[Chimera-users] seeing atom info through surface

Elaine Meng meng at cgl.ucsf.edu
Thu Aug 21 11:49:17 PDT 2008

Hi Fabian,
Both the atom spheres (CPK representation) and molecular surface are  
triangulations rather than the exact smooth surfaces, and when both  
are shown, parts of the spheres poke through above the surface.  The  
ideal surfaces would overlap exactly, at least in the convex areas, so  
even then you might expect some show-through, although it wouldn't  
look so bumpy.

The simplest way to avoid it is to use a different atom  
representation.  However, you must be doing this for some reason, so  
here is my best idea:

You could "fake" the CPK representation by using ball-and-stick  
instead, but with increased ball scale factor (ballScale=0.25 by  
default, whereas 1 would give the VDW radius and be the same as the  
CPK representation).  The ball scale factor can be changed in the  
Selection Inspector ("molecule model" section), or in the molecule  
model attributes panel, or with a command something like:
     setattr m ballScale 0.85

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 21, 2008, at 11:22 AM, Fabian Glaser wrote:

> Thanks for your answer. But even if teh surface is 0% transparent I  
> see the CPK
> balls "sticking out", and they don't look nice. Maybe there is a way  
> of
> slightly enlarging the surface?
> THanks a lot for your kind help,
> Fabian

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