsp;is shown on the graphs is indicated on the bar at the bottom of FG window.&nbsp;Clicking on this bar by mouse will switch from one contact map to another.'''</span></div><div><span style="font-size: 11pt;">'''The contact map &nbsp;is shown on this graph implicitly as well by color of&nbsp;graph bars.'''</span></div><div><span style="font-size: 11pt;">'''&nbsp;For example, on the figure the elements of contact map related to the fragment 21 are shown. The score for fragment 21 to be before the fragments 37, 20 and 17 in protein sequence &nbsp;are shown in magenta which means that these connections being derived from NOESY data are supported by HNCA spectra as well. The score for fragment 21 to be before the fragments 22 and 4 are shown in red meaning that theses connections&nbsp;are not supported by HNCA&nbsp;spectra.'''</span></div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div><span style="font-size: 11pt;">'''['''</span><span style="font-size: 12pt; color: rgb(153, 51, 102);">View&gt;Assignment</span>'''<span style="font-size: 11pt;">] </span>''':'''To display assignment results.'''</div><div>'''&nbsp;'''</div><div><span style="font-size: 11pt;">'''The user is asked to select a directory were assignment probabilities were calculated'''</span></div><div><span style="font-size: 11pt;">'''(sa_run# or rem_run#). '''</span></div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div><span style="font-size: 11pt;">'''New “Assignments Graphs” (AG) window pops up. This window provides user with graphical means to manipulate&nbsp;PB-fragment’s assignments without making changes of assignment status of PB-fragments in memory. The current fragment’s assignment, taken from the memory, altogether with different scores associated with this assignment is shown when AG window is opened. The fragments that currently are not assigned are also shown in the bottom-right part of the AG window. User can modify the current assignment and to observe the resulting changes in the scores. '''</span></div><div><span style="font-size: 11pt;">'''&nbsp;A particular fragment’s assignment is displayed on the left part of the AG window. The graph at the bottom shows ID of fragments assigned to each sequence position, while four graphs on the top show different scores that correspond to this assignment, namely, HNCA score, NOE scores, typing and assignment probabilities that currently loaded in memory. The scroll bar at the bottom allows user to move along protein sequence.'''</span></div><div><span style="font-size: 11pt;">'''In order to modify the assignment user have first to select protein sequence segment of interest by clicking on IDs of two residues that correspond to the edges of the segment. The colour of these residues, for example K56 and D59, will change to red (see Figure).&nbsp;Then pressing on “Select Segment” bar at the bottom of AG window will result in possible assignment for the selected window to be shown on top-right corner of AG window.&nbsp;The possible assignments for the selected sequence segment are taken form the selected directory shown on the title bar and correspond to sub-optimal fragment assignments sampled during SA or REM calculations'''</span></div><div><span style="font-size: 11pt;">'''The new assignment for the sequence segment should be selected from the list of possible assignments using mouse. The color of the selected line will turn red (see Figure). In the case user want to consider an assignment that is not present in the list, he should select any assignment from the list ant modify it by pressing the button “Edit” at the bottom of the AG window. A new window “Edit Assignment” pops up, and user can modify the assignment by typing changes in this window. &nbsp;'''</span></div><div><span style="font-size: 11pt;">'''Once a new assignment for the sequence segment is selected the current fragments assignment shown on the left part of AG window can be modified by pressing button “Update” &nbsp;(see Figure)'''</span><span style="font-size: 11pt;">
</span></div><div></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="6"><span><font size="5">FMCGUI2.2 DATA FORMATS</font></span></font>'''</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="5"><span>''A. Sequence formats.''</span></font>'''</div><div>&nbsp;</div><div>&nbsp;</div><div><span><span style="font-size: 13pt;">'''A1. "Fasta" format'''</span></span>''<u><span style="font-size: 11pt;">.</span></u>''<span style="font-size: 11pt;"> The first line should start with '&gt;'. Next one or more</span></div><div><span style="font-size: 11pt;">lines contain sequence in 1-letter code.</span></div><div>&nbsp;</div><div><span><font size="2">&nbsp;</font></span></div><div><font size="2">Example_A1:</font></div><div>&nbsp;</div><div><font size="2">&gt;&nbsp;</font></div><div><font size="2">MDSKEVLVHVKNLEKNKSNDAAVLEILHVL</font></div><div><font size="2">DKEFVPTE KLLRETKVGVE VNKFKKSTN</font></div><div><font size="2">VEISKLVKKMISSWKDAIN<span>&nbsp;&nbsp;&nbsp; </span></font></div><div>&nbsp;</div><div>&nbsp;</div><div><span><span style="font-size: 13pt;">'''A2. "Standard" format'''</span></span>''<u><span style="font-size: 11pt;">.</span></u>''<span style="font-size: 11pt;"> Each line contains name of one residue in 3-letter code</span></div><div><span style="font-size: 11pt;">and optionally the residues ID. (Only residue ID of the first residue is used).</span></div><div>&nbsp;</div><div><font size="2">Example_A2.1 (position ID is not specified)</font></div><div>&nbsp;</div><div><font size="2">GLN</font></div><div><font size="2">GLY</font></div><div><font size="2">HIS</font></div><div><font size="2">MET</font></div><div><font size="2">PRO</font></div><div><font size="2">GLY</font></div><div><font size="2">ILE</font></div><div><font size="2">ILE</font></div><div><font size="2">TYR</font></div><div><font size="2">GLU</font></div><div><font size="2">GLY</font></div><div><font size="2">LYS</font></div><div><font size="2">GLY</font></div><div><font size="2">THR</font></div><div><font size="2">ASN</font></div><div><font size="2">MET</font></div><div><font size="2">GLU</font></div><div><font size="2">....</font></div><div>&nbsp;</div><div><font size="2">Example_A2.2 (with specified all position ID):</font></div><div>&nbsp;</div><div><font size="2">GLN&nbsp;-3</font></div><div><font size="2">GLY&nbsp;-2</font></div><div><font size="2">HIS &nbsp;-1</font></div><div><font size="2">MET <span>&nbsp;&nbsp;0</span></font></div><div><font size="2">PRO<span>&nbsp;&nbsp; 1</span></font></div><div><font size="2">GLY <span>&nbsp;&nbsp;2</span></font></div><div><font size="2">ILE<span>&nbsp;&nbsp; 3</span></font></div><div><font size="2">ILE<span>&nbsp;&nbsp; 4</span></font></div><div><font size="2">TYR&nbsp;&nbsp;5</font></div><div><font size="2">.....</font></div><div>&nbsp;</div><div><font size="2">Example_A2.3 (with specified first position ID):</font></div><div>&nbsp;</div><div><font size="2">GLN&nbsp;-3</font></div><div><font size="2">GLY&nbsp;</font></div><div><font size="2">HIS</font></div><div><font size="2">MET<span>&nbsp;&nbsp; </span></font></div><div><font size="2">PRO&nbsp;</font></div><div><font size="2">GLY&nbsp;</font></div><div><font size="2">ILE&nbsp;</font></div><div><font size="2">ILE&nbsp;</font></div><div><font size="2">TYR&nbsp;</font></div><div><font size="2">.....</font></div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="5"><span>''B. Peak lists formats.''</span></font>'''</div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="4"><span>B1. Sparky format.</span></font>'''</div><div>&nbsp;</div><div><span style="font-size: 11pt;">Could be both referenced and not referenced, with or without Volume/Height. </span></div><div><span style="font-size: 11pt;">Referencing, if present, has format F#, were # is user defined </span></div><div><span style="font-size: 11pt;">PB-fragment ID.&nbsp;The volume/height could be provided by digit number </span></div><div><span style="font-size: 11pt;">or by float number in E format (0.141E+10)</span></div><div>&nbsp;</div><div><font size="2">Example_B1.1: (referenced HNCA)</font></div><div>&nbsp;</div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; User&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; w1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; w2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; w3&nbsp;</span></font></div><div>&nbsp;</div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F1&nbsp;&nbsp;&nbsp;&nbsp; 55.269&nbsp;&nbsp;&nbsp; 106.560&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.027 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F1&nbsp;&nbsp;&nbsp;&nbsp; 43.558&nbsp;&nbsp;&nbsp; 106.560&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.026 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F2&nbsp;&nbsp;&nbsp;&nbsp; 51.232&nbsp;&nbsp;&nbsp; 114.375&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.101 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F2 &nbsp;&nbsp;&nbsp;&nbsp;59.634&nbsp;&nbsp;&nbsp; 114.375&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.096 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F3&nbsp;&nbsp;&nbsp;&nbsp; 57.686&nbsp;&nbsp;&nbsp; 118.215&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.514 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F3&nbsp;&nbsp;&nbsp;&nbsp; 59.071&nbsp;&nbsp;&nbsp; 118.215&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.519 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F4&nbsp;&nbsp;&nbsp;&nbsp; 55.762&nbsp;&nbsp;&nbsp; 118.966&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.306 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F4&nbsp;&nbsp;&nbsp;&nbsp; 59.071&nbsp;&nbsp;&nbsp; 118.966&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.306 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F5&nbsp;&nbsp;&nbsp;&nbsp; 52.547&nbsp;&nbsp;&nbsp; 119.119&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;9.250 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F5&nbsp;&nbsp;&nbsp;&nbsp; 59.071&nbsp;&nbsp;&nbsp; 119.119&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.249 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F6&nbsp;&nbsp;&nbsp;&nbsp; 59.071&nbsp;&nbsp;&nbsp; 120.109&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.230 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F6&nbsp;&nbsp;&nbsp;&nbsp; 55.128&nbsp;&nbsp;&nbsp; 120.109&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.232 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F7&nbsp;&nbsp;&nbsp;&nbsp; 55.598&nbsp;&nbsp;&nbsp; 122.600&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.599 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F9&nbsp;&nbsp;&nbsp;&nbsp; 56.184&nbsp;&nbsp;&nbsp; 122.430&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.316 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F9&nbsp;&nbsp;&nbsp;&nbsp; 57.616&nbsp;&nbsp;&nbsp; 122.430&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.319 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F11&nbsp;&nbsp;&nbsp;&nbsp; 58.719&nbsp;&nbsp;&nbsp; 122.464&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.158 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F11&nbsp;&nbsp;&nbsp;&nbsp; 55.292&nbsp;&nbsp;&nbsp; 122.464&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.157 </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">Example_B1.2: (not referenced N15NOESY)<span>&nbsp;&nbsp; </span></font></div><div>&nbsp;</div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Assignment&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; w1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; w2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; w3&nbsp;&nbsp; Data Height </span></font></div><div>&nbsp;</div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.592&nbsp;&nbsp;&nbsp; 106.850&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.261&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1435751 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4.244&nbsp;&nbsp;&nbsp; 106.850&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.259&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1096259 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.625&nbsp;&nbsp;&nbsp; 108.915&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.438&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 544482 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6.898&nbsp;&nbsp;&nbsp; 108.915&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.438&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 428124 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;2.017&nbsp;&nbsp;&nbsp; 119.793&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7.851&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 858875 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4.358&nbsp;&nbsp;&nbsp; 119.793&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7.855&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1260421 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4.573&nbsp;&nbsp;&nbsp; 126.081&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.518&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 590579 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.891&nbsp;&nbsp;&nbsp; 126.081&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.522&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 651350 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 5.665&nbsp;&nbsp;&nbsp; 125.092&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.261&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 793816 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.567&nbsp;&nbsp;&nbsp; 125.092&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.264&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1123055 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3.300&nbsp;&nbsp;&nbsp; 125.092&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.262&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 814461 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 4.713&nbsp;&nbsp;&nbsp; 125.092&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.262&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6211645 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 6.976&nbsp;&nbsp;&nbsp; 125.092&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.262&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2048095 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;?-?-?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7.884&nbsp;&nbsp;&nbsp; 125.092&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.261&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 651915 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; </span></font></div><div>&nbsp;</div><div><font size="2">Example_B1.3: (not referenced HNCO)</font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; w1&nbsp;&nbsp;&nbsp; w2&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; w3&nbsp;</span></font></div><div>&nbsp;</div><div><font size="2">&nbsp;176.935<span>&nbsp;&nbsp;&nbsp; 106.560&nbsp;&nbsp;&nbsp; &nbsp;9.025 </span></font></div><div><font size="2">&nbsp;175.679<span>&nbsp;&nbsp;&nbsp; 114.375&nbsp;&nbsp;&nbsp; &nbsp;9.107 </span></font></div><div><font size="2">&nbsp;175.310<span>&nbsp;&nbsp;&nbsp; 118.215&nbsp;&nbsp;&nbsp; &nbsp;9.517 </span></font></div><div><font size="2">&nbsp;174.027<span>&nbsp;&nbsp;&nbsp; 118.966&nbsp;&nbsp;&nbsp; &nbsp;9.307 </span></font></div><div><font size="2">&nbsp;178.232<span>&nbsp;&nbsp;&nbsp; 119.102&nbsp;&nbsp;&nbsp; &nbsp;9.255 </span></font></div><div><font size="2">&nbsp;175.174<span>&nbsp;&nbsp;&nbsp; 120.109&nbsp;&nbsp;&nbsp; &nbsp;9.227 </span></font></div><div><font size="2">&nbsp;173.781<span>&nbsp;&nbsp;&nbsp; 122.600&nbsp;&nbsp;&nbsp; &nbsp;9.599 </span></font></div><div><font size="2">&nbsp;175.720<span>&nbsp;&nbsp;&nbsp; 122.430&nbsp;&nbsp;&nbsp; &nbsp;9.312 </span></font></div><div><font size="2">&nbsp;172.143<span>&nbsp;&nbsp;&nbsp; 122.464&nbsp;&nbsp;&nbsp; &nbsp;9.165 </span></font></div><div><font size="2">&nbsp;173.699<span>&nbsp;&nbsp;&nbsp; 121.269&nbsp;&nbsp;&nbsp; &nbsp;9.058 </span></font></div><div><font size="2">&nbsp;176.102<span>&nbsp;&nbsp;&nbsp; 121.525&nbsp;&nbsp;&nbsp; &nbsp;9.099 </span></font></div><div><font size="2">&nbsp;173.645<span>&nbsp;&nbsp;&nbsp; 123.727&nbsp;&nbsp;&nbsp; &nbsp;9.143 </span></font></div><div><font size="2">&nbsp;173.781<span>&nbsp;&nbsp;&nbsp; 124.819&nbsp;&nbsp;&nbsp; &nbsp;9.113 </span></font></div><div>&nbsp;</div><div>&nbsp;</div><div><font size="2">ExampleB_1.4: (referenced N15HSQC)</font></div><div>&nbsp;</div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; User&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; w1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; w2&nbsp;</span></font></div><div>&nbsp;</div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F34&nbsp;&nbsp;&nbsp; 123.334&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.843 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F99&nbsp;&nbsp;&nbsp; 122.498&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7.685 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F144&nbsp;&nbsp;&nbsp; 117.711&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7.610 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F163&nbsp;&nbsp;&nbsp; 121.227&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.178 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F50&nbsp;&nbsp;&nbsp; 116.577&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.451 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F1&nbsp;&nbsp;&nbsp; 106.560&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.025 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F100&nbsp;&nbsp;&nbsp; 122.361&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7.821 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F101&nbsp;&nbsp;&nbsp; 121.372&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 7.868 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F102&nbsp;&nbsp;&nbsp; 122.361&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.006 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F103&nbsp;&nbsp;&nbsp; 122.378&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.048 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F105&nbsp;&nbsp;&nbsp; 122.703&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.123 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F106&nbsp;&nbsp;&nbsp; 122.327&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.231 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F107&nbsp;&nbsp;&nbsp; 121.440&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.358 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F109&nbsp;&nbsp;&nbsp; 120.570&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.577 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F11&nbsp;&nbsp;&nbsp; 122.464&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 9.164 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F111&nbsp;&nbsp;&nbsp; 120.535&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.306 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F112&nbsp;&nbsp;&nbsp; 121.218&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.200 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F113&nbsp;&nbsp;&nbsp; 120.843&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.157 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F114&nbsp;&nbsp;&nbsp; 121.338&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 8.105 </span></font></div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="4"><span>B2. XEASY format.</span></font>'''</div><div>&nbsp;</div><div><span style="font-size: 11pt;">First (one or a few) lines should start with character '#'. </span></div><div><span style="font-size: 11pt;">There is no referencing in this format.</span></div><div>&nbsp;</div><div>&nbsp;</div><div><font size="2">Example_B2: (not referenced Arom_NOESY)</font></div><div>&nbsp;</div><div><font size="2"># Number of dimensions 3</font></div><div><font size="2">#FORMAT xeasy3D</font></div><div><font size="2">#INAME 1 C</font></div><div><font size="2">#INAME 2 H</font></div><div><font size="2">#INAME 3 HC</font></div><div><font size="2">#CYANAFORMAT ChH</font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 1 132.896&nbsp;&nbsp; 7.221&nbsp;&nbsp; 7.216 1 U&nbsp;&nbsp; 0.141E+10&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 2 132.896&nbsp;&nbsp; 6.799&nbsp;&nbsp; 7.219 1 U&nbsp;&nbsp; 0.177E+09&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 3 132.896&nbsp;&nbsp; 4.695&nbsp;&nbsp; 7.217 1 U&nbsp;&nbsp; 0.205E+08&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 4 132.896&nbsp;&nbsp; 3.271&nbsp;&nbsp; 7.220 1 U&nbsp;&nbsp; 0.274E+08&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 5 132.896&nbsp;&nbsp; 3.006&nbsp;&nbsp; 7.219 1 U&nbsp;&nbsp; 0.180E+08&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 6 132.896&nbsp;&nbsp; 1.848&nbsp;&nbsp; 7.228 1 U&nbsp;&nbsp; 0.108E+08&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp; &nbsp;&nbsp;0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 7 132.896&nbsp;&nbsp; 1.436&nbsp;&nbsp; 7.233 1 U&nbsp;&nbsp; 0.112E+08&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 8 118.540&nbsp;&nbsp; 6.796&nbsp;&nbsp; 6.796 1 U&nbsp;&nbsp; 0.452E+10&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 9 118.540&nbsp;&nbsp; 7.221&nbsp;&nbsp; 6.792 1 U&nbsp;&nbsp; 0.228E+09&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 10 118.540&nbsp;&nbsp; 7.054&nbsp;&nbsp; 6.794 1 U&nbsp;&nbsp; 0.167E+09&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 11 118.540&nbsp;&nbsp; 4.708&nbsp;&nbsp; 6.795 1 U&nbsp;&nbsp; 0.641E+08&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 12 118.540&nbsp;&nbsp; 2.032&nbsp;&nbsp; 6.794 1 U&nbsp;&nbsp; 0.203E+08&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 13 118.540&nbsp;&nbsp; 0.537&nbsp;&nbsp; 6.797 1 U&nbsp;&nbsp; 0.380E+08&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 14 131.288&nbsp;&nbsp; 6.911&nbsp;&nbsp; 6.900 1 U&nbsp;&nbsp; 0.261E+09&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 15 131.288&nbsp;&nbsp; 7.170&nbsp;&nbsp; 6.899 1 U&nbsp;&nbsp; 0.897E+08&nbsp;0.000E+00 e 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp; 0</span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; ...</span></font></div><div><span><font size="2">&nbsp;</font></span></div><div style="margin: 12pt 0cm 3pt;">'''<font size="4"><span>&nbsp;B3. "Standard" ABACUS format.</span></font>'''</div><div><span><font size="2">&nbsp;</font></span></div><div><font size="2">Example_B3.1: (not referenced N15NOESY)</font></div><div>&nbsp;</div><div><font size="2">1<span>&nbsp;&nbsp; 106.850&nbsp;&nbsp; 4.244&nbsp;&nbsp; 8.259&nbsp;&nbsp; 1096259 </span></font></div><div><font size="2">2<span>&nbsp;&nbsp; 108.915&nbsp;&nbsp; 1.625&nbsp;&nbsp; 8.438&nbsp;&nbsp; 544482 </span></font></div><div><font size="2">3<span>&nbsp;&nbsp; 108.915&nbsp;&nbsp; 6.898&nbsp;&nbsp; 8.438&nbsp;&nbsp; 428124 </span></font></div><div><font size="2">4<span>&nbsp;&nbsp; 119.793&nbsp;&nbsp; 2.017&nbsp;&nbsp; 7.851&nbsp;&nbsp; 858875 </span></font></div><div><font size="2">5<span>&nbsp;&nbsp; 119.793&nbsp;&nbsp; 4.358&nbsp;&nbsp; 7.855&nbsp;&nbsp; 1260421 </span></font></div><div><font size="2">6<span>&nbsp;&nbsp; 126.081&nbsp;&nbsp; 4.573&nbsp;&nbsp; 8.518&nbsp;&nbsp; 590579 </span></font></div><div><font size="2">7<span>&nbsp;&nbsp; 126.081&nbsp;&nbsp; 3.891&nbsp;&nbsp; 8.522&nbsp;&nbsp; 651350 </span></font></div><div><font size="2">8<span>&nbsp;&nbsp; 125.092&nbsp;&nbsp; 5.665&nbsp;&nbsp; 8.261&nbsp;&nbsp; 793816 </span></font></div><div><font size="2">9<span>&nbsp;&nbsp; 125.092&nbsp;&nbsp; 3.567&nbsp;&nbsp; 8.264&nbsp;&nbsp; 1123055 </span></font></div><div><font size="2">…</font></div><div>&nbsp;</div><div><font size="2">Example_B3.2: (not referenced C135NOESY)</font></div><div>&nbsp;</div><div><font size="2">1<span>&nbsp;&nbsp; 61.234&nbsp;&nbsp; 2.083&nbsp;&nbsp; 4.157&nbsp;&nbsp; 0.124E+08 </span></font></div><div><font size="2">2<span>&nbsp;&nbsp; 61.234&nbsp;&nbsp; 7.471&nbsp;&nbsp; 4.152&nbsp;&nbsp; 0.751E+07 </span></font></div><div><font size="2">3<span>&nbsp;&nbsp; 31.252&nbsp;&nbsp; 4.219&nbsp;&nbsp; 2.974&nbsp;&nbsp; 0.814E+07 </span></font></div><div><font size="2">4<span>&nbsp;&nbsp; 31.252&nbsp;&nbsp; 4.222&nbsp;&nbsp; 3.029&nbsp;&nbsp; 0.985E+07 </span></font></div><div><font size="2">5<span>&nbsp;&nbsp; 50.670&nbsp;&nbsp; 4.728&nbsp;&nbsp; 3.651&nbsp;&nbsp; 0.114E+09 </span></font></div><div><font size="2">6<span>&nbsp;&nbsp; 17.853&nbsp;&nbsp; 2.445&nbsp;&nbsp; 0.865&nbsp;&nbsp; 0.506E+08 </span></font></div><div><font size="2">7<span>&nbsp;&nbsp; 17.853&nbsp;&nbsp; 3.055&nbsp;&nbsp; 0.868&nbsp;&nbsp; 0.189E+08 </span></font></div><div><font size="2">8<span>&nbsp;&nbsp; 17.853&nbsp;&nbsp; 3.837&nbsp;&nbsp; 0.868&nbsp;&nbsp; 0.285E+08 </span></font></div><div><font size="2">9<span>&nbsp;&nbsp; 17.853&nbsp;&nbsp; 7.122&nbsp;&nbsp; 0.873&nbsp;&nbsp; 0.278E+08 </span></font></div><div><font size="2">10<span>&nbsp;&nbsp; 17.853&nbsp;&nbsp; 6.847&nbsp;&nbsp; 0.868&nbsp;&nbsp; 0.185E+08 </span></font></div><div><font size="2">11<span>&nbsp;&nbsp; 17.853&nbsp;&nbsp; 8.292&nbsp;&nbsp; 0.860&nbsp;&nbsp; 0.263E+08 </span></font></div><div><font size="2">12<span>&nbsp;&nbsp; 17.853&nbsp;&nbsp; 8.393&nbsp;&nbsp; 0.860&nbsp;&nbsp; 0.198E+08 </span></font></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="5"><span>''C. Spin-systems file.''</span></font>'''</div><div>&nbsp;</div><div>&nbsp;</div><div><span style="font-size: 11pt;">One can load&nbsp;both assigned and not assigned spin-systems (fragments)</span></div><div><span style="font-size: 11pt;">There is only one format to load not assigned spin-systems.</span></div><div><span style="font-size: 11pt;">Assigned spin-systems could be loded using&nbsp;two different formats.</span></div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="4"><span>C1. PB-fragments in standard format.</span></font>'''</div><div>&nbsp;</div><div><span style="font-size: 11pt;">Each fragment is represented by a number of lines. The groups of lines </span></div><div><span style="font-size: 11pt;">corresponding to different fragments are separated by empty line. The line </span></div><div><span style="font-size: 11pt;">that follow the last fragment should have 'Q' at the first position.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">A fragment is described by the following format:</span></div><div><span><font size="2">&nbsp;</font></span></div><div><font size="2">&nbsp;31 X<span>&nbsp;&nbsp;&nbsp; 7&nbsp;&nbsp;&nbsp;&nbsp; 0.000&nbsp;</span></font></div><div><font size="2"><span>&nbsp;&nbsp; 9.025&nbsp;HN&nbsp;&nbsp;&nbsp; 106.560&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 5.221&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 55.302&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.940&nbsp;HB*&nbsp;&nbsp;&nbsp; 33.679&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.480&nbsp;HG1&nbsp;&nbsp;&nbsp; 27.976&nbsp;CG </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.775&nbsp;HG2&nbsp;&nbsp;&nbsp; 27.976&nbsp;CG </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 2.943&nbsp;HD1&nbsp;&nbsp;&nbsp; 43.958&nbsp;CD </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 3.205&nbsp;HD2&nbsp;&nbsp;&nbsp; 43.958&nbsp;CD </span></font></div><div>&nbsp;</div><div><span style="font-size: 11pt;">The first line contains userID, 1-letter residue type ('X' if not known), the </span></div><div><span style="font-size: 11pt;">number of the following lines, and chemical shift of CO (0.000 if not known).</span></div><div>&nbsp;</div><div>&nbsp;</div><div><span style="font-size: 11pt;">The fragments user ID could be any digit number &lt; 500.</span></div><div><span style="font-size: 11pt;">There is no restriction on the order of fragments in the file.</span></div><div>&nbsp;</div><div><font size="2">Example_C1:(not assigned PB-fragments)</font></div><div><font size="2">.....</font></div><div><font size="2">&nbsp;90 X<span>&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp; 0.000 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.462&nbsp;HN&nbsp;&nbsp;&nbsp; 122.771 &nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.262&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 56.242&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.880&nbsp;HB1&nbsp;&nbsp;&nbsp; 30.528&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 2.006&nbsp;HB2&nbsp;&nbsp;&nbsp; 30.528&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 2.222&nbsp;HG*&nbsp;&nbsp;&nbsp; 36.201&nbsp;CG </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;91 S<span>&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp; 174.082 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.089&nbsp;HN&nbsp;&nbsp;&nbsp; 123.488&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.626&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 55.058&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 3.413&nbsp;HB1&nbsp;&nbsp;&nbsp; 65.338&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 3.801&nbsp;HB2&nbsp;&nbsp;&nbsp; 65.338&nbsp;CB </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">247 X<span>&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp;&nbsp;&nbsp; 0.000 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.070&nbsp;HN&nbsp;&nbsp;&nbsp; 123.607&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.034&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 62.358&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 2.048&nbsp;HB&nbsp;&nbsp;&nbsp;&nbsp; 32.775&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 0.873&nbsp;HG1*&nbsp;&nbsp; 21.111&nbsp;CG1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 0.884&nbsp;HG2*&nbsp;&nbsp; 20.501&nbsp;CG2 </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;18 X<span>&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp;&nbsp;&nbsp; 0.000 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.110&nbsp;HN&nbsp;&nbsp;&nbsp; 123.044&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 5.042&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 58.559&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.179&nbsp;HB&nbsp;&nbsp;&nbsp;&nbsp; 70.135&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 0.087&nbsp;HG2*&nbsp;&nbsp; 16.018&nbsp;CG2 </span></font></div><div><font size="2">Q</font></div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="4"><span>C2. Assigned AA-fragments in standard format.</span></font>'''</div><div>&nbsp;</div><div><span style="font-size: 11pt;">AA-fragments are ordered in a file according to their assignment to </span></div><div><span style="font-size: 11pt;">protein sequence. Each fragment is described using the following format:</span></div><div>&nbsp;</div><div>&nbsp;</div><div><font size="2">&nbsp;11 T<span>&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp; 174.109&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 106 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.114&nbsp;HN&nbsp;&nbsp;&nbsp; 113.206&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.325&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 61.900&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.283&nbsp;HB&nbsp;&nbsp;&nbsp;&nbsp; 69.855&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.126&nbsp;HG2*&nbsp;&nbsp; 21.639&nbsp;CG2 </span></font></div><div>&nbsp;</div><div>&nbsp;</div><div><span style="font-size: 11pt;">The first line contains protein sequence ID to which the fragment is assigned, </span></div><div><span style="font-size: 11pt;">1-letter residue type, the number of the following lines, chemical shift of </span></div><div><span style="font-size: 11pt;">CO, and user ID of the fragment. The last number, user ID, is optional.</span></div><div>&nbsp;</div><div><font size="2">Example_C2.1:(assigned AA-fragments)</font></div><div><font size="2">.....</font></div><div><font size="2">&nbsp;10 G<span>&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp; 174.136&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 158 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.605&nbsp;HN&nbsp;&nbsp;&nbsp; 110.399&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 3.708&nbsp;HA*&nbsp;&nbsp;&nbsp; 46.225&nbsp;CA </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;11 T<span>&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp; 174.109&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 106 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.114&nbsp;HN&nbsp;&nbsp;&nbsp; 113.206&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.325&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 61.900&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.283&nbsp;HB&nbsp;&nbsp;&nbsp;&nbsp; 69.855&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.126&nbsp;HG2*&nbsp;&nbsp; 21.639&nbsp;CG2 </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;12 N<span>&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp; 175.100&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 999 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.231&nbsp;HN&nbsp;&nbsp;&nbsp; 122.327&nbsp;N </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;16 A<span>&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp; 179.269&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 50 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 3.224&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 56.082&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.518&nbsp;HB*&nbsp;&nbsp;&nbsp; 18.860&nbsp;CB </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;17 D<span>&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp; 179.378&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 74 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.451&nbsp;HN&nbsp;&nbsp;&nbsp; 116.577&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.370&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 57.335&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 2.656&nbsp;HB*&nbsp;&nbsp;&nbsp; 39.698&nbsp;CB </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;18 V<span>&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp; 177.276&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 117 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 7.579&nbsp;HN&nbsp;&nbsp;&nbsp; 122.993&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 3.720&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 65.701&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 2.068&nbsp;HB&nbsp;&nbsp;&nbsp;&nbsp; 31.930&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.160&nbsp;HG1*&nbsp;&nbsp; 22.719&nbsp;CG1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 0.642&nbsp;HG2*&nbsp;&nbsp; 20.806&nbsp;CG2 </span></font></div><div><font size="2">...........<span>&nbsp;&nbsp; </span></font></div><div><span><font size="2">&nbsp;&nbsp; </font></span></div><div>&nbsp;</div><div><font size="2">Example_C2.2:(assigned AA-fragments)</font></div><div><font size="2">.....</font></div><div><font size="2">&nbsp;10 G<span>&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp; 174.136&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.605&nbsp;HN&nbsp;&nbsp;&nbsp; 110.399&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 3.708&nbsp;HA*&nbsp;&nbsp;&nbsp; 46.225&nbsp;CA </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;11 T<span>&nbsp;&nbsp;&nbsp; 4&nbsp;&nbsp; 174.109&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.114&nbsp;HN&nbsp;&nbsp;&nbsp; 113.206&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.325&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 61.900&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.283&nbsp;HB&nbsp;&nbsp;&nbsp;&nbsp; 69.855&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.126&nbsp;HG2*&nbsp;&nbsp; 21.639&nbsp;CG2 </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;12 N<span>&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp; 175.100&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.231&nbsp;HN&nbsp;&nbsp;&nbsp; 122.327&nbsp;N </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;16 A<span>&nbsp;&nbsp;&nbsp; 2&nbsp;&nbsp; 179.269&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 3.224&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 56.082&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.518&nbsp;HB*&nbsp;&nbsp;&nbsp; 18.860&nbsp;CB </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;17 D<span>&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp; 179.378&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 8.451&nbsp;HN&nbsp;&nbsp;&nbsp; 116.577&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 4.370&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 57.335&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 2.656&nbsp;HB*&nbsp;&nbsp;&nbsp; 39.698&nbsp;CB </span></font></div><div><span><font size="2">&nbsp;&nbsp;&nbsp; </font></span></div><div><font size="2">&nbsp;18 V<span>&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp; 177.276&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 7.579&nbsp;HN&nbsp;&nbsp;&nbsp; 122.993&nbsp;N </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 3.720&nbsp;HA&nbsp;&nbsp;&nbsp;&nbsp; 65.701&nbsp;CA </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 2.068&nbsp;HB&nbsp;&nbsp;&nbsp;&nbsp; 31.930&nbsp;CB </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 1.160&nbsp;HG1*&nbsp;&nbsp; 22.719&nbsp;CG1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp; 0.642&nbsp;HG2*&nbsp;&nbsp; 20.806&nbsp;CG2 </span></font></div><div><font size="2">...........&nbsp;</font></div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="4"><span>C3. CYANA chemical shift file (prot-file).</span></font>'''</div><div>&nbsp;</div><div><font size="2">Example_C3:(assigned chemical shifts)</font></div><div>&nbsp;</div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 1&nbsp;&nbsp; 8.414&nbsp;&nbsp; 0.000 H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 2 123.795&nbsp;&nbsp; 0.000 N&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 3&nbsp;&nbsp; 4.723&nbsp;&nbsp; 0.000 HA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 4&nbsp;53.298&nbsp;&nbsp; 0.000 CA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 5&nbsp;&nbsp; 1.898&nbsp;&nbsp; 0.000 HB3&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 6&nbsp;32.288&nbsp;&nbsp; 0.000 CB&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 7&nbsp;&nbsp; 2.030&nbsp;&nbsp; 0.000 HB2&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 8&nbsp;&nbsp; 2.475&nbsp;&nbsp; 0.000 HG3&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp;&nbsp; 9&nbsp;32.024&nbsp;&nbsp; 0.000 CG&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 10&nbsp;&nbsp; 2.547&nbsp;&nbsp; 0.000 HG2&nbsp;&nbsp;&nbsp;&nbsp; 1 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 11 177.440&nbsp;&nbsp; 0.000 C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 12&nbsp;&nbsp; 4.379&nbsp;&nbsp; 0.000 HA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 13&nbsp;63.455&nbsp;&nbsp; 0.000 CA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 14&nbsp;&nbsp; 1.914&nbsp;&nbsp; 0.000 HB3&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 15&nbsp;32.194&nbsp;&nbsp; 0.000 CB&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 16&nbsp;&nbsp; 2.268&nbsp;&nbsp; 0.000 HB2&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2">&nbsp;<span>&nbsp;&nbsp;17&nbsp;&nbsp; 1.971&nbsp;&nbsp; 0.000 HG3&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 18&nbsp;27.313&nbsp;&nbsp; 0.000 CG&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 19&nbsp;&nbsp; 2.008&nbsp;&nbsp; 0.000 HG2&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 20&nbsp;&nbsp; 3.650&nbsp;&nbsp; 0.000 QD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 21&nbsp;50.670&nbsp;&nbsp; 0.000 CD&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 2 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 22 173.945&nbsp;&nbsp; 0.000 C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 23&nbsp;&nbsp; 8.438&nbsp;&nbsp; 0.000 H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 24 108.915&nbsp;&nbsp; 0.000 N&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 25&nbsp;&nbsp; 3.941&nbsp;&nbsp; 0.000 QA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3 </span></font></div><div><font size="2"><span>&nbsp;&nbsp;&nbsp; 26&nbsp;45.341&nbsp;&nbsp; 0.000 CA&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 3 </span></font></div><div><font size="2">..................................</font></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div style="margin: 12pt 0cm 3pt;">'''<font size="6"><span><font size="5">FMCGUI2.2&nbsp;HOW-TOs</font></span></font>'''</div><div style="margin: 12pt 0cm 3pt;">'''<font size="5"><span>''Spin-system identification''</span></font>'''</div><div>&nbsp;</div><div><span style="font-size: 11pt;">Normally, the NMR spectra shown in Table 1 should be collected for ABCUS. Spectra should ideally be collected from the same protein preparation and under the same conditions to make sure peaks are within tolerance between spectra. All spectra need to be appropriately synchronized <span style="color: black;">and calibrated against reference spectra of your choice. It is a good idea to use as a reference for spectra calibration the 2D HN-projection of 15N-NOESY and the 2D CH-projection of the 13C-NOESY. </span></span></div><div>&nbsp;</div><div>&nbsp;</div><div><span style="font-size: 11pt;">Step 1. Generate HN-rooted spin-systems (''b''PB-fragments) . </span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.1 &nbsp;These spin-systems can be identified using the following spectra </span></div><div><span style="font-size: 11pt;">
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15N_HSQC</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; HNCO</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CBCA(CO)NH</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; HBHAC (CO)NH</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; HNCA</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 15N_NOESY</span></div><div><span style="font-size: 11pt;">&nbsp;It is a good idea to analyze all these spectra simultaneously, for example, &nbsp;using SPARKY,&nbsp;in order to obtain &nbsp;peak lists of 15N_HSQC, HNCA, &nbsp;and CBCA(CO)HN spectra (see Figure 4.1A). The first two spectra should be referenced.</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 1.2. Create initial HN-rooted spin-systems (bPB-fragments) using FMCGUI:</span></div><div>&nbsp;</div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">start new project PRJ_1 ['''<span style="color: rgb(153, 51, 102);">Poject&gt;new</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load protein sequence ['''<span style="color: rgb(153, 51, 102);">DATA&gt;Protein Sequence&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load&nbsp;referenced HNCA peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;HNCA&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load&nbsp;referenced CBCA(CO)NH peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;CBCACONH&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load&nbsp;referenced HBHA(CO)NH peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;HBHACONH&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load&nbsp;referenced 15N_HSQC peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;N15 HSQC&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">set tolerances for matching of resonances in different spectral dimensions&nbsp;['''<span style="color: rgb(153, 51, 102);">DATA&gt;Tolerances</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">create bPB-fragments ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;create&gt;fawn</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt;"><span style="font-size: 11pt;">First, a referenced C13_hsqc peak list is created and shown in new window ‘fake C13 HSQC’. Warning messages are shown in the project main window. You have to check the list and modify it if needed. Then, press ‘OK’ button in the ‘‘fake C13 HSQC’ window. In the result, new window ‘Create Fragment’ pops up. The window consists of three sections. The left sections contains suggested ''b''PB-fragments, while the other sections contains two reports of fragments scoring with&nbsp;both C and H resonances and with only C&nbsp;resonances, respectively. Consider warning messages shown in the project main window and check/modify generated ''b''PB-fragments in the left section of “Create Fragment” window. When satisfied, the ''b''PB-fragments will be loaded in the memory by&nbsp;clicking on “OK” button.</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp; -&nbsp;&nbsp;&nbsp; save project PRJ_1. ['''<span style="color: rgb(153, 51, 102);">Project&gt;Save</span>'''] or ['''<span style="color: rgb(153, 51, 102);">Project&gt;Quit</span>''']</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div style="margin: 0cm 0cm 0pt 36pt;">&nbsp;</div><div><span style="font-size: 11pt;">Step 2. Complete ''b''PB-fragments with aliphatic side-chain resonances and generating additional spin-systems (without HN) using the following spectra. </span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13C_HSQC</span></div><div>''<span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>''<span style="font-size: 11pt;">(H)CCH-TOCSY</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; H(C)CH-TOCSY</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 13C_NOESY</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;2.1. Generate expected peak lists for C13HSQC, (H)CCH_TOCSY, and&nbsp;H(C)CH_TOCSY spectra&nbsp;using created ''b''PB-gfragments:</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;- open project PRJ1 ['''<span style="color: rgb(153, 51, 102);">Project&gt;load</span>''']</span></div><div><span style="font-size: 11pt;">&nbsp;- generate expected C13hsqc_exp.list that consists of C<sub></sub>-H<sub></sub> and C<sub></sub>-H<sub></sub> moieties </span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp; ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Expected Peaks&gt;C13HSQC</span>''']</span></div><div><span style="font-size: 11pt;">&nbsp;- generate expected CCH_tocsy.list&nbsp;['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Expected Peaks&gt;(H)CCH</span>''']</span></div><div><span style="font-size: 11pt;">&nbsp;- generate expected HCH_tocsy.list&nbsp;['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Expected Peaks&gt;H(C)CH</span>''']</span></div><div>&nbsp;</div><div style="margin: 0cm 0cm 0pt 21pt; text-indent: -21pt;"><span style="font-size: 11pt;">2.2<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">Read the generated peaks into SPARKY.&nbsp;</span></div><div>&nbsp;</div><div style="margin: 0cm 0cm 0pt 21pt; text-indent: -21pt;"><span style="font-size: 11pt;">2.3<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">Using SPARKY, complete ''b''PB-fragments with aliphatic side-chain resonances by analyzing </span><span style="font-size: 11pt;">C<sub></sub>-H<sub></sub> &nbsp;and&nbsp;C<sub></sub>-H<sub></sub> strips in all CH_rooted spectra (see Figure 2.B,C). New resonances should be peaked and referenced ''<u>only</u>'' in 13C_HSQC spectrum.</span></div><div>&nbsp;</div><div style="margin: 0cm 0cm 0pt 21pt; text-indent: -21pt;"><span style="font-size: 11pt;">2.4<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">When all peaks corresponding to HN-rooted spin-systems are peaked in 13C_HSQC spectrum, the unpicked peaks are used as a starting point for identification of spin-systems without backbone HN resonances (PB-fragments corresponding to residues before prolines in the protein sequence, last residue and residues missing in HN-rooted spectra).</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">Step 3. Spin-systems validation and correction.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">Validate PB-fragments using FMCGUI:</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;&nbsp;&nbsp; start a new project PRJ2 ['''<span style="color: rgb(153, 51, 102);">Project&gt;new</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load protein sequence ['''<span style="color: rgb(153, 51, 102);">DATA&gt;Protein Sequence&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load&nbsp;referenced 15N_HSQC peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;N15 HSQC&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load&nbsp;referenced 13C_HSQC peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;C13 HSQC&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load&nbsp;referenced HNCA peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;HNCA&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load&nbsp;&nbsp;CBCA(CO)HN peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;CBCACOHN&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">load&nbsp;&nbsp;HNCO peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;HNCO&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">set tolerances for matching of resonances in different spectral dimensions&nbsp;['''<span style="color: rgb(153, 51, 102);">DATA&gt;Tolerances</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">create PB-fragments ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;create&gt;abacus</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt;"><span style="font-size: 11pt;">This command starts script ‘''sps_create’''. In the result, a new window ‘Create Fragment’ pops up. The warning messages of the ‘''sps_create’'' script are shown in the main window and indicate spin-system that have low score, namely, S<sub>max</sub> &lt; 10<sup>-4</sup>. Following the warnings check and modify, if necessary, generated PB-fragments in the left section of “Create Fragment’ window. Alternatively, go back to spectra, fix peak lists accordingly, and repeat the fragment generation/validation again.</span></div><div style="margin: 0cm 0cm 0pt 36pt;"><span style="font-size: 11pt;">When satisfied, the PB-fragments will be saved (file ‘sps_pb.dat’ into directory PRJ2/sps) and loaded in the memory by&nbsp;pressing OK button in “Create Fragment’ window.</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;&nbsp;&nbsp; save project PRJ2 ['''<span style="color: rgb(153, 51, 102);">Project&gt;Save</span>'''] or ['''<span style="color: rgb(153, 51, 102);">Project&gt;Quit</span>''']</span></div><div>'''&nbsp;'''</div><div>'''&nbsp;'''</div><div style="margin: 12pt 0cm 3pt;">'''<font size="5"><span>''Sequence specific assignment of PB-fragments''</span></font>'''</div><div>'''<span style="font-size: 11pt;">&nbsp;</span>'''</div><div><span style="font-size: 11pt;">&nbsp;&nbsp; Step 1. Peak picking of NOESY spectra.</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; To facilitate peak-picking of NOESY spectra, you can&nbsp;first generate expected tocsy peaks of PB-fragments using FMCGUI:&nbsp;&nbsp; </span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">open project PRJ2 ['''<span style="color: rgb(153, 51, 102);">Project&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">generate tocsy peaks of N15 NOESY spetrum ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Expected Peaks&gt;N15NOESY</span>''']</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">generate tocsy peaks of C13NOESY spectrum ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Expected Peaks&gt;C13NOESY</span>''']</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Then, using SPARKY, read in the expected peaks into corresponding spectra and complete peak picking manually.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp; Step 2.&nbsp;Probabilistic assignment of PB-fragments to protein sequence.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">According to FMC procedure (see Introduction) you have to do the following:</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - Probabilistic typing of PB-fragments.</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - </span><span style="font-size: 11pt;">To calculate &nbsp;two fragments “contact” maps&nbsp;C<sub>NOE&nbsp;</sub>andC<sub>HNCA . </sub>C<sub>NOE</sub> is a contact map based on 15N_ and 13C_NOESY data (it could be calculated by 2 methods, “abacus” and “fawn”) and&nbsp;C<sub>HNCA</sub> is a map based on HNCA data. </span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - </span><span style="font-size: 11pt;">To calculate</span><span style="font-size: 11pt;"> assignment probabilities by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo simulations</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp; This can be done by the following commands:</span><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;open project PRJ2 ['''<span style="color: rgb(153, 51, 102);">Project&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;load 15N NOESY peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;N15 NOESY&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;load 13C NOESY peak list&nbsp;'''<span style="color: rgb(153, 51, 102);">[DATA&gt;C13NOESY H2O&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;set tolerances&nbsp;['''<span style="color: rgb(153, 51, 102);">Data&gt;Tolerances</span>''']</span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;calculate typing probabilities for all fragments ['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Type&gt;calculate&gt;abacus</span>''']</span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp; You have to consider the warning messages shown in the project main window and to analyze/modify typing probabilities manually by using “Fragment Property Modification” (FPM) window.&nbsp;To open FPM window click on <span style="color: rgb(153, 51, 102);">['''Fragment&gt;Type&gt;fix'''</span>]. This window has 3 sections.&nbsp;Top section allows you to select a fragment (by user ID) and modify its typing probabilities. The middle section shows typing probabilities that correspond to the selected amino acid type for all fragments. Here you can fix for any fragment it’s &nbsp;typing probability corresponding to the selected amino acid type to the values of 1 or 0.</span></div><div style="margin: 0cm 0cm 0pt 18pt;">&nbsp;</div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;calculate fragment contact map from HNCA data ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Contacts&gt;HNCA</span>'''].&nbsp;In the result the </span><span style="font-size: 11pt;">map is calculated and loaded in the memory. It is strongly recommended to check the messages in the project main window regarding HNCA peak list. In case there are inconsistencies present in the input HNCA peak list, go back to spectra and fix the list.</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - calculate fragment contact map from NOESY data ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Contacts&gt;NOE&gt;abacus</span>'''].&nbsp;In the result, two contact maps, </span><span style="font-size: 11pt;">and </span><span style="font-size: 11pt;">C<sub>NOE_F </sub>are calculated and loaded in the memory. Calculation of </span><span style="font-size: 11pt;">&nbsp;involves use of BACUS procedure for NOESY data interpretation, while </span><sub><span style="font-size: 11pt;">&nbsp;</span></sub><span style="font-size: 11pt;">&nbsp;</span><span style="font-size: 11pt;">does not.</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">Calculate assignment probabilities. It can be done using two different Monte Carlo simulation methods. Namely, Simulating Annealing (SA) ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Calculate Probability&gt;SA</span>'''] and Replica Exchange Method (REM) ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Calculate Probability&gt;REM</span>''']. Before starting calculations you have to specify control parameters. The main parameters to consider are: ‘Name of the SA/REM run’, ‘Size of the pool for unassigned fragments’, ‘number of SA runs’, ‘Final Temperature’ (SA), ‘Low Temperature’ (REM), and ‘NOE contact map’.&nbsp;The results of the calculations will be stored in the directory under specified name which is created inside PRJ2/assign/ directory. The main result consists of optimal and sub-optimal fragments assignments and assignment probability map. The last one will be automatically loaded in the memory as well.</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Calculation of assignment probabilities could be repeated a few times using different methods and parameters. Result of each calculation is stored in a separate directory. Therefore, there could be a few different directories (for example, sa_run1, sa_run2, rem_run0, rem_run1, rem_run3… ) within PRJ2/assign/ directory that contain different assignment probability maps.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">Step 3.&nbsp;Sequence-specific assignment of PB-fragments by analyzing probabilities </span><span style="font-size: 11pt;">.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp; A fragment assignment to a sequence position using FMCGUI could be done in two ways, manually and using assignment probability map, respectively. </span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - manual assignment ['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Fix Assignment&gt;manually</span>'''].</span></div><div><span style="font-size: 11pt;">This command pops up ‘Fragment Property Modification’ window. You can change the assignment ID of any selected fragment using the bottom section of the window. </span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - assignment using probability map&nbsp;['''<span style="color: rgb(153, 51, 102);">Assignment&gt;Fix Assignment&gt;using probability map</span>'''].&nbsp;You have to select a calculation directory (sa_run# or rem_run#) that contains assignment probability map, </span><span style="font-size: 11pt;">, </span><span style="font-size: 11pt;">and to specify the probability threshold </span><span style="font-size: 11pt;">. A fragments ''k'' will be assigned to position ''s'' if the condition&nbsp;</span><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;is satisfied (see Figure 1.).</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">Step 4. Assignment analysis.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">In the case of poor data, only a part of the fragments get assigned unambiguously. The uncertainty in fragments assignment could be resolved manually with the help of FMCGUI command ['''<span style="color: rgb(153, 51, 102);">View&gt;Assignment</span>''']. This command pops up “Assignment Graph” window that provides you with graphical tool to visualize the current assignment and to analyze sub-optimal fragment assignments.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">Step 5. Final resonance assignment.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">When sequence specific PB-fragment assignment is done you have to put in order assigned fragments and to assignCO resonances using command&nbsp;['''<span style="color: rgb(153, 51, 102);">Fragment&gt;Modify assigned</span>'''].</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><span style="font-size: 11pt;">&nbsp;</span></div><div style="margin: 12pt 0cm 3pt;">'''<font size="5"><span>''Structure calculation using FMCGUI''</span></font>'''</div><div>'''&nbsp;'''</div><div>&nbsp;</div><div><span style="font-size: 11pt;">Step 1. Load Data.</span></div><div>&nbsp;</div><div>'''<span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''<span style="font-size: 11pt;">- &nbsp;open new project PRJ3 ['''<span style="color: rgb(153, 51, 102);">Project&gt;new</span>''']</span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;load 15N NOESY peak list ['''<span style="color: rgb(153, 51, 102);">DATA&gt;N15 NOESY&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;load 13C_aliphatic NOESY peak list&nbsp;'''<span style="color: rgb(153, 51, 102);">[DATA&gt;C13NOESY H2O&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;load 13C_aromatic NOESY peak list&nbsp;'''<span style="color: rgb(153, 51, 102);">[DATA&gt;AromNOESY&gt;load</span>''']</span></div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">-&nbsp;set tolerances&nbsp;['''<span style="color: rgb(153, 51, 102);">Data&gt;Tolerances</span>''']</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; - &nbsp;load&nbsp;13C NOESY peak list&nbsp;'''<span style="color: rgb(153, 51, 102);">[DATA&gt;C13NOESY H2O&gt;load</span>''']</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;load&nbsp;''<u>assigned </u>''chemical shifts&nbsp;'''<span style="color: rgb(153, 51, 102);">[Fragment&gt;Load&gt;assigned</span>''']</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The file with assigned chemical shifts could be either in “standard” format&nbsp;&nbsp; (assigned AA-fragments) or in cyana&nbsp;format (prot-file).</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div><span style="font-size: 11pt;">Step 2. Set up constraints</span></div><div>&nbsp;</div><div>'''<span style="font-size: 11pt;">&nbsp;</span>'''<span style="font-size: 11pt;">The structure calculation requires dihedral angle constraints in the cyana format (aco-file). These constraints are usually prepared using the results of dihedral angle prediction by TALOS.&nbsp;H-bond constraints are optional.</span></div><div style="margin: 0cm 0cm 0pt 18pt;">&nbsp;</div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">calculate dihedral angle constraints ['''<span style="color: rgb(153, 51, 102);">Structure&gt;Constraints&gt;Talos&gt;Calculate</span>''']&nbsp;</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">set up H-bond&nbsp;constraints ['''<span style="color: rgb(153, 51, 102);">Structure&gt;Constraints&gt;H-bonds&gt;Specify</span>''']&nbsp;</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div style="margin: 0cm 0cm 0pt 36pt;"><span style="font-size: 11pt;">In the cased&nbsp;dihedral angle or H-bond constraints in cyana format (aco-file or upl-file, respectively) already are &nbsp;prepared, &nbsp;then the constraints&nbsp;can&nbsp;be loaded &nbsp;from the corresponding files &nbsp;&nbsp;['''<span style="color: rgb(153, 51, 102);">Structure-&gt;Constraints-&gt;Talos&gt;Load</span>''']&nbsp;or ['''<span style="color: rgb(153, 51, 102);">Structure&gt;Constraints&gt;H-bonds&gt;Load</span>''']</span></div><div>&nbsp;</div><div>&nbsp;</div><div><span style="font-size: 11pt;">Step 3. Specify ligands coordinating ZN ions (if there are any).</span></div><div>&nbsp;</div><div style="margin: 0cm 0cm 0pt 18pt;"><span style="font-size: 11pt;">If there are ZN ions as a part of a protein structure the file “zn_ligands” should be present inside FMCGUI project directory. This file can be created by the following command</span></div><div style="margin: 0cm 0cm 0pt 18pt;">'''&nbsp;'''</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;specify residues that coordinate ZN ion(s) ['''<span style="color: rgb(153, 51, 102);">Structure&gt;Add ZN ion</span>''']</span></div><div>'''&nbsp;'''</div><div>&nbsp;</div><div><span style="font-size: 11pt;">Step 4. Set up CYANA calculations</span></div><div style="margin: 0cm 0cm 0pt 18pt;">&nbsp;</div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;setting up structure calculations with CYANA&nbsp;['''<span style="color: rgb(153, 51, 102);">Structure&gt;Calcuate&gt;cyana</span>''']</span></div><div>'''<span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''<span style="font-size: 11pt;">All files that are necessary for CYANA&nbsp;run are prepared and saved&nbsp;in the user specified directory, crun#,&nbsp;which is&nbsp;located inside the project directory. These files include chemical shifts (belok.prot file), sequence file, peak lists, dihedral angles constraints (file belok.aco), H-bond constraints, if available, (file hbond.upl), and constraints for ZN ions, if present, (files zn.upl,&nbsp;zn.lol).</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">Step 5. Water refinement</span></div><div>'''&nbsp;'''</div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">set up water refinement&nbsp;calculations of the ensemble of structures obtained by CYANA&nbsp;['''<span style="color: rgb(153, 51, 102);">Structure&gt;Water Refinement&gt;calculate</span>''']. The popped up window allows user to select file with cyana structural ensemble (final.pdb),&nbsp;cyana dihedral angle constraints (belok.aco), cyana distance constraints (final.upl) , H-bond constraints (hbond.upl), RDC data,&nbsp;ZINC ligands file, and to specify cis-Proline residues and proton state of HIS residues. The command will set up the water refinement calculations in the user specified directory WRdir.</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">curry out water refinement calculations (on linux cluster is recommended) following the instruction given in the project main window</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">analp.comyze and superimpose refined structures ['''<span style="color: rgb(153, 51, 102);">Structure&gt;Water Refinement&gt;Summary</span>''']. The refined structural models are superimposed and combined in one file. Also, for each refined structure, different energy component are calculated and analysis of constraint violations is performed. The results of this analysis are placed in the created directory WRdir_results.</span></div><div>'''&nbsp;'''</div><div><span style="font-size: 11pt;">Step 6. Structure evaluation and peak list refinement.</span></div><div>&nbsp;</div><div><span style="font-size: 11pt;">RPF analysis and&nbsp;DP score allow one to estimate goodness-of-fit&nbsp;of a structural ensemble to NOESY peak lists. The results of RPF analysis can serve both for structure validation and peak lists &nbsp;refinement. </span></div><div><span style="font-size: 11pt;">&nbsp;</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">to run RPF analysis ['''<span style="color: rgb(153, 51, 102);">Structure&gt;RPF&gt;RP</span>''']. </span><span style="font-size: 11pt;">The results of the RPF analysis include peak lists in the SPARKY format of both false negative and false positive peaks for C13_aliphatic_NOESY, C13_aromatic_NOESY, and N15_NOESY spectra in separate files.</span></div><div style="margin: 0cm 0cm 0pt 36pt; text-indent: -18pt;"><span style="font-size: 11pt;">-<span style="font-family: 'times new roman'; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span><span style="font-size: 11pt;">to set up DP-score calculations with AutoStructure&nbsp;</span><span style="font-size: 11pt;">['''<span style="color: rgb(153, 51, 102);">Structure&gt;RPF&gt;DP</span>'''].</span></div><div>&nbsp;</div><div style="margin: 0cm 0cm 0pt 18pt;">&nbsp;</div><div style="margin: 0cm 0cm 0pt 18pt;">&nbsp;<br></div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div><div>&nbsp;</div></font></font></font></font></font></font></div>
 
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Latest revision as of 23:48, 5 January 2010

  1. Introduction to ABACUS
  2. FMCGUI objects
  3. FMCGUI commands
  4. FMCGUI Data Formats
  5. FMCGUI HOW-TOs
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