[Chimera-users] Save marker sets from command line or python

Elaine Meng meng at cgl.ucsf.edu
Sun Jan 29 11:56:56 PST 2017


Hi Kyle,
Sorry, there is no Chimera command to save marker sets in the cmm format.  (As far as I know, the manual page you were looking at is up to date.)

I’m sure it can be done in Python but somebody else would have to shed light on that.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jan 28, 2017, at 1:46 PM, Kyle Morris <kylelmorris at berkeley.edu> wrote:
> 
> Dear Chimera dev and community,
> 
> I would like to save a marker set from the command line and ultimately do so in a script. Using the write command which I would use for PDB's, marker sets get saved in PDB format, of course. Is there a command to save the marker set as XML .cmm as it would from the volume tracer menu?
> 
> I notice at the bottom of the following page this is a suggested development:
> 
> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html
> 	• supply Python code for reading and writing the XML files containing saved marker sets
> Is it there already and I can't find perhaps?
> 
> Thanks for your help as ever!
> 
> Best wishes,
> Kyle




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