[Chimera-users] Molecular Representations

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 28 09:11:30 PDT 2014

Dear Jian,

Ball size = VDW radius X "ball scale"

The ball scale is a model-level setting (same for whole structure) and the default is 0.25.  You can change it in the molecule model attributes (choose "attributes…" in Model Panel, or use Selection Inspector  to inspect: Molecule model) or with command "setattr", for example:

setattr m ballScale 0.3


I should make this clearer in the page on molecular representations.  There is a similar setting for the stick thickness, stickScale.  

If you want to measure the distance between two specific atoms (atom center to atom center) you should use the "distance" command.  The "measure distance" command can report the closest distance among two sets of atoms, but if your specification includes a surface, it will also look at the distance to the surface (which is in a different place than the atomic centers, because it goes over the VDW surfaces of the atoms) and only report that one if it is closer.  Both ways are reliable, it just depends on what you want to measure.


There is also a GUI for the atom-atom pairwise distance measurements, menu: Tools… Structure Analysis… Distances.  You can pick the two atoms from the screen (Ctrl-click, Shift-Ctrl-click) and then click the "Create" button on that tool.

I hope this helps,
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 28, 2014, at 7:42 AM, "Jian Guan" <jug25 at psu.edu> wrote:

> Dear all,
> I have one question about the Molecular Representations.
> In chimera, molecule can be represented by ball and sphere. Sphere is with the VDW radius for atoms and stick bonds. What about the ball? What is the ball size?
> I tried to measure the distance between two molecules. I used command line of “measure distance #1 #2”. It shows closest distance between two sets of atoms. When I made surface map for the same two molecules, I used the same command, it showed different number. I understand it is the distance of VDW. But what is the distance between atoms if I used PDB file instead of surface map? Which one is more reliable?
> Thanks,
> Jian

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