Heather's notes

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Setting up

Download molecular viewing applications

Chimera using Dock Blaster link - select snapshot 2376

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.

Help text was very useful. It was easy to learn the basics.

PyMol using Dock Blaster link - click Download - select desired platform and follow instruction

Users manual - [1] or type help keyword

Getting Started

Tutorial on how to prepare files for Dock Blaster using Chimera (it uses snapshot 2309 but it is still relevant)[2]

Dock Blaster:FAQ has a nice troubleshooting section in the works.[3]

To convert file types: 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



2316 - vegfr2 - dud files

2317 - 2bhe - pdb files - failed -- deleted

2318 - 2bhe - mol2 file using babel - cal. report empty - electrostatic scores lousy - lesson: use convert.py rather than babel

2319 - 2bhe - pdb files - cal report "special case with no ligand control" - cal. runs - only extrema and random

2321 - 2bhe - rec:2bhe_other_data.pdb; lig:xtal_lig2bhe.pdb - calibration files:see 2319

2322 - 2bhe - rec:rec2bhe.pdb; lig:xtal_lig_2bhe_hetatom.pdb - failed - file contained 'A'

2323 - 2bhe - rec:rec2bhe.pdb; lig:xtal_lig_2bhe_hetatom.pdb - failed

2324 - 2bhe - rec:rec2bhe.pdb; lig:xtal_lig_2bhe_hetatom.pdb

2325 - 2bhe - mol2 file using convert.py

2326 - 2bhe - used .ism file - failed

To Do

run 2bhe with and without terminus.

look at runs

start a gold run


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)

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 tollerant.

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.