[Chimera-users] New Chimera molecular surface code

[Tom Goddard]

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

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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
-----
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
                     http://www.cgl.ucsf.edu/home/meng/index.html




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:
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>>
>> 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
>>
>