[Chimera-users] SAS values for single atoms and residues

Elaine Meng meng at cgl.ucsf.edu
Tue Oct 6 09:24:09 PDT 2009

Hi Dave,
It is not clear to me what you did to list values in the Reply Log.

After you display surface to create those surface area attributes,  
then start "Render by Attribute" (for example, from under Tools...  
Depiction) and in that dialog, choose "File... Save Attributes."  In  
the resulting file-save dialog you can specify not only which  
attribute you want to save, but there is a checkbox "Restrict save to  
current selection" that you will want to activate before saving the  

For example, you could select all the LYS and then this would be used  
to write a file listing the areaSAS of each of those residues.   
Alternatively you could select all the :lys at nz and then write the  
areas of the selected atoms.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 6, 2009, at 9:23 AM, David Chenoweth wrote:

> Hi Elaine,
> I'm trying to calculate the solvent accessible surface area for  
> several lysine residues in a protein  to evaluate which are most  
> likely to be free on the surface for functionalization. My thought  
> was to just calculate the SAS area and rank order them. When I  
> select just the primary amine of all the lysine residues and go to  
> the reply log I get several numbers in a row under SAS and I'm not  
> sure which are correct. These numbers don't seem to change if I  
> select different residues so I'm not sure how to get the SAS values  
> just for my lysine amines.
> Thanks,
> Dave

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