[Chimera-users] (no subject)

[Elaine Meng]

Hi Cedric,
When a molecular surface is calculated (the first time it is shown),  
the solvent-excluded and solvent-accessible areas are also  
calculated.  The overall totals and total per disconnected part  
("component") are reported in the Reply Log.  At the same time, it  
creates atom and residue attributes named areaSES and areaSAS.   
Chimera only shows the solvent-excluded surface, but areas for both  
types of surfaces are computed:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces 
 >

So after you show a surface, you can use these atomic or residue  
attributes in various ways.  To see a histogram of the values, start  
Render/Select by Attribute (under Tools... Structure Analysis, among  
other places).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#render 
 >

With this tool, you could color by the values, or select only atoms  
(or residues) with values in a certain range, or write out the values  
for all atoms or just the selected atoms to a text file with "File...  
Save Attributes".

The values can also be used in command-line specifications, and you  
can show them as labels.  Example commands:

open 1zik
surf
color green @/areaSAS>40
~surf
labelopt info areaSAS
la @n

You can get totals over selected atoms using Attribute Calculator  
(under Tools... Structure Analysis).
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html 
 >

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Apr 21, 2009, at 6:23 AM, Cédric Govaerts wrote:

> Hi there,
> I want to compute accessible surface area for the backbone, as I  
> want to
> compare the predicted amide deuteration between two conformations of a
> protein (I have PDBs for both). I tried with VADAR but the results are
> puzzling, I suspect they are not correct (the more open structure  
> gets a
> lower score).
>
> Is there a way I can do something like that in Chimera ?
>
> In other word I need to compute how exposed to the solvent are the  
> backbone
> atoms (in fact just the NH) and get a table for every position.
> Cannot seem to find a simple way to do that with Chimera...
>
> Thanks again for your help
> Cedric