Resonance Assignment/Abacus/Structure calculation setup and analysis: Difference between revisions

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(Created page with '<div>Step 1. Load Data.</div><div> </div> **open new project PRJ3 ['''<span>Project>new</span>'''] **load 15N NOESY peak list ['''<span>DATA>N15 NOESY>load</span>'…')
 
 
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<div>Step 1. Load Data.</div><div>&nbsp;</div>
=== Step 1. Load Data ===
**open new project PRJ3 ['''<span>Project&gt;new</span>''']  
<div>&nbsp;</div>  
**load 15N NOESY peak list ['''<span>DATA&gt;N15 NOESY&gt;load</span>''']  
**open new project PRJ3 { [[FMCGUI_commands#Project.3ENew|Project&gt;new]] }
**load 13C_aliphatic NOESY peak list&nbsp;'''<span>[DATA&gt;C13NOESY H2O&gt;load</span>''']  
**load 15N NOESY peak list { [[FMCGUI commands#Data.3EN15_NOESY.3E|DATA&gt;N15 NOESY&gt;load]] }
**load 13C_aromatic NOESY peak list&nbsp;'''<span>[DATA&gt;AromNOESY&gt;load</span>''']  
**load 13C_aliphatic NOESY peak list&nbsp; { [[FMCGUI commands#Data.3EC13_NOESY.3E|DATA&gt;C13NOESY H2O&gt;load]] }
**set tolerances&nbsp;['''<span>Data&gt;Tolerances</span>''']
**load 13C_aromatic NOESY peak list&nbsp; { [[FMCGUI commands#Data.3EArom_NOESY.3E|DATA&gt;AromNOESY&gt;load]] }
**<span>load&nbsp;13C NOESY peak list&nbsp;'''[DATA&gt;C13NOESY H2O&gt;load''']</span>  
**set tolerances&nbsp; { [[FMCGUI commands#Data.3ETolerances|Data&gt;Tolerances]] } <span />  
**<span>load&nbsp;''<u>assigned </u>''chemical shifts&nbsp;'''[Fragment&gt;Load&gt;assigned'''] </span>
**<span>load&nbsp;''<u>assigned </u>''chemical shifts&nbsp; { [[FMCGUI commands#Fragment.3ELoad.3Eassigned|Fragment&gt;Load&gt;assigned]] }
<div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The file with assigned chemical shifts could be either in “standard” format&nbsp;&nbsp; (assigned AA-fragments) or in cyana&nbsp;format (prot-file).</span></div><div>&nbsp;</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div>Step 2. Set up constraints</div><div>&nbsp;</div><div>'''&nbsp;'''The structure calculation requires dihedral angle constraints in the cyana format (aco-file). These constraints are usually prepared using the results of dihedral angle prediction by TALOS.&nbsp;H-bond constraints are optional.</div><div>&nbsp;</div><div><span>-<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>calculate dihedral angle constraints ['''<span>Structure&gt;Constraints&gt;Talos&gt;Calculate</span>''']&nbsp;</div><div><span>-<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up H-bond&nbsp;constraints ['''<span>Structure&gt;Constraints&gt;H-bonds&gt;Specify</span>''']&nbsp;</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div>In the cased&nbsp;dihedral angle or H-bond constraints in cyana format (aco-file or upl-file, respectively) already are &nbsp;prepared, &nbsp;then the constraints&nbsp;can&nbsp;be loaded &nbsp;from the corresponding files <span>&nbsp;&nbsp;['''Structure-&gt;Constraints-&gt;Talos&gt;Load''']&nbsp;or ['''Structure&gt;Constraints&gt;H-bonds&gt;Load'''] </span></div><div>&nbsp;</div><div>&nbsp;</div><div>Step 3. Specify ligands coordinating ZN ions (if there are any).</div><div>&nbsp;</div><div>If there are ZN ions as a part of a protein structure the file “zn_ligands” should be present inside FMCGUI project directory. This file can be created by the following command</div><div>'''&nbsp;'''</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;specify residues that coordinate ZN ion(s) ['''Structure&gt;Add ZN ion'''] </span></div><div>'''&nbsp;'''</div><div>&nbsp;</div><div>Step 4. Set up CYANA calculations</div><div>&nbsp;</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; -&nbsp;setting up structure calculations with CYANA&nbsp;['''Structure&gt;Calcuate&gt;cyana'''] </span></div><div>'''<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''All files that are necessary for CYANA&nbsp;run are prepared and saved&nbsp;in the user specified directory, crun#,&nbsp;which is&nbsp;located inside the project directory. These files include chemical shifts (belok.prot file), sequence file, peak lists, dihedral angles constraints (file belok.aco), H-bond constraints, if available, (file hbond.upl), and constraints for ZN ions, if present, (files zn.upl,&nbsp;zn.lol).</div><div>&nbsp;</div><div>Step 5. Structure evaluation and peak list refinement.</div><div>&nbsp;</div><div>RPF analysis and&nbsp;DP score allow one to estimate goodness-of-fit&nbsp;of a structural ensemble to NOESY peak lists. The results of RPF analysis can serve both for structure validation and peak lists&nbsp;refinement. </div><div>&nbsp;</div><div><span>-<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>run RPF analysis ['''<span>Structure&gt;RPF&gt;RP</span>The results of the RPF analysis include peak lists in the SPARKY format of both false negative and false positive peaks for C13_aliphatic_NOESY, C13_aromatic_NOESY, and N15_NOESY spectra in separate files.''']. </div><div><span>-<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp;['''<span>Structure&gt;RPF&gt;DP</span>'''].</div>
</span>
<div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The file with assigned chemical shifts could be either in “standard” format&nbsp;&nbsp; ([[Spin systems format|assigned AA-fragments]]) or in [[Spin systems format|cyana format]] (prot-file).</span></div><div>&nbsp;</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div>
 
=== Step 2. Set up constraints ===
<div>&nbsp;</div><div>'''&nbsp;'''The structure calculation requires dihedral angle constraints in the cyana format (aco-file). These constraints are usually prepared using the results of dihedral angle prediction by TALOS.&nbsp;H-bond constraints are optional.</div><div>&nbsp;</div>  
*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>calculate dihedral angle constraints { [[FMCGUI_commands#Structure.3EConstraints.3ETalos.3Ecalculate|Structure&gt;Constraints&gt;Talos&gt;Calculate]] }&nbsp;  
*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up H-bond&nbsp;constraints { [[FMCGUI_commands#Structure.3EConstraints.3EH-bonds.3ESpecify|Structure&gt;Constraints&gt;H-bonds&gt;Specify]] }&nbsp;
<div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div><div>In the cased&nbsp;dihedral angle or H-bond constraints in cyana format (aco-file or upl-file, respectively) already are &nbsp;prepared, &nbsp;then the constraints&nbsp;can&nbsp;be loaded &nbsp;from the corresponding files <span>&nbsp;&nbsp; { [[FMCGUI_commands#Structure.3EConstraints.3ETalos.3Eload|Structure-&gt;Constraints-&gt;Talos&gt;Load]] }&nbsp;or { [[FMCGUI_commands#Structure.3EConstraints.3EH-bonds.3ESpecify|Structure&gt;Constraints&gt;H-bonds&gt;Load]] } </span></div><div>&nbsp;</div><div>&nbsp;</div>
 
=== Step 3. Specify ligands coordinating ZN ions (if there are any) ===
<div>&nbsp;</div><div>If there are ZN ions as a part of a protein structure the file “zn_ligands” should be present inside FMCGUI project directory. This file can be created by the following command</div><div>'''&nbsp;'''</div>  
*<span>&nbsp;&nbsp;&nbsp; specify residues that coordinate ZN ion(s) { [[FMCGUI commands#Structure.3EAdd_ZN_ligands|Structure&gt;Add ZN ion]] }
</span>
<div>'''&nbsp;'''</div><div>&nbsp;</div>
 
=== '''Step 4. Set up CYANA calculations'''  ===
<div>'''&nbsp;'''</div>  
*<span>&nbsp;&nbsp;&nbsp; setting up structure calculations with CYANA&nbsp; { [[FMCGUI commands#Structure.3ECalculate.3ECyana|Structure&gt;Calcuate&gt;cyana]] }
</span>
<div>'''<span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span>'''All files that are necessary for CYANA&nbsp;run are prepared and saved&nbsp;in the user specified directory, crun#,&nbsp;which is&nbsp;located inside the project directory. These files include chemical shifts (belok.prot file), sequence file, peak lists, dihedral angles constraints (file belok.aco), H-bond constraints, if available, (file hbond.upl), and constraints for ZN ions, if present, (files zn.upl,&nbsp;zn.lol).</div><div>&nbsp;</div>
 
=== Step 5. Structure evaluation and peak lists refinement ===
<div>&nbsp;</div><div>RPF analysis and&nbsp;DP score allow one to estimate goodness-of-fit&nbsp;of a structural ensemble to NOESY peak lists. The results of RPF analysis can serve both for structure validation and peak lists&nbsp;refinement. </div><div>&nbsp;</div>  
*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>run RPF analysis { [[FMCGUI commands#Structure.3ERPF.3ERP|Structure&gt;RPF&gt;RP]] }. The results of the RPF analysis include peak lists in the SPARKY format of both false negative and false positive peaks for C13-aliphatic NOESY, C13-Aromatic NOESY, and N15-NOESY spectra in separate files.  
*<span><span>&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp; { [[FMCGUI commands#Structure.3ERPF.3EDP|Structure&gt;RPF&gt;DP]] }.

Latest revision as of 23:49, 5 January 2010

Step 1. Load Data

 

            The file with assigned chemical shifts could be either in “standard” format   (assigned AA-fragments) or in cyana format (prot-file).
 
     

Step 2. Set up constraints

 
 The structure calculation requires dihedral angle constraints in the cyana format (aco-file). These constraints are usually prepared using the results of dihedral angle prediction by TALOS. H-bond constraints are optional.
 
           
In the cased dihedral angle or H-bond constraints in cyana format (aco-file or upl-file, respectively) already are  prepared,  then the constraints can be loaded  from the corresponding files    { Structure->Constraints->Talos>Load } or { Structure>Constraints>H-bonds>Load }
 
 

Step 3. Specify ligands coordinating ZN ions (if there are any)

 
If there are ZN ions as a part of a protein structure the file “zn_ligands” should be present inside FMCGUI project directory. This file can be created by the following command
 

 
 

Step 4. Set up CYANA calculations

 

          All files that are necessary for CYANA run are prepared and saved in the user specified directory, crun#, which is located inside the project directory. These files include chemical shifts (belok.prot file), sequence file, peak lists, dihedral angles constraints (file belok.aco), H-bond constraints, if available, (file hbond.upl), and constraints for ZN ions, if present, (files zn.upl, zn.lol).
 

Step 5. Structure evaluation and peak lists refinement

 
RPF analysis and DP score allow one to estimate goodness-of-fit of a structural ensemble to NOESY peak lists. The results of RPF analysis can serve both for structure validation and peak lists refinement.
 
  •       run RPF analysis { Structure>RPF>RP }. The results of the RPF analysis include peak lists in the SPARKY format of both false negative and false positive peaks for C13-aliphatic NOESY, C13-Aromatic NOESY, and N15-NOESY spectra in separate files.
  •      set up DP-score calculations with AutoStructure  { Structure>RPF>DP }.
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