Can multiple marker sets be batch-saved into individual .cmm files?
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/v...), 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.
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.p... <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. Tom
On Aug 28, 2019, at 9:59 AM, Jun Ha Song <junhasong@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/v... <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. _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Jun Ha Song -
Tom Goddard