[Chimera-users] COX inhibitor demo discrepancy

Elaine Meng meng at cgl.ucsf.edu
Sat Sep 9 17:49:42 PDT 2017


Hi Simon,
I see in the screenshot image you sent in the earlier e-mail (yesterday) that your ViewDock dialog with the “ras.mol2” data opened in it says “Created by: Discovery Studio”.  Thus I can only guess that you’d saved the “ras.mol2” file from that program, and that it either removed or reformatted the energy information so that Chimera could not read it.  Try downloading the ras.mol2 file again from the link in the tutorial, saving it as plain text and using it in Chimera WITHOUT opening it in DIscovery Studio first and it should work.

Kudos on making your own demo!  By the way, all of the User Guide is included with your download, and you can search it from the Help menu.
Best,
Elaine


> On Sep 9, 2017, at 6:42 AM, simon chapman <rowanlodge19 at gmail.com> wrote:
> 
> 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 that.
> 
> 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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