[Chimera-users] holes in molecular surface

Elaine Meng meng at cgl.ucsf.edu
Fri Jul 28 13:39:25 PDT 2017

Hi Marcus, 
Thanks for the kind words!

I assume you mean the hole is a weird artifact, not just when you have two chains and see a big hole where one contacts the other because the surface encloses both of them together.  That second issue is easily solved by making each chain have its own enclosing surface.

For the weird artifacts, I’ve also seen them occasionally with the MSMS-calculated molecular surface in Chimera (for example, 4hhb Lys 90 in chain C gets a weirdly truncated surface, at least on my computer).   

If tweaking parameters like probe radius and surface-vertex density don’t help, there are at least two different approaches you could try that don’t depend on the MSMS algorithm:

(1) use “molmap” to simulate a density map from the atoms and show an isosurface of that map. The shape will be a bit different from the SES, however.  See under #3 in the surface workarounds page.  

(2)  use the semi-secret grid SES implemented in Chimera, see:

In both cases, be VERY careful to only specify the protein atoms, for example:

molmap #0&protein 4 gridSpacing 0.5
- or -
surf #0&protein grid .5

…otherwise all the other atoms (solvent, ligands, etc.) will be assimilated into the blob. Also, these alternative-method surfaces aren't automatically associated with atoms, so if you want to color patches based on their underlying atom or residue, you would have to use the Color Zone tool.

The grid SES is more fully implemented in our next-gen software ChimeraX, so it’s much easier to color patches specified by the underlying atoms/residues/chains. ChimeraX is available for download now, but it's in early dev. and far from a complete replacement for Chimera at this point.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 28, 2017, at 11:19 AM, Marcus Mendes <marcus.famendes at gmail.com> wrote:
> Hi All,
> First of all I want to thanks for the great software. I'm having a problem with the surface calculation. My molecules have 384 aa, with a mutation in 9 positions between them (always in the Chain C). In some molecules there is a hole in the middle of surface (I'm using the Headless chimera). I already tried to customizing some options like probeRadius and Density, but I still have some molecules with a hole. There's anything that I can do to fix this?
> Best regards
> Marcus Mendes

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