AlexLemak at 22:58, 29 November 2009

2009-11-29T22:58:10Z

← Older revision		Revision as of 22:58, 29 November 2009
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	<div>Step 1. Load Data.</div><div> </div>		<div>Step 1. Load Data.</div><div> </div>
	*open new project PRJ3 ['''<span>Project>new</span>''']		**open new project PRJ3 ['''<span>Project>new</span>''']
	*load 15N NOESY peak list ['''<span>DATA>N15 NOESY>load</span>''']		**load 15N NOESY peak list ['''<span>DATA>N15 NOESY>load</span>''']
	*load 13C_aliphatic NOESY peak list '''<span>[DATA>C13NOESY H2O>load</span>''']		**load 13C_aliphatic NOESY peak list '''<span>[DATA>C13NOESY H2O>load</span>''']
	*load 13C_aromatic NOESY peak list '''<span>[DATA>AromNOESY>load</span>''']		**load 13C_aromatic NOESY peak list '''<span>[DATA>AromNOESY>load</span>''']
	*set tolerances ['''<span>Data>Tolerances</span>''']		**set tolerances ['''<span>Data>Tolerances</span>''']
	*<span>load 13C NOESY peak list '''[DATA>C13NOESY H2O>load''']</span>		**<span>load 13C NOESY peak list '''[DATA>C13NOESY H2O>load''']</span>
	*<span>load ''<u>assigned </u>''chemical shifts '''[Fragment>Load>assigned'''] </span>		**<span>load ''<u>assigned </u>''chemical shifts '''[Fragment>Load>assigned'''] </span>
	<div><span>            The file with assigned chemical shifts could be either in “standard” format   (assigned AA-fragments) or in cyana format (prot-file).</span></div><div> </div><div><span>      </span></div><div>Step 2. Set up constraints</div><div> </div><div>''' '''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.</div><div> </div><div><span>-<span>          </span></span>calculate dihedral angle constraints ['''<span>Structure>Constraints>Talos>Calculate</span>'''] </div><div><span>-<span>          </span></span>set up H-bond constraints ['''<span>Structure>Constraints>H-bonds>Specify</span>'''] </div><div><span>            </span></div><div>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 <span>  ['''Structure->Constraints->Talos>Load'''] or ['''Structure>Constraints>H-bonds>Load'''] </span></div><div> </div><div> </div><div>Step 3. Specify ligands coordinating ZN ions (if there are any).</div><div> </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>''' '''</div><div><span>      - specify residues that coordinate ZN ion(s) ['''Structure>Add ZN ion'''] </span></div><div>''' '''</div><div> </div><div>Step 4. Set up CYANA calculations</div><div> </div><div><span>       - setting up structure calculations with CYANA ['''Structure>Calcuate>cyana'''] </span></div><div>'''<span>          </span>'''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).</div><div> </div><div>Step 5. Structure evaluation and peak list refinement.</div><div> </div><div>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. </div><div> </div><div><span>-<span>          </span></span>run RPF analysis ['''<span>Structure>RPF>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>          </span></span>set up DP-score calculations with AutoStructure ['''<span>Structure>RPF>DP</span>'''].</div>		<div><span>            The file with assigned chemical shifts could be either in “standard” format   (assigned AA-fragments) or in cyana format (prot-file).</span></div><div> </div><div><span>      </span></div><div>Step 2. Set up constraints</div><div> </div><div>''' '''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.</div><div> </div><div><span>-<span>          </span></span>calculate dihedral angle constraints ['''<span>Structure>Constraints>Talos>Calculate</span>'''] </div><div><span>-<span>          </span></span>set up H-bond constraints ['''<span>Structure>Constraints>H-bonds>Specify</span>'''] </div><div><span>            </span></div><div>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 <span>  ['''Structure->Constraints->Talos>Load'''] or ['''Structure>Constraints>H-bonds>Load'''] </span></div><div> </div><div> </div><div>Step 3. Specify ligands coordinating ZN ions (if there are any).</div><div> </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>''' '''</div><div><span>      - specify residues that coordinate ZN ion(s) ['''Structure>Add ZN ion'''] </span></div><div>''' '''</div><div> </div><div>Step 4. Set up CYANA calculations</div><div> </div><div><span>       - setting up structure calculations with CYANA ['''Structure>Calcuate>cyana'''] </span></div><div>'''<span>          </span>'''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).</div><div> </div><div>Step 5. Structure evaluation and peak list refinement.</div><div> </div><div>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. </div><div> </div><div><span>-<span>          </span></span>run RPF analysis ['''<span>Structure>RPF>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>          </span></span>set up DP-score calculations with AutoStructure ['''<span>Structure>RPF>DP</span>'''].</div>

AlexLemak: Created page with '
Step 1. Load Data.

open new project PRJ3 ['''Project>new'''] load 15N NOESY peak list ['''DATA>N15 NOESY>load''']…'

2009-11-29T22:56:30Z

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>''']…'

New page

<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>''']
*load 13C_aliphatic NOESY peak list '''<span>[DATA>C13NOESY H2O>load</span>''']
*load 13C_aromatic NOESY peak list '''<span>[DATA>AromNOESY>load</span>''']
*set tolerances ['''<span>Data>Tolerances</span>''']
*<span>load 13C NOESY peak list '''[DATA>C13NOESY H2O>load''']</span>
*<span>load ''<u>assigned </u>''chemical shifts '''[Fragment>Load>assigned'''] </span>
<div><span>            The file with assigned chemical shifts could be either in “standard” format   (assigned AA-fragments) or in cyana format (prot-file).</span></div><div> </div><div><span>      </span></div><div>Step 2. Set up constraints</div><div> </div><div>''' '''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.</div><div> </div><div><span>-<span>          </span></span>calculate dihedral angle constraints ['''<span>Structure>Constraints>Talos>Calculate</span>'''] </div><div><span>-<span>          </span></span>set up H-bond constraints ['''<span>Structure>Constraints>H-bonds>Specify</span>'''] </div><div><span>            </span></div><div>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 <span>  ['''Structure->Constraints->Talos>Load'''] or ['''Structure>Constraints>H-bonds>Load'''] </span></div><div> </div><div> </div><div>Step 3. Specify ligands coordinating ZN ions (if there are any).</div><div> </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>''' '''</div><div><span>      - specify residues that coordinate ZN ion(s) ['''Structure>Add ZN ion'''] </span></div><div>''' '''</div><div> </div><div>Step 4. Set up CYANA calculations</div><div> </div><div><span>       - setting up structure calculations with CYANA ['''Structure>Calcuate>cyana'''] </span></div><div>'''<span>          </span>'''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).</div><div> </div><div>Step 5. Structure evaluation and peak list refinement.</div><div> </div><div>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. </div><div> </div><div><span>-<span>          </span></span>run RPF analysis ['''<span>Structure>RPF>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>          </span></span>set up DP-score calculations with AutoStructure ['''<span>Structure>RPF>DP</span>'''].</div>

Structure calculation - Revision history

AlexLemak at 22:58, 29 November 2009

AlexLemak: Created page with 'Step 1. Load Data. *open new project PRJ3 ['''Project>new'''] *load 15N NOESY peak list ['''DATA>N15 NOESY>load''']…'

AlexLemak: Created page with '
Step 1. Load Data.

open new project PRJ3 ['''Project>new'''] load 15N NOESY peak list ['''DATA>N15 NOESY>load''']…'