Resonance Assignment/Abacus/Water refinement setup and analysis: Difference between revisions

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*open new project PRJ4 [<span>Project&gt;new</span>] or
*open new project PRJ4 { [[FMCGUI commands#Project.3ENew|Project&gt;new]] } or
<div>&nbsp;&nbsp;&nbsp;&nbsp; load&nbsp;old one PRJ3 [<span>Project&gt;load&lt;/span</span>]  
<div>&nbsp;&nbsp;&nbsp;&nbsp; load&nbsp;old one PRJ3 { [[FMCGUI commands#Project.3ELoad|Project&gt;load]] }
*set up water refinement&nbsp;calculations of the ensemble of structures obtained by CYANA&nbsp;[<span>Structure&gt;Water Refinement&gt;calculate</span>]. The popped up window allows user to select file with cyana structural ensemble (final.pdb),&nbsp;cyana dihedral angle constraints (belok.aco), cyana distance constraints (final.upl) , H-bond constraints (hbond.upl), RDC data,&nbsp;ZINC ligands file, and to specify cis-Proline residues and proton state of HIS residues. The command will set up the water refinement calculations in the user specified directory WRdir.  
*set up water refinement&nbsp;calculations of the ensemble of structures obtained by CYANA&nbsp; { [[FMCGUI commands#Structure.3ERWater_refinment.3Ecalculate|Structure&gt;Water Refinement&gt;calculate]] }. The popped up window allows user to select file with cyana structural ensemble (final.pdb),&nbsp;cyana dihedral angle constraints (belok.aco), cyana distance constraints (final.upl) , H-bond constraints (hbond.upl), RDC data,&nbsp;ZINC ligands file, and to specify cis-Proline residues and proton state of HIS residues. The command will set up the water refinement calculations in the user specified directory WRdir.  
*curry out water refinement calculations (on linux cluster is recommended) following the instruction given in the project main window  
*curry out water refinement calculations (on linux cluster is recommended) following the instruction given in the project main window  
*analyze and superimpose refined structures [<span>Structure&gt;Water Refinement&gt;Summary</span>]. The refined structural models are superimposed and combined in one file. Also, for each refined structure, different energy component are calculated and analysis of constraint violations is performed. The results of this analysis are placed in the created directory WRdir_results.
*analyze and superimpose refined structures { [[FMCGUI commands#Structure.3ERWater_refinment.3Esummary|Structure&gt;Water Refinement&gt;Summary]] }. The refined structural models are superimposed and combined in one file. Also, for each refined structure, different energy component are calculated and analysis of constraint violations is performed. The results of this analysis are placed in the created directory WRdir_results.
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Revision as of 00:02, 3 December 2009

     load old one PRJ3 { Project>load }
  • set up water refinement calculations of the ensemble of structures obtained by CYANA  { Structure>Water Refinement>calculate }. The popped up window allows user to select file with cyana structural ensemble (final.pdb), cyana dihedral angle constraints (belok.aco), cyana distance constraints (final.upl) , H-bond constraints (hbond.upl), RDC data, ZINC ligands file, and to specify cis-Proline residues and proton state of HIS residues. The command will set up the water refinement calculations in the user specified directory WRdir.
  • curry out water refinement calculations (on linux cluster is recommended) following the instruction given in the project main window
  • analyze and superimpose refined structures { Structure>Water Refinement>Summary }. The refined structural models are superimposed and combined in one file. Also, for each refined structure, different energy component are calculated and analysis of constraint violations is performed. The results of this analysis are placed in the created directory WRdir_results.
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