[Chimera-users] chimera batch process

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 8 09:27:55 PDT 2017


Dear Yagmur Turgay,
You would first see if it’s possible to do all the things you want with Chimera commands, then you could use Python to loop through multiple data sets as described here:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

>From your description, I can’t really tell if you can do everything with Chimera commands.  Certainly you can open data with the “open” command; set isosurface display, threshold level, and step size with the “volume” command; hide dust with command “sop hideDust”; select with “select”.  However, when you say “segmented tomogram” I don’t know if you mean just the volume data set or some previously calculated segmentation surfaces.  The “volume” command I mentioned would work on the volume data set.  Secondarily, it wasn’t clear to me whether you needed to judge the connectivity interactively to decide what step value to use.  If so, it would be harder to automate.

For details on each command, see:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

Operations that are GUI-only (that don’t have Chimera commands) could be executed with python, but somebody else would have to advise on the details.

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 8, 2017, at 8:05 AM, y.turgay at bioc.uzh.ch wrote:
> 
> Dear chimera users,
> I was wondering if you could help me automate the following procedure in order to batch process all my tomograms.
> What I want to do is to open a segmented tomogram, apply parameters like surface, the step size (1 of 8) to increase the connectivity of what has been segmented, to hide the dust (size: 50) and to threshold the tomogram to 0.5. Afterwards I would select all remaining objects and open a script to invert the surface and execute "mask #0 sel invert true" using the command line in chimera to substract the background from the tomogram. Finally I would save this as new map.
> Can anyone help me with the commands I have to write in the Terminal to iterate through 200 tomogram folder and automate and batch process this.
> Best
> Yagmur Turgay




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