[Chimera-users] Can multiple marker sets be batch-saved into individual .cmm files?

Tom Goddard goddard at sonic.net
Wed Aug 28 14:52:02 PDT 2019

Hi Junha,

  I think the only way to save a Chimera marker file (.cmm) is through the Volume tracer gui File menu.  There is no command as far as I know.  But there is a Python script that adds a savemarkers command on the Chimera Python scripts web page.

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

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

It look like it would be pretty trivial to add a "for" loop in that code so it saves each markerset in a separate file with a numeric suffix.  Or you could just use the "perframe" command to save each markerset to a separate file.


> On Aug 28, 2019, at 9:59 AM, Jun Ha Song <junhasong at berkeley.edu> wrote:
> Dear RBVI,
> I need to save around 340 market sets into individual .cmm files, 1 .cmm for each marker set I have in my Chimera session. I have been looking at UCSF Chimera documentation for some time (https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#activeset <https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#activeset>), and I wanted to ask if multiple marker sets (each with its own unique model ID) can be saved in single batch command line.
> Is there a possibility of specifying commands like save or write or export with atom specification of all the model that I want to save to make Chimera save all my 340 marker sets as their individual .cmm files? I was hoping that I could simply use something like
> save #1-340 individual UseModelIDasFilename format .cmm directory E:\LBNL\Individual_Models
> to make it happen, but all the commands that I thought of as potential candidate for batch-save command doesn't mention whether it can work with volume tracer's "Save current marker set as...".
> or, if I can use Volume Tracer's "Save current marker set as..." using a script, I could handle this by making myself very simple macro, but I don't know whether volume tracer's codes would allow some quick script to substitute its "Save current marker set as..." function.
> So, in summary, I wanted to know if...
> Q1 : Is there a command in UCSF Chimera that allows batch saving multiple market sets as individual .cmm files?
> Q2 : Can Volume Tracer's "Save current marker set as..." function be used by using some kind of script?
> Sincerely,
> Junha Song.
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