[Chimera-users] Closest Waters

Tom Goddard goddard at sonic.net
Tue Nov 30 11:17:43 PST 2010

Hi Elaine,

   This question has come up several times and requires some steps to 
answer.  It strikes me as a good question to base a screen-capture video 
demo on.


> 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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> Chimera-users at cgl.ucsf.edu
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