[Chimera-users] New Chimera molecular surface code

Tom Goddard goddard at cgl.ucsf.edu
Wed Mar 21 18:36:24 PDT 2007

Elaine Meng explains how to fake a solvent accessible surface in Chimera.


Hi Miguel,
In the meanwhile, you can approximate a solvent-accessible surface by 
inflating all the atomic radii by 1.4 A and reducing the MSMS probe size.

  Command: vdwdefine +1.4

Probe size can be decreased by choosing the molecular surface in the 
Model Panel, clicking "attributes" on the right, and entering a new 
value.  However, the minimum probe radius allowed is 0.5 A, so there 
will be more smoothing of crevices than in a true SAS; it's definitely 
just an approximation.  However, it may suffice for coloring by 
electrostatic potential if you don't have a GRASP surface handy.
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 21, 2007, at 8:47 AM, Tom Goddard wrote:

> Hi Miguel,
>  Conrad Huang is writing new molecular surface code and I believe it 
> will also calculate solvent accessible surfaces.  We recently decided 
> it will not be ready for the next Chimera production release in a few 
> months.  It is a complex calculation and I'm not sure when it will be 
> available.
>  Chimera can read a GRASP surface from a file (just use File / Open, 
> file suffix .srf) and color it in the same way it colors MSMS surfaces.
>    Tom
> Miguel Ortiz Lombardia wrote:
>> Hash: SHA1
>> Hi Tom,
>> I would like to know if there has been any advancement in changing the
>> surfaces code. I know you had plans to write your own so that chimera
>> would not rely on msms, and I am very interested in this development
>> because it would allow the use of solvent accessible surfaces apart from
>> molecular surfaces. The former are more appropriate, among other
>> questions, to map electrostatic potential maps (less local effects). I
>> would be happy to test around, if you need testers. Unfortunately my
>> programming skills are quite minimal.
>> But I'll be patient anyway ;-)
>> Thanks to all of you for this great tool!
>> Cheers,
>> Miguel

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