Save marker sets from command line or python
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/v... - 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
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@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/v... • 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
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/v... • 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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participants (3)
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Elaine Meng -
Kyle Morris -
Tom Goddard