[Chimera-users] Identifying surface residues

Elaine Meng meng at cgl.ucsf.edu
Thu May 14 10:53:28 PDT 2009


Dear Soumya,
When you show a surface, the surface area values are automatically  
assigned to atoms and residues.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces 
 >

You can select resides with surface area greater than some value,  
which will be the residues at the surface.  The residues with small or  
zero surface area will be the ones buried on the inside.

For example,

open a structure (I opened PDB 2gbp as an example)
use menu "Actions... Surface... show"
then you can hide the surface, "Actions... Surface... hide"
then to select by surface area value, choose "Select... by Attribute  
Value"
     in that dialog:
        change from attributes of "atoms" to "residues" if you want to  
select whole residues
        choose Attribute: "areaSAS" (if you want solvent-accessible  
surface area)
                         or "areaSES" (if you want solvent-excluded  
surface area)
        move the vertical green bars to enclose the values of  
interest, click Apply
It is the solvent-excluded surface that is displayed in Chimera.
For example, I chose residues with areaSES values >30 (one green bar  
near 30, the other near the maximum value). You could use a different  
cutoff, but probably it should be bigger than zero.  That generally  
selects the residues on the surface, and now you can use the Actions  
menu to do something else to those residues (color them, label them,  
write list of residues to a file, etc.)

Instead of a dialog you could also select them with a command, e.g.

select :/areaSES>30

One thing to think about is that usually there are surface bubbles on  
the inside, and some of the residues may have surface area from these  
bubbles and not the real outer surface of the protein.  You can change  
the surface to not include these inside bubbles:

open Model Panel (menu "Favorites... Model Panel")
    in that dialog:
        choose the MSMS surface model in the left side
        click "attributes" button on the right side
           in that, change "show disjoint surfaces" to "false"
        Close dialog
now choose "Select... by Attribute Value" again
     in that dialog:
        Refresh... Values
        and proceed as above to choose residues by surface area value
(or again, you could use the command instead)

Here is a previous answer to a similar question:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-November/003291.html 
 >

I hope this helps,
Elaine

On May 14, 2009, at 5:46 AM, Soumya Ghosh (Systembiologie) wrote:

> Dear Dr. Elaine C. Meng,
> Thanks a lot for your kind help. It really worked nicely.Can I  
> afford to have some more questions. When I put my protein in the  
> CHIMERA, I get the 3D module of it and it exhibits the &#945;- 
> helices and the ß-sheets very nicely. Now if I want to highlight the  
> aminoacids that are specifically on the surface of the N -terminal  
> or the amino acids that specifically embedded in the core, is there  
> any provision to that. I tried with the Action; surface; show. With  
> these commands it is visible that a structure appears that cover  
> sometime the loops/helices/sheets fully or partially. Now my problem  
> is, that is the sructure which is visible is it the surface? The  
> amino acids  which are highlighted are also from the surface? Can  
> you kindly help me in this regard.
>
> Thanks with regards,
>
> Soumya




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