[Chimera-users] Identifying surface residues

Soumya Ghosh (Systembiologie) ghosh at wzw.tum.de
Fri May 15 01:22:45 PDT 2009


Dear Dr.Elaine Meng,
Thanks  a lot for your kind advise. It really helped me a lot.

Regards,
Soumya



Elaine Meng wrote ..
> 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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