[Chimera-users] Question on Chimera

[Elaine Meng]

Hi Ki,
I'll answer in two parts,
(A) how to tell Chimera that certain water molecules should be  
included with the protein when drawing a surface
(B) how to show only part of the surface that forms a binding site or  
pocket

(A) Chimera automatically puts atoms into groups it thinks are  
reasonable for surface calculation.  This default approach keeps  
water molecules and ligands outside of the protein.  To make a  
surface that combines other molecules together with the protein, use  
the command "surfcat" to specify the group and then "surface" to  
display the surface of the group.
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html

For example, the surface for 1nzy automatically includes the protein  
part of chains A,B,C.  Let's say you wanted it to enclose the protein  
part of chains A,B plus 367 and 402 in chain "water" (in a different  
structure, the waters could be in the same chains as the protein  
residues, or in chain "het").

    surfcat mysurface protein & :.a-b | :367.water,402.water
    surface mysurface

This example is a little complicated - the reason for including the  
"protein &" is that chains A and B include ligand molecules, not just  
protein, and I didn't want the surface to enclose them.  It might be  
simpler for your protein.  If you want all the protein in your model  
plus a couple of waters, you could just select the two waters with  
Ctrl-click on the first, Shift-Ctrl-click on the second, then use:

    surfcat mysrf protein | sel
    surface mysrf

(B) I should mention here are many different ways to do the same  
things in Chimera.  The following things could also be done using  
selection from the screen and the Actions... Surface menu.

If you know what residues line the pocket, you can just display the  
surface for those residues, for example:
    ~surface
    surface :64.b,90.b,114.b,137.b,145.b

Or, if there is a ligand in the pocket, or an atom in the protein or  
a water that is approximately in the middle of the pocket, you can  
use it to define a zone:

    surface :bca.b z<6 & mysurface
(show surface for residues with any atoms within 6 angstroms of  
residue BCA in chain B and that are in the "mysurface" group)

  If the surface is displayed already, you could hide the part that  
is outside of the zone:

  ~surf :402.water za>8
(undisplay surface for atoms farther than 8 angstroms from water 402)

Currently zones are based only on atom-atom distances; there is no  
way to define them using atom-surface distances, so sometimes it  
takes more steps of displaying or undisplaying atomic surface patches  
(with surface/~surface or using the menu) to show just the part you  
want.

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

On Jun 24, 2007, at 12:23 PM, Ki Kim wrote:
> Hello,
> I would like to know what is the best way to draw the surface of the
> binding site of a protein.  I would like to add some water molecules
> to the protein and treat these water as part of the protein.
> Thank you for your help.
> Sincerely,
> Ki Kim