http://wiki.docking.org/index.php?action=history&feed=atom&title=Heather%27s_notesHeather's notes - Revision history2026-04-07T06:14:48ZRevision history for this page on the wikiMediaWiki 1.39.1http://wiki.docking.org/index.php?title=Heather%27s_notes&diff=3155&oldid=prevTherese: 35 revisions2012-10-08T20:25:28Z<p>35 revisions</p>
<p><b>New page</b></p><div>=Setting up=<br />
==Download molecular viewing applications==<br />
'''Chimera''' using Dock Blaster link - select snapshot 2376<br />
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Open Chimera - click on Favorites>Preferences, select 'Web Access' as Category, change Confirm open of commands or code to 'never' and Accept web data to 'true', save and close.<br />
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Help text was very useful. It was easy to learn the basics.<br />
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'''PyMol''' using Dock Blaster link - click Download - select desired platform and follow instruction<br />
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Users manual - [http://pymol.sourceforge.net/newman/user/toc.html] or type ''help keyword''<br />
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==Getting Started==<br />
Tutorial on how to prepare files for Dock Blaster using Chimera (it uses snapshot 2309 but it is still relevant)[http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.htm]<br />
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Dock Blaster:FAQ has a nice troubleshooting section in the works.[http://wiki.compbio.ucsf.edu/wiki/index.php/DOCK_Blaster:FAQ#I.27m_having_trouble_using_DOCK_Blaster]<br />
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To convert file types:<br />
Use ssh or equivalent to ftp file to blur.compbio.ucsf.edu; log onto unix; ssh nirvana, enter password; convert.py --i=filename --o=filename<br />
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=Jobs=<br />
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'''5/17/07'''<br />
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2316 - vegfr2 - dud files<br />
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2317 - 2bhe - pdb files - failed -- deleted<br />
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2318 - 2bhe - mol2 file using babel - cal. report empty - electrostatic scores lousy - lesson: use convert.py rather than babel<br />
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2319 - 2bhe - pdb files - cal report "special case with no ligand control" - cal. runs - only extrema and random<br />
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2321 - 2bhe - rec:2bhe_other_data.pdb; lig:xtal_lig2bhe.pdb - calibration files:see 2319<br />
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2322 - 2bhe - rec:rec2bhe.pdb; lig:xtal_lig_2bhe_hetatom.pdb - failed - file contained 'A'<br />
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2323 - 2bhe - rec:rec2bhe.pdb; lig:xtal_lig_2bhe_hetatom.pdb - failed<br />
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2324 - 2bhe - rec:rec2bhe.pdb; lig:xtal_lig_2bhe_hetatom.pdb<br />
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2325 - 2bhe - mol2 file using convert.py<br />
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2326 - 2bhe - used .ism file - failed<br />
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=To Do=<br />
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run 2bhe with and without terminus.<br />
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look at runs<br />
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start a gold run<br />
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=Comments=<br />
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On Target Prep page clicked Reload Page button got "we have no idea what we were asked to do" expected page to refresh (assume that this feature is not working yet)<br />
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Typo - On Get Started page, last bullet - You may be one of those people, like me, who tries to do as much as possible before reading the documentation, on the grounds that the software should be intuitive and tol'''''l'''''erant.<br />
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Browse Jobs page - headings, e.g. Job ID are linked, is clicking on the links supposed to sort by that column or take you to another page.</div>Therese