Resonance Assignment/Abacus/Structure calculation setup and analysis

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Contents

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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