https://nesgwiki.chem.buffalo.edu/index.php?action=history&feed=atom&title=Water_refinementWater refinement - Revision history2026-04-13T18:25:48ZRevision history for this page on the wikiMediaWiki 1.38.2https://nesgwiki.chem.buffalo.edu/index.php?title=Water_refinement&diff=2355&oldid=prevAlexLemak at 00:31, 30 November 20092009-11-30T00:31:52Z<p></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 00:31, 30 November 2009</td>
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<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 PRJ4['''<span>Project&gt;new</span>'''] or</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;">*</ins>open new project PRJ4['''<span>Project&gt;new</span>'''] or</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>load&nbsp;old one PRJ3['''<span>Project&gt;load</span''']<del style="font-weight: bold; text-decoration: none;"></div><div></del>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.<del style="font-weight: bold; text-decoration: none;"></div><div></del>curry out water refinement calculations (on linux cluster is recommended) following the instruction given in the project main window<del style="font-weight: bold; text-decoration: none;"></div><div></del>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.</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><ins style="font-weight: bold; text-decoration: none;">&nbsp;&nbsp;&nbsp;&nbsp; </ins>load&nbsp;old one PRJ3['''<span>Project&gt;load<ins style="font-weight: bold; text-decoration: none;">&lt;/span</ins></span<ins style="font-weight: bold; text-decoration: none;">></ins>''']</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>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.</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>curry out water refinement calculations (on linux cluster is recommended) following the instruction given in the project main window</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>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.</div></td></tr>
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</table>AlexLemakhttps://nesgwiki.chem.buffalo.edu/index.php?title=Water_refinement&diff=2354&oldid=prevAlexLemak: Created page with 'open new project PRJ4['''<span>Project>new</span>'''] or <div>load old one PRJ3['''<span>Project>load</span''']</div><div>set up water refinement calculations of …'2009-11-30T00:30:48Z<p>Created page with 'open new project PRJ4['''<span>Project>new</span>'''] or <div>load old one PRJ3['''<span>Project>load</span''']</div><div>set up water refinement calculations of …'</p>
<p><b>New page</b></p><div>open new project PRJ4['''<span>Project&gt;new</span>'''] or<br />
<div>load&nbsp;old one PRJ3['''<span>Project&gt;load</span''']</div><div>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.</div><div>curry out water refinement calculations (on linux cluster is recommended) following the instruction given in the project main window</div><div>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.</div></div>AlexLemak