[Chimera-users] Display solvent-accessible surface?

Elaine Meng meng at cgl.ucsf.edu
Fri Sep 17 10:08:38 PDT 2010

Hi Darrell,
You're definitely right in that the potential at the solvent-accessible surface (SAS) is more directly what the contacting atom centers would "see."  It also varies less sharply there as compared to the solvent-excluded surface (SES) that Chimera displays.  For these reasons, both Electrostatic Surface Coloring and Coulombic Surface Coloring tools (by default) actually use the values 1.4 angstroms out from the SES (so approximately at the SAS) even though the coloring is at the SES.  


There are options in those tools to change the offset, so it could be zero to just show the values exactly at the displayed surface.

You can simulate an SAS in Chimera by increasing all the VDW radii by 1.4 and making the probe for surface calculation as small as possible.  You can't get exactly the SAS because the probe cannot be zero.  For example, commands:

open 1zik; preset apply int 2
del solvent; rep sphere
vdwdef +1.4 
setattr s probeRadius 0.5

I find that many papers and programs claim to be showing the SAS but aren't really.  It has an interesting soap-bubbly appearance that I rarely see in published images.  Nevertheless you can change the offset to zero in the ESP-coloring tool and try this almost-SAS surface to see what it looks like.  Just remember to avoid calculations that rely on reasonable VDW radii after inflating their values.

I hope this helps,

P.S. I thought your name sounded familiar..  We were happy to see that you teach some molecular graphics classes including Chimera!  Thanks!

Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 17, 2010, at 8:46 AM, Hurt, Darrell (NIH/NIAID) [E] wrote:

> Hi there,
> I’ve tried searching the archives and found some interesting information, but nothing specific to this question. Elaine’s response was particularly helpful:
> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-February/003597.html
>> From the documentation, it seems that Chimera only displays solvent-excluded surfaces:
> http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/representation.html#surfaces
> I understand that I can map solvent-accessibility to this surface using “Render Attributes”, but I would like to display the actual solvent-accessible surface. I want to do this because it is my understanding that electrostatic potential mapping to a solvent-accessible surface is often more informative than to a solvent-excluded surface:
> http://www.poissonboltzmann.org/apbs/examples/visualization/apbs-electrostatics-in-pymol#TOC-Surface-potentials
> Can it be done?
> Thanks,
> Darrell
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
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