[Chimera-users] Closest Waters

[Elaine Meng]

On Nov 30, 2010, at 4:55 AM, Beale, John wrote:

> I have another question that maybe you can answer. Is there a way in Chimera to select only internal amino acids of a protein (I would like to select hydrophobic amino acids away under the surface of my protein to try and identify hydrophobic core groups)?

Hi John,
After you have displayed a surface, then (even if you hide the surface), the atoms and residues will have surface area values assigned as an attribute.  Amino acid hydrophobicity is another attribute.  You can select by attribute values or combinations of attribute values, for example, residues with little exposed surface area but high hydrophobicity values.

Example:

open 2gbp
surface
~surf
select :/areaSES<10 and kdHydrophobicity>1

... you wouldn't necessarily use those cutoffs, may want to experiment and see what works best in your case.  Then you could choose "Actions... Write List" from the menu to save a list of the selected residues to a text file.

More details:  

The surface area attributes are named areaSES (solvent-excluded, where the probe surface goes; this is the type of surface Chimera displays) and areaSAS (solvent-accessible, where the probe sphere center goes), as described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

The hydrophobicity attribute is named kdHydrophobicity and is described here:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html>

The names of the attributes are relevant because you would choose them in the "Select by Attribute" dialog (menu Select... By Attribute Value), or enter the names in the Command Line to select residues by their values.  To use a combination of multiple attributes, I would use the Command Line approach. 
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors>  
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#resprops>

 However, the "Select by Attribute" dialog can still be useful for showing you histograms of the values in your structure; you would need to change to attributes of "residues" and then choose the particular attribute by name to see its histogram.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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