[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>


> 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
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170130/19c01bd8/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: savemarkers.py
Type: text/x-python-script
Size: 1013 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170130/19c01bd8/attachment.bin>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20170130/19c01bd8/attachment-0001.html>

More information about the Chimera-users mailing list