[Chimera-users] Chimera bug: intermolecular surfaces missing

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 4 09:59:45 PDT 2012

Hi Peter,
I believe what you are describing is not a bug, it is merely that by default Chimera lumps all the contacting macromolecules into a single enclosed surface.  However, you can tell it to enclose sets of atoms separately as you wish.

One way is to use the command "split" to make each chain a separate model.

Another way (allowing you to retain the whole structure in a single model) is to use "surfcat" to define categories (the groups of atoms you want lumped together) and then "surface" those categories, for example:

open 1zik
rain chain
surfcat achain protein & :.a
surfcat bchain protein & :.b
surface achain
surface bchain

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 Jul 4, 2012, at 5:55 AM, Peter Hornbeck wrote:
> Hi Scooter et al,
> When displaying the surfaces of compound structures (e.g., 1O6K.pdb), surfaces are not displayed in the areas of intermolecular contact.
> I am using Chimera v 1.6 (build 37500), Mac OSX v10.6.8. We encountered this bug with a previous version, but I don't remember the resolution
> Image enclosed.
> Thanks, Peter Hornbeck

More information about the Chimera-users mailing list