View source for Resonance Assignment/Abacus/FMCGUI objects

&nbsp; 
<div>Most of FMCGUI commands operate mainly with the following three objects that are located in computer memory:&nbsp;</div>
*protein sequence
*peak list 
*and PB fragments.
<div>&nbsp;</div> 
== '''Protein sequence'''  ==
<div>This object can be created in memory using {[[FMCGUI commands#Data&gt;Protein_Sequence&gt;Load|Data&gt;Protein Sequence&gt;Load ]]} or {[[FMCGUI commands#Project.3ELoad|Project&gt;Load]]} commands. <br></div><div>&nbsp;</div><div>&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, then the loaded sequence should be numbered accordingly starting with a negative position ID of the first residue.</div><div>&nbsp;</div>

== Peak list  ==
<div>Different peak lists objects can be created in memory using {[[FMCGUI commands#Data.3EN15_NOESY.3E|Data&gt;”Peak list name”&gt;Load]]} or {[[FMCGUI commands#Project.3ELoad|Project&gt;Load]]}</div><div></div><div></div><div><br> </div> 
*(+)&nbsp;&nbsp;&nbsp; peak list is required to be referenced 
*(+/-)&nbsp; peak lists could be referenced optionally&nbsp; 
*(-) &nbsp; &nbsp; peak lists for which referencing is not used even if it is present&nbsp;in the input file<br>
<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; </span></div> 
{| cellspacing="0" cellpadding="0" border="1"
|-
| width="176" valign="top" | <div align="center">N15 NOESY<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div> 
| width="88" valign="top" | <div align="center">-</div>
|-
| width="176" valign="top" | <div align="center">C13 NOESY H2O<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div> 
| width="88" valign="top" | <div align="center">-</div>
|-
| width="176" valign="top" | <div align="center">Arom NOESY<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div> 
| width="88" valign="top" | <div align="center">-</div>
|-
| width="176" valign="top" | <div align="center">N15 HSQC</div> 
| width="88" valign="top" | <div align="center">+</div>
|-
| width="176" valign="top" | <div align="center">C13 HSQC</div> 
| width="88" valign="top" | <div align="center">+</div>
|-
| width="176" valign="top" | <div align="center">HNCA</div> 
| width="88" valign="top" | <div align="center">+/-</div>
|-
| width="176" valign="top" | <div align="center">HNCO</div> 
| width="88" valign="top" | <div align="center">-</div>
|-
| width="176" valign="top" | <div align="center">CBCACONH</div> 
| width="88" valign="top" | <div align="center">+/-</div>
|-
| width="176" valign="top" | <div align="center">HBHACONH</div> 
| width="88" valign="top" | <div align="center">+</div>
|}
<div align="center"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div>&nbsp;</div>

== &nbsp;List of PB fragments  ==
<div></div><div>This object can be created in memory using {[[FMCGUI commands#Fragment.3ELoad.3EPB_fragments|Fragment&gt;Load&gt;]]}, {[[FMCGUI commands#Fragment.3ECreate.3Eabacus|Fragment&gt;Create&gt;abacus]]}, or {[[FMCGUI commands#Project.3ELoad|Project&gt;Load]]} commands. </div><div></div><div>Each PB fragment in the list has the following main properties:</div> 
==== User ID&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  ====

&nbsp;&nbsp;&nbsp; &nbsp;Fragment ID assigned by user, ''U_id''<span style="font-style: italic;">. </span>''U_id'' can’t be changed within FMCGUI.

==== Assignment ID  ====

&nbsp;&nbsp;&nbsp; Assignment ID, ''A_id'',&nbsp; indicates the sequence position ID to which the fragment is assigned.<br> 

''A_id'' = -99 if&nbsp;the fragment is not assigned to any position in the sequence. 

''A_id'' could be set up or modified by the following commands {[[FMCGUI commands#Assignment.3EFix_Assignment.3EManually|Assignment&gt;Fix Assignment&gt;Manually]]}, {[[FMCGUI commands#Assignment.3EFix_Assignment.3EUsing_Probability_map|Assignment&gt;Fix Assignment&gt;Using probability Map]]}, and {[[FMCGUI commands#Assignment.3EFix_Assignment.3EReset_all|Assignment&gt;Fix Assignment&gt;Reset all]] }.

==== Typing probabilities  ====

&nbsp;&nbsp;&nbsp;&nbsp; <span>T<sup>t </sup>(f)&nbsp; </span><span>is a probability for fragment ''f ''to have amino acid type ''t''</span><span>. Here ''t ''corresponds to one of 20 amino acid residue types, and f </span><span>is fragment user ID. </span> 

Typing probbilities&nbsp; could be calculated or modified manually by the commands {[[FMCGUI commands#Fragment.3EType.3ECalculate.3E|Fragment&gt;Type&gt;Calculate]]} and&nbsp; {[[FMCGUI commands#Fragment.3EType.3Efix|Fragment&gt;Type&gt;Fix]]}, respectively.

=== Contact map  ===

:There are three fragment contact maps: C<sup>f1</sup><sub>CA</sub><span>(f2)&nbsp; , </span>C<sup>f1</sup><sub>B</sub><span>(f2) ,</span><span>&nbsp; and </span>C<sup>f1</sup><sub>F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f1'' in protein sequence. Here ''f''1 and ''f2'' stand for&nbsp;fragment's user ID. </span>
<div><span>&nbsp;Fragment contact map&nbsp; </span>C<sup>f1</sup><sub>CA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command&nbsp;&nbsp; {[[FMCGUI commands#Assignment.3EContacts.3EHNCA|Assignment&gt;Contacts&gt;HNCA]]}<div>&nbsp;Fragment<span>&nbsp;&nbsp; contact maps </span>C<sup>f1</sup><sub>B</sub><span>(f2)&nbsp;</span><span>&nbsp; and </span>C<sup>f1</sup><sub>F</sub><span>(f2) </span>&lt;span /&gt;<span>&nbsp; are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>&nbsp;&nbsp;</span><span> </span>C<sup>f1</sup><sub>F</sub><span>(f2)&nbsp;&nbsp;</span><span> can be calculated for all values of f1 and f2 by both commands&nbsp;&nbsp; {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn|Assignment&gt;Contacts&gt;NOE&gt;fawn]]} &nbsp; and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus|Assignment&gt;Contact&gt;NOE&gt;abacus]]}, while &nbsp; </span>C<sup>f1</sup><sub>B</sub><span>(f2) </span>&lt;span /&gt;<span> is calculated by&nbsp; command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus|Assignment&gt;Contact&gt;NOE&gt;abacus]]}.<div>&nbsp;</div></span></div></span></div>

=== Assignment probabilities  ===

:&nbsp;&nbsp;

<span>P<sup>s</sup>(f) is a probability of fragment f to be assigned to sequense position s, where f is fragment user ID, and s is sequence position ID.</span> <span>There are two assignment probabilities associated with a fragment - P<sup>s</sup><sub>SA</sub>(f) and P<sup>s</sup><sub>REM</sub>(f) - that are calculated using Simulates Annealing (SA) and 
</span> <span>Replica Exchange Method (REM) Monte Carlo simulations, respistively.</span> <span>
</span> 

<br> 
<div>&nbsp;<span>P<sup>s</sup><sub>SA</sub>(f)&nbsp;&nbsp;&nbsp; is calclated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3ESA|Assignment&gt;Calculate Probabilities&gt;SA]]}&nbsp; </span><br></div><div>'''&nbsp;'''<span>P<sup>s</sup><sub>REM</sub>(f)&nbsp;  is calculated&nbsp;by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3EREM|Assignment&gt;Calculate probabilities&gt;REM]]}.</span></div><div><br></div><div><span>Both assignment probabilities could be also&nbsp; loaded in memory from already performed calculations using command {[[FMCGUI commands#Assignment.3ELoad_Probabilities|Assignment&gt;Load probabilities]]}.</span></div><div>&nbsp;</div><div><br></div><div>'''&nbsp;'''</div><div>'''&nbsp;<br>'''</div>

== Main window  ==
<div></div> 
==== Figure 2.1  ====
<div></div><div>[[Image:Fmcgui mainwindow.jpg|thumb|left|500px]]</div><div></div><div></div><div></div><div></div><div><br><br><br><br><br><br><br><br><br><br><br><br></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)<br></div> 
*&nbsp;the title bar displays the name of the current project and the directory inside which the project is located; 
*&nbsp;the bar with six menus: [[FMCGUI commands#Project_Menu|Project]], [[FMCGUI commands#Data_Menu|Data]], [[FMCGUI commands#Fragment_Menu|Fragment]], [[FMCGUI commands#Assignment_Menu|Assignment]], [[FMCGUI commands#Structure_Menu|Structure]], and [[FMCGUI commands#View_Menu|View]], respectively; 
*the project main window, where all messages from the last executed command are displayed&nbsp;; 
*the log window,&nbsp;where the history of executed commands is shown.
<div>&nbsp;</div><div>&nbsp;</div>