[Chimera-users] Surface rendering

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 6 09:28:24 PDT 2012

Hi George,
Sometimes by making small changes in the surface calculation parameters, you can get it to work, but there is no guaranteed fix.  Here is some text from an earlier post to chimera-users at cgl.ucsf.edu on this topic:
The first thing to do is make sure you have a fairly recent version of Chimera, say 1.4 from Dec 2009 or newer.  Although we have not eliminated the failures, we have made some improvements that reduce their frequency.

Sometimes when there is an error, it can still fall back to a "single component" calculation.  The problem may be in some inside bubble, whereas the "single component" is the main outer surface.  If that's what happened, but it still looks like you got the surface you want, you can ignore the message.

If you didn't get any surface, however, there are several things to try, as mentioned in several previous posts (links below). Unfortunately none is a magic bullet that works in all situations.

Different things may work for different structures, and for some, you may not be able to find any fix.

On Jul 6, 2012, at 8:20 AM, George Tzotzos wrote:

> Hi everybody,
> I'm using SiteComp to detect differences in binding affinities between two similar structures. The _clusters.pdb file produced by SiteComp is a standard PDB file in which the grid points corresponding to the difference clusters are represented by hydrogen atoms. They can be treated as any molecule in Chimera.
> Usually I find it useful to represent them as a mesh surface. Usually, I load in Chimera the protein.pdb, the ligand.pdb and the _clusters.pdb. After this, I select the _clusters.pdb and show it as mesh or solid using Actions-> Surface. In some cases, I fail to render the surface, or to be precise only one part of the clusters is rendered.
> I understand that this is a frequent problem with this type of discontinuous pdb. I'm attaching one such file and I would be grateful for any help
> Best regards
> George

More information about the Chimera-users mailing list