[Chimera-users] selecting surface waters

Walter Novak wnovak at brandeis.edu
Fri Nov 21 10:01:51 PST 2008

Hi Elaine,

Thanks, this worked great!!!


On Nov 21, 2008, at 12:48 PM, Elaine Meng wrote:

> 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
> ~surf
> 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.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces 
> >
> 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 areaSAS.
> 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
> -----
> 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
>                     http://www.cgl.ucsf.edu/home/meng/index.html
> 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

Walter R.P. Novak, Ph.D.
Postdoctoral Fellow
Rosenstiel Basic Medical Research Center
Brandeis University
415 South St. MS 029
Waltham, MA 02454-9110
Phone: (781) 736-4944
Fax: (781) 736-2405

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