[Chimera-users] chimera help - surface exposed sides

[Elaine Meng]

On Nov 22, 2007, at 1:07 AM, Thomas C. Marlovits wrote:

> Hi Elaine,
> I am trying to find an easy way to determine solvent  
> accessible/surface exposed side chains but also buried side chains  
> from atomic structures.
> The idea would be to:
> - display the surface
> - have a command that would highlight (color) surface exposed side  
> chains/amino acids
> Optional: color the identified aa by physical property, etc
> - show all the identified amino acids on a primary sequence
> - write out the amino acids into a text file.
>
> Would be great if you can let me know, how to do this most efficiently.
> Thanks,
> -Thomas
> ----------------------------------------------------------------------- 
> --------
> Thomas C. Marlovits, PhD, M.A.S.
> IMP-IMBA Research Center
>        - Research Institute of Molecular Pathology (IMP)
>    - Institute of Molecular Biotechnology, Austrian Academy of  
> Sciences (IMBA)
>
Hi Thomas,
- First assign atoms (or residues) an attribute with values equal to  
their solvent-accessible surface areas (more details below).

- Then you can use Select... By Attribute Value to select any subset of  
those based on some cutoff, for example all atoms with surface area >  
0.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ 
render.html#select
The selection can be written as a list of atoms (or residues) with  
Actions... Write List, and the Sequence tool will show the current  
selection on the protein sequence (it would also be shown on a multiple  
sequence alignment associated with the structure, if you have such an  
alignment).
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/seqpanel.html

- Of course you could also color the selection, but now that numerical  
attributes are assigned, you can map values to colors that will  
gradually shade from one to another with "Render by Attribute" or the  
command "rangecolor"
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ 
render.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rangecolor.html

Now, back to how to get the attribute values assigned.  Currently it is  
necessary to use the "Area/Volume from Web" tool (under Tools...  
Surface/Binding Analysis). It sends coordinates to the NIH StrucTools  
server.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ 
surfvol.html

We are in the process of generating our own surface-calculation code  
that will provide these values within Chimera, but it is not done yet.   
The main inconvenience of this server approach is that you should first  
delete things like water and ligands if you don't want them lumped with  
the protein during the calculation.

"Area/Volume from Web" has a few different options of what is  
calculated.  You can use its MSMS method to calculate both molecular  
surface and solvent-accessible surface (this will generate two  
attributes) or the Gerstein method to calculate solvent-accessible  
surface.  Atom attribute values will automatically be assigned by this  
tool.  If you want them summed to residue attribute values, you must  
also use "Attribute Calculator".
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/ 
calculator.html

There are examples of using Area/Volume from Web, Attribute Calculator,  
and Render by Attribute in the Attributes tutorial, part 2:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
attributes.html#part2

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