[Chimera-users] New Chimera molecular surface code

Miguel Ortiz Lombardia molatwork at yahoo.es
Thu Mar 22 06:39:34 PDT 2007

Hash: SHA1

Dear Tom, Elaine and Conrad,

Thank you for your answers. Elaine's suggestion is quite all right to
check out how it looks like, though the "real" SAS would be better ;-)

Thank you very much for your efforts, I know you have a long list of
features requested!

Best regards,


Tom Goddard escribió:
> 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
> -----
> 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:
>>> 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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> Chimera-users at cgl.ucsf.edu
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- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: molatwork at yahoo.es
www: http://www.pangea.org/mol/spip.php?rubrique2
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.                          (Raoul Vaneigem)
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