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]]
+#[[FMCGUI commands]]
-= '''<font size="6"><span><font size="5">INTRODUCTION TO ABACUS</font></span></font>''' =
+#FMCGUI Data Formats
-<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>
+#*[[Protein Sequence format]]
-{| width="666" cellspacing="0" cellpadding="0" border="0" style="width: 499.75pt; border-collapse: collapse;" class="FCK__ShowTableBorders"
+#*[[Peak Lists format]]
-|- style="height: 269.1pt;"
+#*[[Spin systems 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>
+#FMCGUI HOW-TOs
-| 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 identification]]
-|}
+#*[[Sequence specific assignment of PB fragments]]
-<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>
+#*[[Structure calculation setup and analysis]]
-== <font size="4"><span>NMR spectra required for ABACUS</span></font>  ==
+#*[[Water refinement setup and analysis]]
-&nbsp;
-<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"
-|-
-| 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>
-|-
-| 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>
-|-
-| 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>
-|-
-| 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>
-|-
-| 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>
-|-
-| 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>
-|-
-| 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>
-|-
-| 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>
-== '<font size="4">Spin-system identification strategy</font> ==
-<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>
-== <font size="4">Fragments assignment by FMC</font> ==
-== '''''&nbsp;''''' ==
-<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><div><span style="font-size: 11pt;">''Figure 1.4.''</span>'''''<span style="font-size: 11pt;">&nbsp;PB-fragments mapping onto protein sequence.</span>'''''</div><div>'''''&nbsp;'''''</div><div><span style="font-size: 11pt; color: rgb(51, 153, 102);">''Set of PB-frsagments''</span>'''''<b><span style="font-size: 16pt; color: rgb(51, 153, 102);">:</span></b><span style="font-size: 16pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; F<sub>1</sub> F<sub>2</sub> F<sub>3</sub> F<sub>4</sub> ....</span>'''''</div><div>'''''&nbsp;'''''</div><div>''<span style="color: rgb(51, 153, 102);">Positions:</span>'''<span>&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; <span style="color: blue;">protein sequence</span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <span style="color: red;">recycle bin</span></span>'''''</div><div><span>'''&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; 1 2 3 ……&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;… N<sub>s</sub>… .N<sub>total</sub>'''</span></div><div>&nbsp;</div><div><span style="font-size: 11pt; color: rgb(51, 153, 102);">Scoring function:</span></div><div>'''''&nbsp;'''''</div><div>'''''&nbsp;'''''</div><div>'''''&nbsp;'''''</div>
-<br> <br>
-<div><span style="font-size: 11pt;">Where</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;'''''A '''''is any possible fragment’s mapping (assignment) onto protein sequence;</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; N<sub>f</sub> is number of PB-fragments;</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; N<sub>s</sub> is number of residues in protein sequence;</span></div><div><span style="font-size: 11pt;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; &nbsp;N<sub>totl</sub> is number of total positions for fragment mapping; Positions in the “recycle bin” are reserved for discarded (not assigned)&nbsp;PB-fragments.</span></div><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>
-= '''<font size="6"><span><font size="5">FMCGUI_2.2 COMMANDS</font></span></font>''' =
-<div>&nbsp;</div>
-== '''<font size="4"><span>''0. FMCGUI objects.''</span></font>''' ==
-<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>
-{| cellspacing="0" cellpadding="0" border="1" style="margin: auto auto auto 4cm; border-collapse: collapse;"
-|-
-| 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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-|-
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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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-|-
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-<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>
-== '''<font size="4"><span>''&nbsp; ''</span></font>'''<font size="4">''1. Main window''</font> ==
-== '''&nbsp;''' ==
-<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></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></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></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></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></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>
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Resonance Assignment/Abacus: Difference between revisions

Latest revision as of 23:48, 5 January 2010

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Resonance Assignment/Abacus: Difference between revisions

Latest revision as of 23:48, 5 January 2010

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