Resonance Assignment/Abacus/FMCGUI objects: Difference between revisions

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<div>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. </div><div>&nbsp;</div>
<div>Most of FMCGUI commands operate mainly with the following three objects that are loaded into computer memory:&nbsp;</div>
*protein sequence  
*peak list  
*PB fragments
<div>&nbsp;</div>
== '''Protein sequence'''  ==
== '''Protein sequence'''  ==
<div>This object can be created in memory using [<span>Data&gt;Protein sequence&gt;load] or [Project&gt;load] commands. </span></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 in the loaded sequence, it should be numbered accordingly starting with a negative position ID of the first residue.</div><div>&nbsp;</div>
<div>The protein sequence can be loaded into the program using {[[FMCGUI commands#Data.3EProtein_Sequence.3ELoad|Data&gt;Protein Sequence&gt;Load ]]} or {[[FMCGUI commands#Project.3ELoad|Project&gt;Load]]} commands. <br></div><div>The position ID of the first residue in the sequence should be specified by the user when loading the&nbsp;sequence file (when it is not specified in the input file). Some commands in FMCGUI&nbsp;assume that the first residue of the protein sequence has position ID of 1. Therefore, if there is a HIS-tag, the loaded sequence should be numbered&nbsp;accordingly with a negative position ID for the first residue.</div><div>&nbsp;</div>
== Peak list ==
== Peak list ==
<div>Different peak lists objects can be created in memory using ['''<span>Data&gt;</span>'''”Peak list name'''”&gt;load'''] or ['''Project&gt;load'''] commands. For some peak-lists, peaks in the list could be referenced by spin-system (fragment) user ID.</div><div>The following table shows what peak lists are required referencing (+), peak lists </div><div>that are optionally referenced (+/-), and peak lists for which referencing is not used </div><div>even if present&nbsp;in the input file (-):</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; </span></div>
<div>Different peak lists can be loaded into the program 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 needs to be referenced
*(+/-)&nbsp; peak lists could be referenced, but it isn't necessary
*(-) &nbsp; &nbsp; peak lists&nbsp;could be&nbsp;referenced, but it won't be used by FMCGUI<br><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; </span>
 
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<div align="center"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div>&nbsp;</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  ==
== List of PB fragments  ==
<div></div><div>This object can be created in memory using ['''<span>Fragment&gt;Load</span>'''], ['''Fragment&gt;Create'''], or ['''Project&gt;load'''] commands. </div><div></div><div>Each PB fragment in the list has the following main properties:</div>
<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;
==== User ID&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;  ====
*&nbsp;&nbsp;&nbsp;&nbsp; Fragment ID assigned by user, ''U_id'';''U_id'' can’t be changed within FMCGUI.
 
&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;can 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  ====


*Assignment ID
:There are three fragment contact maps: C<sup>f1</sup><sub>HNCA</sub><span>(f2)&nbsp; , </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) ,</span><span>&nbsp; and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f2'' in protein sequence. Here ''f''1 and ''f2'' stand for&nbsp;fragment's user ID. </span>
*:&nbsp;&nbsp;&nbsp; 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).''A_id'' could be set up or modified by the commands['''<span>Assignment&gt;Fix Assignment&gt;Manually</span>'''], ['''Assignment&gt;Fix Assignment&gt;Using probability Map'''], and ['''Assignment&gt;Fix Assignment&gt;Reset all'''].
<div><span>&nbsp;Fragment contact map&nbsp; </span>C<sup>f1</sup><sub>HNCA</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>NOE_B</sub><span>(f2)&nbsp;</span><span>&nbsp; and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2)&nbsp;</span><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>NOE_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>NOE_B</sub><span>(f2)&nbsp;</span><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  ====


*Typing probabilities
:&nbsp;&nbsp;
*:&nbsp;&nbsp;&nbsp; Typing probabilities <span>&nbsp;&nbsp; , where&nbsp;''t ''correspond to one of 20 amino acid residue types.</span><span>is a probability for fragment ''U_id'' to have a type ''t''. It could be calculated or modified by the commands ['''Fragment&gt;Type&gt;Calculate'''] and ['''Fragment&gt;Type&gt;Fix'''].</span>


*Contact map
<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 />
*:&nbsp;&nbsp;&nbsp; Each fragment has three Fragment contact maps:&nbsp;<span>, &nbsp;, and , respectively.&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><span>is calculated from HNCA spectrum by the command&nbsp;&nbsp; ['''Assignment&gt;Contact&gt;HNCA''']</span></div><div>&nbsp;Fragment<span>&nbsp;&nbsp; contact maps &nbsp;and , calculated from NOESY spectra with and without using BACUS procedure, respectively;</span></div><div><span>&nbsp;&nbsp; &nbsp;can be calculated by the commands&nbsp;&nbsp; ['''Assignment&gt;Contact&gt;NOE&gt;fawn''']&nbsp;&nbsp;&nbsp; and ['''Assignment&gt;Contact&gt;NOE&gt;abacus'''], while &nbsp;is calculated by ['''Assignment&gt;Contact&gt;NOE&gt;abacus'''].</span></div><div>&nbsp;</div>
*Assignment probabilities
*:&nbsp;&nbsp;&nbsp; FragmentFragment assignment probabilities <span>&nbsp;and &nbsp;are calculated using SA and REM Monte Carlo simulations, respectively. Here ''s'' stands for protein sequence position ID. </span>
<div>&nbsp;<span> &nbsp;is calculated&nbsp;by command ['''Assignment&gt;Calculate probabilities&gt;SA'''] or it can be loaded in memory using command ['''Assignment&gt;Load probabilities'''];</span></div><div>&nbsp;<span> &nbsp;is calculated&nbsp;by command ['''Assignment&gt;Calculate probabilities&gt;REM'''] or it can be loaded in memory using command ['''Assignment&gt;Load probabilities'''];</span></div><div>&nbsp;</div><div>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>View&gt;Fragment</span>''']</div><div>&nbsp;</div><div>&nbsp;<br></div>


== Main window ==
<br>
<div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)</div><div>&nbsp;- the title bar displays the name of the current project and the directory where the project is located;</div><div>&nbsp;- the bar with six menu: Project, Data, Fragment, Assignment, Structure, and View, respectively;</div><div>- the main message window, where message from the last executed command is displayed&nbsp;;</div><div>- the log window,&nbsp;where the history of executed commands is shown.</div><div>&nbsp;</div><div>&nbsp;</div>
<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>
== 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)<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>

Latest revision as of 00:23, 9 January 2010

 

Most of FMCGUI commands operate mainly with the following three objects that are loaded into computer memory: 
  • protein sequence
  • peak list
  • PB fragments
 

Protein sequence

The protein sequence can be loaded into the program using {Data>Protein Sequence>Load } or {Project>Load} commands.
The position ID of the first residue in the sequence should be specified by the user when loading the sequence file (when it is not specified in the input file). Some commands in FMCGUI assume that the first residue of the protein sequence has position ID of 1. Therefore, if there is a HIS-tag, the loaded sequence should be numbered accordingly with a negative position ID for the first residue.
 

Peak list

Different peak lists can be loaded into the program using {Data>”Peak list name”>Load} or {Project>Load}

  • (+)    peak list needs to be referenced
  • (+/-)  peak lists could be referenced, but it isn't necessary
  • (-)     peak lists could be referenced, but it won't be used by FMCGUI
                                 
N15 NOESY             
-
C13 NOESY H2O     
-
Arom NOESY            
-
N15 HSQC
+
C13 HSQC
+
HNCA
+/-
HNCO
-
CBCACONH
+/-
HBHACONH
+
          
 

List of PB fragments

This object can be created in memory using {Fragment>Load>}, {Fragment>Create>abacus}, or {Project>Load} commands.
Each PB fragment in the list has the following main properties:

User ID      

     Fragment ID assigned by user, U_id. U_id can’t be changed within FMCGUI.

Assignment ID

    Assignment ID, A_id,  indicates the sequence position ID to which the fragment is assigned.

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

A_id could be set up or modified by the following commands {Assignment>Fix Assignment>Manually}, {Assignment>Fix Assignment>Using probability Map}, and {Assignment>Fix Assignment>Reset all }.

Typing probabilities

     Tt (f)  is a probability for fragment f to have amino acid type t. Here t corresponds to one of 20 amino acid residue types, and f is fragment user ID.

Typing probbilities can be calculated or modified manually by the commands {Fragment>Type>Calculate} and  {Fragment>Type>Fix}, respectively.

Contact map

There are three fragment contact maps: Cf1HNCA(f2)  , Cf1NOE_B(f2) ,  and Cf1NOE_F(f2) , respectively. Each contact map scores the possibility for any fragment f1 to be next to the fragment f2 in protein sequence. Here f1 and f2 stand for fragment's user ID.
 Fragment contact map  Cf1HNCA(f2) is calculated based on HNCA spectrum by the command   {Assignment>Contacts>HNCA}
 Fragment   contact maps Cf1NOE_B(f2)   and Cf1NOE_F(f2)   are calculated from NOESY spectra with or without using BACUS procedure, respectively.
   Cf1NOE_F(f2)   can be calculated for all values of f1 and f2 by both commands   {Assignment>Contacts>NOE>fawn}   and {Assignment>Contact>NOE>abacus}, while   Cf1NOE_B(f2)  is calculated by  command {Assignment>Contact>NOE>abacus}.
 

Assignment probabilities

  

Ps(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. There are two assignment probabilities associated with a fragment - PsSA(f) and PsREM(f) - that are calculated using Simulates Annealing (SA) and Replica Exchange Method (REM) Monte Carlo simulations, respistively.


 PsSA(f)    is calclated by command {Assignment>Calculate Probabilities>SA} 
 PsREM(f)  is calculated by command {Assignment>Calculate probabilities>REM}.

Both assignment probabilities could be also  loaded in memory from already performed calculations using command {Assignment>Load probabilities}.
 

Main window

Figure 2.1

Fmcgui mainwindow.jpg












The main frame of FMC Graphical Interface consist of 4 sections (see Figure)
  •  the title bar displays the name of the current project and the directory inside which the project is located;
  •  the bar with six menus: Project, Data, Fragment, Assignment, Structure, and View, respectively;
  • the project main window, where all messages from the last executed command are displayed ;
  • the log window, where the history of executed commands is shown.
 
 
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