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Resonance Assignment/Abacus/Structure calculation setup and analysis - Revision history
2026-05-24T04:11:08Z
Revision history for this page on the wiki
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https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=3499&oldid=prev
Agutmana: moved Structure calculation setup and analysis to Resonance Assignment/Abacus/Structure calculation setup and analysis
2010-01-05T23:49:04Z
<p>moved <a href="/index.php/Structure_calculation_setup_and_analysis" class="mw-redirect" title="Structure calculation setup and analysis">Structure calculation setup and analysis</a> to <a href="/index.php/Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis" title="Resonance Assignment/Abacus/Structure calculation setup and analysis">Resonance Assignment/Abacus/Structure calculation setup and analysis</a></p>
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<td colspan="1" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:49, 5 January 2010</td>
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Agutmana
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=2937&oldid=prev
AlexLemak at 23:57, 2 December 2009
2009-12-02T23:57:10Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:57, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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. </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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. </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp; { [[FMCGUI commands#Structure.3ERPF.<del style="font-weight: bold; text-decoration: none;">3ERP</del>|Structure&gt;RPF&gt;DP]] }.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp; { [[FMCGUI commands#Structure.3ERPF.<ins style="font-weight: bold; text-decoration: none;">3EDP</ins>|Structure&gt;RPF&gt;DP]] }.</div></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=2936&oldid=prev
AlexLemak at 23:56, 2 December 2009
2009-12-02T23:56:36Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:56, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 5. Structure evaluation and peak lists refinement ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 5. Structure evaluation and peak lists refinement ===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>run RPF analysis { [[<del style="font-weight: bold; text-decoration: none;">FMCGUI_commands</del>#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 <del style="font-weight: bold; text-decoration: none;">C13_aliphatic_NOESY</del>, <del style="font-weight: bold; text-decoration: none;">C13_aromatic_NOESY</del>, and <del style="font-weight: bold; text-decoration: none;">N15_NOESY </del>spectra in separate files. </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>run RPF analysis { [[<ins style="font-weight: bold; text-decoration: none;">FMCGUI commands</ins>#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 <ins style="font-weight: bold; text-decoration: none;">C13-aliphatic NOESY</ins>, <ins style="font-weight: bold; text-decoration: none;">C13-Aromatic NOESY</ins>, and <ins style="font-weight: bold; text-decoration: none;">N15-NOESY </ins>spectra in separate files. </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp;[<del style="font-weight: bold; text-decoration: none;"><span></del>Structure&gt;RPF&gt;DP<del style="font-weight: bold; text-decoration: none;"></span></del>].</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp; <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[FMCGUI commands#Structure.3ERPF.3ERP|</ins>Structure&gt;RPF&gt;DP]<ins style="font-weight: bold; text-decoration: none;">] }</ins>.</div></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=2935&oldid=prev
AlexLemak at 23:55, 2 December 2009
2009-12-02T23:55:14Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:55, 2 December 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l28">Line 28:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>=== Step 5. Structure evaluation and peak lists refinement ===</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>=== Step 5. Structure evaluation and peak lists refinement <ins style="font-weight: bold; text-decoration: none;"> </ins>===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>run RPF analysis [<del style="font-weight: bold; text-decoration: none;"><span></del>Structure&gt;RPF&gt;RP<del style="font-weight: bold; text-decoration: none;"></span></del>] .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></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>run RPF analysis <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[FMCGUI_commands#Structure.3ERPF.3ERP|</ins>Structure&gt;RPF&gt;RP]<ins style="font-weight: bold; text-decoration: none;">] }</ins>. 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></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp;[<span>Structure&gt;RPF&gt;DP</span>].</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp;[<span>Structure&gt;RPF&gt;DP</span>].</div></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=2933&oldid=prev
AlexLemak at 23:53, 2 December 2009
2009-12-02T23:53:51Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:53, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''Step 4. Set up CYANA calculations''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''Step 4. Set up CYANA calculations''' ===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span>&nbsp;&nbsp;&nbsp; setting up structure calculations with CYANA&nbsp; { [[<del style="font-weight: bold; text-decoration: none;">[[FMCGUI_commands</del>#Structure.3ECalculate.3ECyana|Structure&gt;Calcuate&gt;cyana]] }</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span>&nbsp;&nbsp;&nbsp; setting up structure calculations with CYANA&nbsp; { [[<ins style="font-weight: bold; text-decoration: none;">FMCGUI commands</ins>#Structure.3ECalculate.3ECyana|Structure&gt;Calcuate&gt;cyana]] }</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></span></ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=2931&oldid=prev
AlexLemak at 23:53, 2 December 2009
2009-12-02T23:53:29Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:53, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div><div>&nbsp;</div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div><div>&nbsp;</div></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>=== '''Step 4. Set up CYANA calculations''' ===</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>=== '''Step 4. Set up CYANA calculations''' <ins style="font-weight: bold; text-decoration: none;"> </ins>===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span>&nbsp;&nbsp;&nbsp; setting up structure calculations with CYANA&nbsp;[<del style="font-weight: bold; text-decoration: none;">'''</del>Structure&gt;Calcuate&gt;cyana<del style="font-weight: bold; text-decoration: none;">'''</del>] <del style="font-weight: bold; text-decoration: none;"></span></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span>&nbsp;&nbsp;&nbsp; setting up structure calculations with CYANA&nbsp; <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[[[FMCGUI_commands#Structure.3ECalculate.3ECyana|</ins>Structure&gt;Calcuate&gt;cyana]<ins style="font-weight: bold; text-decoration: none;">] }</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 5. Structure evaluation and peak lists refinement ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 5. Structure evaluation and peak lists refinement ===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&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></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&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></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp;[<span>Structure&gt;RPF&gt;DP</span>].</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up DP-score calculations with AutoStructure&nbsp;[<span>Structure&gt;RPF&gt;DP</span>].</div></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=2930&oldid=prev
AlexLemak at 23:51, 2 December 2009
2009-12-02T23:51:42Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:51, 2 December 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l18">Line 18:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 3. Specify ligands coordinating ZN ions (if there are any) ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 3. Specify ligands coordinating ZN ions (if there are any) ===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span>&nbsp;&nbsp;&nbsp; specify residues that coordinate ZN ion(s) { [[<del style="font-weight: bold; text-decoration: none;">FMCGUI_commands</del>#Structure.<del style="font-weight: bold; text-decoration: none;">3EAss_ZN_ligands</del>|Structure&gt;Add ZN ion]] }</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span>&nbsp;&nbsp;&nbsp; specify residues that coordinate ZN ion(s) { [[<ins style="font-weight: bold; text-decoration: none;">FMCGUI commands</ins>#Structure.<ins style="font-weight: bold; text-decoration: none;">3EAdd_ZN_ligands</ins>|Structure&gt;Add ZN ion]] }</div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></span></ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div><div>&nbsp;</div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div><div>&nbsp;</div></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=2929&oldid=prev
AlexLemak at 23:50, 2 December 2009
2009-12-02T23:50:51Z
<p></p>
<table style="background-color: #fff; color: #202122;" data-mw="interface">
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:50, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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; { [[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></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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; { [[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></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>=== Step 3. Specify ligands coordinating ZN ions (if there are any) ===</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>=== Step 3. Specify ligands coordinating ZN ions (if there are any) <ins style="font-weight: bold; text-decoration: none;"> </ins>===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span>&nbsp;&nbsp;&nbsp; specify residues that coordinate ZN ion(s) [Structure&gt;Add ZN ion] <del style="font-weight: bold; text-decoration: none;"></span></del></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span>&nbsp;&nbsp;&nbsp; specify residues that coordinate ZN ion(s) <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[FMCGUI_commands#Structure.3EAss_ZN_ligands|</ins>Structure&gt;Add ZN ion]<ins style="font-weight: bold; text-decoration: none;">] }</ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div><div>&nbsp;</div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div><div>&nbsp;</div></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''Step 4. Set up CYANA calculations''' ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== '''Step 4. Set up CYANA calculations''' ===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>'''&nbsp;'''</div></div></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=2928&oldid=prev
AlexLemak at 23:49, 2 December 2009
2009-12-02T23:49:13Z
<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:49, 2 December 2009</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><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></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><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></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>=== Step 2. Set up constraints ===</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>=== Step 2. Set up constraints <ins style="font-weight: bold; text-decoration: none;"> </ins>===</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>calculate dihedral angle constraints [<del style="font-weight: bold; text-decoration: none;"><span></del>Structure&gt;Constraints&gt;Talos&gt;Calculate<del style="font-weight: bold; text-decoration: none;"></span></del>]&nbsp;</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>calculate dihedral angle constraints <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[FMCGUI_commands#Structure.3EConstraints.3ETalos.3Ecalculate|</ins>Structure&gt;Constraints&gt;Talos&gt;Calculate]<ins style="font-weight: bold; text-decoration: none;">] }</ins>&nbsp; </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up H-bond&nbsp;constraints [<del style="font-weight: bold; text-decoration: none;"><span></del>Structure&gt;Constraints&gt;H-bonds&gt;Specify<del style="font-weight: bold; text-decoration: none;"></span></del>]&nbsp;</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>*<span><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></span>set up H-bond&nbsp;constraints <ins style="font-weight: bold; text-decoration: none;">{ [</ins>[<ins style="font-weight: bold; text-decoration: none;">FMCGUI_commands#Structure.3EConstraints.3EH-bonds.3ESpecify|</ins>Structure&gt;Constraints&gt;H-bonds&gt;Specify]<ins style="font-weight: bold; text-decoration: none;">] }</ins>&nbsp;</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><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; <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[FMCGUI_commands#Structure.3EConstraints.3ETalos.3Eload|</ins>Structure-&gt;Constraints-&gt;Talos&gt;Load]<ins style="font-weight: bold; text-decoration: none;">] }</ins>&nbsp;or <ins style="font-weight: bold; text-decoration: none;">{ </ins>[<ins style="font-weight: bold; text-decoration: none;">[FMCGUI_commands#Structure.3EConstraints.3EH-bonds.3ESpecify|</ins>Structure&gt;Constraints&gt;H-bonds&gt;Load]<ins style="font-weight: bold; text-decoration: none;">] } </ins></span></div><div>&nbsp;</div><div>&nbsp;</div></div></td></tr>
<tr><td colspan="2" class="diff-side-deleted"></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div> </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 3. Specify ligands coordinating ZN ions (if there are any) ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 3. Specify ligands coordinating ZN ions (if there are any) ===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><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></td></tr>
</table>
AlexLemak
https://nesgwiki.chem.buffalo.edu/index.php?title=Resonance_Assignment/Abacus/Structure_calculation_setup_and_analysis&diff=2924&oldid=prev
AlexLemak at 23:42, 2 December 2009
2009-12-02T23:42:22Z
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">← Older revision</td>
<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 23:42, 2 December 2009</td>
</tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1">Line 1:</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 1. Load Data ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 1. Load Data ===</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div> </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div><div>&nbsp;</div> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**open new project PRJ3 { <del style="font-weight: bold; text-decoration: none;">{{</del>FMCGUI_commands#Project.3ENew|Project&gt;new]] } </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**open new project PRJ3 { <ins style="font-weight: bold; text-decoration: none;">[[</ins>FMCGUI_commands#Project.3ENew|Project&gt;new]] } </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**load 15N NOESY peak list { [[FMCGUI commands#Data.3EN15_NOESY.3E|DATA&gt;N15 NOESY&gt;load]] } </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**load 15N NOESY peak list { [[FMCGUI commands#Data.3EN15_NOESY.3E|DATA&gt;N15 NOESY&gt;load]] } </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**load 13C_aliphatic NOESY peak list&nbsp; { [[FMCGUI commands#Data.3EC13_NOESY.3E|DATA&gt;C13NOESY H2O&gt;load]] } </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**load 13C_aliphatic NOESY peak list&nbsp; { [[FMCGUI commands#Data.3EC13_NOESY.3E|DATA&gt;C13NOESY H2O&gt;load]] } </div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**load 13C_aromatic NOESY peak list&nbsp; { [[FMCGUI commands#Data.3EArom_NOESY.3E|DATA&gt;AromNOESY&gt;load]] } </div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>**load 13C_aromatic NOESY peak list&nbsp; { [[FMCGUI commands#Data.3EArom_NOESY.3E|DATA&gt;AromNOESY&gt;load]] } </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**set tolerances&nbsp; { [[FMCGUI commands#Data.3ETolerances|Data&gt;Tolerances]] } </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**set tolerances&nbsp; { [[FMCGUI commands#Data.3ETolerances|Data&gt;Tolerances]] } <span /> </div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><del style="font-weight: bold; text-decoration: none;">**</del><span<del style="font-weight: bold; text-decoration: none;">>load&nbsp;13C NOESY peak list&nbsp;[DATA&gt;C13NOESY H2O&gt;load]<</del>/<del style="font-weight: bold; text-decoration: none;">span</del>> </div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>**<span>load&nbsp;''<u>assigned </u>''chemical shifts&nbsp; { [[<ins style="font-weight: bold; text-decoration: none;">FMCGUI commands</ins>#Fragment.3ELoad.3Eassigned|Fragment&gt;Load&gt;assigned]] }</div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>**<span>load&nbsp;''<u>assigned </u>''chemical shifts&nbsp; { [[<del style="font-weight: bold; text-decoration: none;">FMCGUI_commands</del>#Fragment.3ELoad.3Eassigned|Fragment&gt;Load&gt;assigned]] }</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;"></span></ins></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div><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; ([[<del style="font-weight: bold; text-decoration: none;">Spin_systems_format</del>|assigned AA-fragments]]) or in [[<del style="font-weight: bold; text-decoration: none;">[[Spin_systems_format</del>|cyana format]] (prot-file).</span></div><div>&nbsp;</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div></div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><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; ([[<ins style="font-weight: bold; text-decoration: none;">Spin systems format</ins>|assigned AA-fragments]]) or in [[<ins style="font-weight: bold; text-decoration: none;">Spin systems format</ins>|cyana format]] (prot-file).</span></div><div>&nbsp;</div><div><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; </span></div></div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><br/></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 2. Set up constraints ===</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>=== Step 2. Set up constraints ===</div></td></tr>
</table>
AlexLemak