[Chimera-users] Command line equivalence for Render by Attribute radii
pett at cgl.ucsf.edu
Mon Sep 16 15:43:09 PDT 2019
This is really simple to do in Python though. The code is:
from chimera import openModels, Molecule
for m in openModels.list(modelTypes=[Molecule]):
for a in m.atoms:
a.radius = a.bfactor
If you put the above into a file with a “.py” suffix, you can execute it simply by opening it with the “open” command. Keep in mind that indentation is relevant in Python, so preserve the indentation.
UCSF Computer Graphics Lab
> On Sep 13, 2019, at 8:25 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hello Jurgen,
> Sorry, there is no command-line equivalent for the “Radii” section of Render by Attribute, nor is there one for “Worms” — there’s only one for coloring, the “rangecolor” command.
> Surely it could be done with python scripting, but somebody else would have to advise on that.
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On Sep 12, 2019, at 1:09 PM, Sygusch Jurgen <jurgen.sygusch at umontreal.ca> wrote:
>> I cannot seem to find the command line equivalence for Render by Attribute radii. I am trying to display a tunnel where the atom B-factors represent the tunnel radius. I am able to display the tunnel as expected by using the GUI.
>> In the GUI, when I do Tools --> Depiction --> Render by Attribute --> atoms --> My Model; then Render Attribute --> bfactor; Radii --> Atom Style --> Sphere, I get the expected result of the tunnel diameter varying according to Bfactor (tunnel radius).
>> What is the command line equivalence for doing this? I cannot seem to find it.
>> Thank you for looking into this.
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