[Chimera-users] COX inhibitor demo discrepancy

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 8 09:16:27 PDT 2017


Hi Simon,
You missed a step or two in the ViewDock tutorial.  You have to use the Columns menu to control what the dialog is showing.  See the paragraph in the tutorial starting “The docked compounds are enumerated…”
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/vdtut.html>

There are several options to the “roll” command including number of degrees per frame.  For a slower roll, you can set this to a low number, e.g. “roll y 0.1”.  Use command “help roll” to see the manual page, or view the copy at our website:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/roll.html>
… it says the default is 1.5 degrees per frame.

If you already started a roll with inifinite frames, you can use “freeze” to halt it.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/freeze.html>

If you mean the COX demo credits, yes, I created that demo.  It is really a series of  Chimera commands to execute for each “panel."   Users can create their own demos, but it requires some familiarity with the commands.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/demos/demos.html>

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Sep 8, 2017, at 6:57 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
> 
> Hello again Elaine. I understand now about the COX demo... I used DSV and PDB to generate the structures. Obviously had incorrect co-ordinates. Will watch out for that next time.
> 
> However, following the tutorial exactly for ViewDock still doesn't quite match. Attached screenshot shows tutorial pic and the version  that I get... the onscreen background molecular structure is identical with the 'official' one. So, not sure why the energy data isn't showing up??
> 
> Also, is there a way to slow down rotation of a molecule after  command 'roll'?
> 
> I  notice your name is at the top of the data slide...is the video your production?
> 
> Best wishes   Simon
> 




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