Get map contour level with python script or command
Dear chimera users and dev, Is there a chimera or python command that can report the current contour level of a volume that is in model number #n back to the reply log or equivalent? I want to do this after executing 'volume #n sdLevel 3’ such that I can programmatically retrieve the contour level associated with a particular sigma level of a currently loaded volume. Apologies if in my searching I have missed this on the boards, I think this is a novel question though. Thanks as always for your help. Best wishes, Kyle
Hi Kyle, There isn’t a Chimera command, sorry; I’m sure it can be done in python, but somebody else would have to advise on that. It may be a couple days, as our expert is away. However, ChimeraX has a “volume settings #N” command that reports the levels of volume model #N (among many other things) to the Log. Otherwise, it has essentially the same “volume” command options as in Chimera, including “sdLevel”. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html> 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 27, 2019, at 5:55 AM, Kyle Morris <kylelmorris@gmail.com> wrote:
Dear chimera users and dev,
Is there a chimera or python command that can report the current contour level of a volume that is in model number #n back to the reply log or equivalent?
I want to do this after executing 'volume #n sdLevel 3’ such that I can programmatically retrieve the contour level associated with a particular sigma level of a currently loaded volume.
Apologies if in my searching I have missed this on the boards, I think this is a novel question though. Thanks as always for your help.
Best wishes, Kyle _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Kyle, In Python with a Volume model v you can get its surface level(s) with v.surface_levels.
import chimera ml = chimera.openModels.list() ml [<VolumeViewer.volume.Volume object at 0x7f8c914f2d88>] v = ml[0] v.surface_levels [0.97360895273109072]
Not sure what you are trying to do so it is hard to advise. You could simply edit the Chimera Python code for the volume command sdLevel option to print the level so it appears in the reply log. The code to modify would be in chimera/share/VolumeViewer/volumecommand.py, search for sdLevel in that file. Alternatively why not use the "measure mapStats #0" command which prints the SD to the reply log emd_1080.map: mean = 0.081329, SD = 0.32454, RMS = 0.33457 then whatever code you have that is parsing the reply log could multiply that SD value by 3. Tom
On Aug 27, 2019, at 5:55 AM, Kyle Morris <kylelmorris@gmail.com> wrote:
Dear chimera users and dev,
Is there a chimera or python command that can report the current contour level of a volume that is in model number #n back to the reply log or equivalent?
I want to do this after executing 'volume #n sdLevel 3’ such that I can programmatically retrieve the contour level associated with a particular sigma level of a currently loaded volume.
Apologies if in my searching I have missed this on the boards, I think this is a novel question though. Thanks as always for your help.
Best wishes, Kyle _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Elaine Meng -
Kyle Morris -
Tom Goddard