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

David Chenoweth dchen at caltech.edu
Tue Oct 6 10:23:10 PDT 2009

Thanks Elaine!
Your a life saver.

On Oct 6, 2009, at 12:24 PM, Elaine Meng wrote:

> 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 file.
> 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
> -----
> 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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