[Chimera-users] Surface function question

Elaine Meng meng at cgl.ucsf.edu
Thu May 25 09:42:27 PDT 2017

Hi Frances,
By default the surface is calculated to enclose all the protein chains in one model in one envelope.  I see that 3fmg has the VP7 protein as chain A and the antibody as chains H and L.  The trivial solution is to simply delete the antibody (e.g. command: delete :.h:.l) but more generally, there are a couple different ways to tell Chimera to instead enclose each protein chain in its own envelope.

(1) use “surfcat” to define the set(s) of atoms you want enclosed separately, e.g. commands:

surfcat vp7 :.a&protein
surface vp7

- OR -

(2) before calculating the surface, use “split” to make each chain a separate model (#0 with all three chains would become instead #0.1 with A chain, #0.2 with H, #0.3 with L):

open 3fmg

If you use the “split” command after you already made the first surface, it won’t go away automatically.  You would have to show the Model Panel (from favorites menu) and close the #0 surface.

Peraonally I prefer the “surfcat” approach but some other people find the “split” approach easier. 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 May 24, 2017, at 6:29 AM, Frances Shepherd <sheph085 at umn.edu> wrote:
> Hi,
> I am modeling a rotavirus VP7 protein using Chimera (PDB 3fmg), and I’m having trouble with the surface function.  This protein is modeled with a monoclonal antibody conjugated to it, which I am able to hide.  But when I show the surface for just the VP7 protein, there are gaps in the surface.  The gaps appear to be in the areas where the VP7 protein comes into contact with the antibody.  Is there a way to fill in these gaps?  I’ve seen other publications that have used this protein (same PDB number), but the surface is complete.  If you have any suggestions, I’d appreciate it.  Thanks!
> -Frances

More information about the Chimera-users mailing list