[chimera-dev] adjust contour to mass

[Tom Goddard]

Hi Martin,

  Here's some example Python code that opens a map an sets the contour level to 1.2 and displays it.

from chimera import openModels
vlist = openModels.open('/Users/goddard/Downloads/Chimera/EMDB/emd_1080.map')
v = vlist[0]
v.set_parameters(surface_levels = [1.2])
v.show()

Or you can simply run a Chimera command from Python

from chimera import runCommand
runCommand("volume #0 level 1.2")

There are more examples of Python code at the Chimera Python scripts web page

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

Unfortunately there is not a reference manual listing all the available Python functions -- something we will remedy in Chimera 2, but that will not be out for perhaps a year.  The density map data structure called "Volume" is defined in Python code included in Chimera

	chimera/share/VolumeViewer/volume.py

so you can look at what Python methods are available by looking at that source code.

	Tom


On Nov 18, 2013, at 6:10 AM, Martin Turk <turk at lmb.uni-muenchen.de> wrote:

> Hi,
> 
> I am trying to write a simple python script that will iterate over opened volumes and adjust the contour level to a certain mass. This shouldn't be more than ~10 lines. However, I can't find chimera's python library reference to look up the class structure and operator names.
> 
> Does someone know how, for example, set volume level to 0.01 would look like in python?
> in the command line it would be for all models: volume #0-99 level 0.01
> 
> for models I've found chimera.openModels and then you can list over them, but that's about it.
> 
> Thanks,
> Martin Turk
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