Hi Jon, If you can come up with the equivalent Chimera commands, you can use the runcommand method in Python: <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> There isn’t necessarily a Chimera command for every GUI action, but it sounds like there may be for what you describe. - “open" to open PDB file - “sym” with “surfaces all” option is like making Multiscale surfaces <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> - “export” to export scene file <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/export.html> You can start up Chimera from the system command line with the nogui option and specify as an input file your python script: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/options.html> I hope this helps, 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 Aug 24, 2016, at 2:45 PM, Jon David <jdavid@cs.unm.edu> wrote:

Hi Friends,

I would like to use Python to perform operations equivalent to the following GUI operations; I'd like to be able to do this as a batch script (e.g., I don't want the Chimera GUI to appear because I don't want to have to close it.):

1) Open a PDB file (I know how to do this part).

2) Tools > Higher-Order Structure > Multiscale Models (this opens the MultiScale Models popup window).

3) Click on the "Make models" button.

4) File > Export Scene... (this opens the Export Scene popup window)

5) In the Export Scene popup window, select File type to be "OBJ [.obj]", enter file name "test.obj"

6) Click on the "Save" button.

I have used Python to open a PDB file, and translate, and rotate it around before. But I don't know where to begin with selecting Multiscale Models' parameters. Any tips? Any help would be much appreciated.

Thanks,

--Jon