[Chimera-users] New Chimera molecular surface code

[Miguel Ortiz Lombardia]

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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,


Miguel

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:
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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
>>>
> _______________________________________________
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> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

- --
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
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Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.                          (Raoul Vaneigem)
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