[Chimera-users] Chimera bug: intermolecular surfaces missing

Elaine Meng meng at cgl.ucsf.edu
Wed Jul 4 10:09:58 PDT 2012

Hi Peter,  
Just a P.S.: for your example, the following is sufficient to separate the bound peptide and protein:

open 1o6k
surfcat peplig protein & :.c

This puts the peptide into a surface category named peplig, where the rest of the protein is still in the main surface.  The "protein &" part is necessary because chain C also includes waters, but you don't want them included inside the "peplig" surface.


On Jul 4, 2012, at 9:59 AM, Elaine Meng wrote:

> 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
> -----
> 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
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