[Chimera-users] Command line equivalence for Render by Attribute radii

Sygusch Jurgen jurgen.sygusch at umontreal.ca
Mon Sep 16 15:50:06 PDT 2019

Wow, thank you very much.

On 2019-09-16 6:43 p.m., Eric Pettersen wrote:
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.

Eric Pettersen
UCSF Computer Graphics Lab

On Sep 13, 2019, at 8:25 AM, Elaine Meng <meng at cgl.ucsf.edu<mailto: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<mailto: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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