[Chimera-users] Chimera - Surface Residue Identification

[Elaine Meng]

On Apr 7, 2008, at 9:33 AM, Thiruvarangan Ramaraj wrote:

> Thanks for your reply.
> I can find out the residues from one chain that are from certain  
> distances from another chain. But it will give all the residues,  
> instead I want only the residues that are in the surface of the  
> chain. Is there any way to do identify the residues that lie on the  
> surface of a chain.
>
> I tried to use surfcat, but it is not working, I am sure I am not  
> doing it correct.
> Any help would be greatly appreciated.
> Thank You
> Sincerely
> Thiru

Dear Thiru,
You can just add another step that says a residue just have a certain  
amount of surface area.  Some new surface-area features were recently  
added to Chimera,  so I recommend getting a daily build.

  First you would need to use "surfcat" and show the surfaces you want.

I don't know what you tried, or what chains are in your structure, so  
I can't give exact steps.  However, here is an example.  If you have  
chains A,B,C and you want one surface around A and another around B,C  
together, you would use these commands:

surfcat group1 :.a
surfcat group2 :.b:.c
surface group1
surface group2

Then, use Select by Attribute ("Select... by Attribute Value" in the  
Chimera menu):  in that tool, choose attributes of "residues" and in  
the "Attribute" menu, choose the name of the surface area attribute.   
The name is areaSAS if you want solvent-accessible surface area,  
areaSES if you want solvent-excluded surface area.   The values in  
the structure are shown in a histogram, and you would move the  
vertical bars to enclose the range of values you want the residues to  
have.  Lots of residues have a tiny amount of surface area, so you  
would probably want to set the minimum at some positive number.   
Click Apply to select that set of residues.

Then you can narrow the set of residues to only those in the zone,  
for example:

select :.a & :.b zr<4.5 & sel

(like my previous example plus "& sel" which means "and also already  
selected").  In the future it should be easier, with a command  
something like

select :.a & :.b zr<4.5 & :/areaSES>50.0

(avoiding the separate "Select by Attribute" step) but currently,  
there is a bug that prevents using areaSAS and areaSES in the command  
line.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




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