[Chimera-users] COX inhibitor demo discrepancy

simon chapman rowanlodge19 at gmail.com
Sat Sep 9 06:42:20 PDT 2017

Hello Elaine, apologies for another email..!

I selected 'Columns' on the first occasion I followed the tutorial. It only
selects Show, Hide ,Read and Display. clicking the first two just shows
'Number' . Selecting that does nothing at all. 'Display' shows 2D
structures as expected. I get the same result every time I've tried since.
   I've left- and right-clicked all the options several times,but it seems
the energy data simply isn't available...

Got the rotate speed sorted immediately along all 3 axes, so thanks for

I have also made a (shaky) demo from the instruction link you provided.

Best wishes   Simon

On 8 September 2017 at 17:16, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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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