[Chimera-users] selecting surface waters

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 21 09:48:37 PST 2008

Hi Wally,
Here's one idea:
while only the protein is included in the default (main) surface, you  
could use the command "surfcat" to lump the waters in with it.  Then  
the surface waters should be the ones with nonzero surface area, or  
bigger than some small cutoff.  Surface area per atom is an attribute,  
so you can use it in command-line specification, selection, etc.

Detailed example (commands):

open 2gbp
surfcat blob protein | solvent
surf blob

When you create a molecular surface, the solvent-accessible and  
solvent-excluded areas per atom are automatically assigned as the atom  
attributes areaSAS and areaSES, respectively.  There are also residue  
attributes by the same names.

I undisplayed the surface after I made it so I could see the atoms,  
but the area values are still there.  You could then select (or color,  
etc.) just the waters with area above some cutoff, for example:

sel :hoh & :/areaSAS>20

  - OR - (since areaSAS is the name of an atom attribute and residue  
attribute, which for only-O water is the same value)

sel :hoh & @/areaSAS>20

  - OR -

sel @/areaSAS>20
~sel protein

First I tried using "solvent" instead of ":hoh" but that doesn't work,  
which made sense upon more thought:  the "surfcat" command reassigned  
those atoms from the solvent surface category into the blob surface  
category, because surface categories are by definition mutually  
exclusive.  Your waters might be named WAT instead of HOH, and of  
course you might want to use a different cutoff or areaSES instead of  

You can see a histogram of the area values in Render/Select by  
Attribute, and select interactively on the histogram with the Select  
part of that dialog, but be aware that would include the nonsolvent  
atoms as well.  You would then have to ~sel protein, as in the last  
example above.

I hope this helps!  Best,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 21, 2008, at 9:02 AM, Walter Novak wrote:

> Hi All,
> I think there might be an easy way to do this, but haven't figured it
> out yet. I am interested in only selecting the waters on the surface
> of the protein, not those that are buried. Any suggestions?
> Thanks,
> Wally

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