Resonance Assignment/Abacus/Water refinement setup and analysis - Revision history

Agutmana: moved Water refinement setup and analysis to Resonance Assignment/Abacus/Water refinement setup and analysis

2010-01-05T23:49:20Z

moved Water refinement setup and analysis to Resonance Assignment/Abacus/Water refinement setup and analysis

← Older revision	Revision as of 23:49, 5 January 2010
(No difference)

AlexLemak at 00:07, 3 December 2009

2009-12-03T00:07:15Z

← Older revision		Revision as of 00:07, 3 December 2009
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	*open new project PRJ4 { [[FMCGUI commands#Project.3ENew\|Project>new]] } or		*open new project PRJ4 { [[FMCGUI commands#Project.3ENew\|Project>new]] } or
	<div>     load old one PRJ3 { [[FMCGUI commands#Project.3ELoad\|Project>load]] }		<div>     load old one PRJ3 { [[FMCGUI commands#Project.3ELoad\|Project>load]] }
	*set up water refinement calculations of the ensemble of structures obtained by CYANA  { [[FMCGUI commands#Structure.~~3ERWater_refinement~~.3Ecalculate\|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,  [[FMCGUI commands#Structure.3EAdd_ZN_ligands\|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 calculations of the ensemble of structures obtained by CYANA  { [[FMCGUI commands#Structure.3EWater_refinement.3Ecalculate\|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,  [[FMCGUI commands#Structure.3EAdd_ZN_ligands\|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 { [[FMCGUI commands#Structure.~~3ERWater_refinement~~.3Esummary\|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.		*analyze and superimpose refined structures { [[FMCGUI commands#Structure.3EWater_refinement.3Esummary\|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.
	</div>		</div>

AlexLemak at 00:04, 3 December 2009

2009-12-03T00:04:55Z

← Older revision		Revision as of 00:04, 3 December 2009
Line 1:		Line 1:
	*open new project PRJ4 { [[FMCGUI commands#Project.3ENew\|Project>new]] } or		*open new project PRJ4 { [[FMCGUI commands#Project.3ENew\|Project>new]] } or
	<div>     load old one PRJ3 { [[FMCGUI commands#Project.3ELoad\|Project>load]] }		<div>     load old one PRJ3 { [[FMCGUI commands#Project.3ELoad\|Project>load]] }
	*set up water refinement calculations of the ensemble of structures obtained by CYANA  { [[FMCGUI commands#Structure.~~3ERWater_refinment~~.3Ecalculate\|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.		*set up water refinement calculations of the ensemble of structures obtained by CYANA  { [[FMCGUI commands#Structure.3ERWater_refinement.3Ecalculate\|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,  [[FMCGUI commands#Structure.3EAdd_ZN_ligands\|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 { [[FMCGUI commands#Structure.~~3ERWater_refinment~~.3Esummary\|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.		*analyze and superimpose refined structures { [[FMCGUI commands#Structure.3ERWater_refinement.3Esummary\|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.
	</div>		</div>

AlexLemak at 00:02, 3 December 2009

2009-12-03T00:02:04Z

← Older revision		Revision as of 00:02, 3 December 2009
Line 1:		Line 1:
	*open new project PRJ4 [~~<span>~~Project>new~~</span>~~] or		*open new project PRJ4 { [[FMCGUI commands#Project.3ENew\|Project>new]] } or
	<div>     load old one PRJ3 [~~<span>~~Project>load~~</span</span>~~]		<div>     load old one PRJ3 { [[FMCGUI commands#Project.3ELoad\|Project>load]] }
	*set up water refinement calculations of the ensemble of structures obtained by CYANA [~~<span>~~Structure>Water Refinement>calculate~~</span>~~]. 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.		*set up water refinement calculations of the ensemble of structures obtained by CYANA  { [[FMCGUI commands#Structure.3ERWater_refinment.3Ecalculate\|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		*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>Water Refinement>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>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.
	</div>		</div>

AlexLemak at 16:06, 1 December 2009

2009-12-01T16:06:46Z

← Older revision		Revision as of 16:06, 1 December 2009
Line 1:		Line 1:
	*open new project PRJ4[~~'''~~<span>Project>new</span>~~'''~~] or		*open new project PRJ4 [<span>Project>new</span>] or
	<div>     load old one PRJ3[~~'''~~<span>Project>load</span</span>~~'''~~]		<div>     load old one PRJ3 [<span>Project>load</span</span>]
	*set up water refinement calculations of the ensemble of structures obtained by CYANA [~~'''~~<span>Structure>Water Refinement>calculate</span>~~'''~~]. 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.		*set up water refinement calculations of the ensemble of structures obtained by CYANA [<span>Structure>Water Refinement>calculate</span>]. 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		*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>Water Refinement>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 [<span>Structure>Water Refinement>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.
	</div>		</div>

AlexLemak: Created page with 'open new project PRJ4['''Project>new'''] or
load old one PRJ3['''Project>load</span'''] set up water refi…'

2009-11-30T00:37:53Z

Created page with '*open new project PRJ4['''<span>Project>new</span>'''] or <div> load old one PRJ3['''<span>Project>load</span</span>'''] *set up water refi…'

New page

*open new project PRJ4['''<span>Project>new</span>'''] or
<div>     load old one PRJ3['''<span>Project>load</span</span>''']
*set up water refinement calculations of the ensemble of structures obtained by CYANA ['''<span>Structure>Water Refinement>calculate</span>''']. 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 ['''<span>Structure>Water Refinement>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.
</div>