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

Tom Goddard goddard at sonic.net
Mon Jan 30 10:59:48 PST 2017


Hi Kyle,

  Here is a Python script that adds a savemarkers command.  You open the Python file in Chimera (command open savemarkers.py) to register the command, then the command looks like

	savemarkers #1 ~/Desktop/mymarkers.cmm

I’ve added this script to the Chimera Python scripts page.

	http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts <http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts>

  Tom



> On Jan 29, 2017, at 11:56 AM, Elaine Meng  wrote:
> 
> 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 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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