[Chimera-users] select by residue type or category

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 19 11:45:32 PDT 2013


Hi Francesco,
You could either just select by residue type and chain ID, for example command

select :asp.j,glu.j

... or by amino acid category, for example command

select :.j & hydrophobic

see command-line atom specification (amino acid category is one of the built-in classifications):
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

These same things can be done with the Actions... Select menu, see submenus "Selection Mode... append" (allows building up a selection instead of always replacing it, or intersecting, as with a specific chain), "Chain...[chain ID]", "Residue... amino acid category" and/or "Residue... [residue name]" but the menu approach is more tedious/longer than commands.

The amino acid categories have default assignments taken from a literature reference as shown here,
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/resprop/resprop.html#aacat>
... but you can change the assignments as you like using the ResProp tool, in menu under Tools... Structure Analysis.

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

On Mar 19, 2013, at 11:17 AM, Francesco Malatesta wrote:

> Hello
> I would like to ask a simple question on selection. In the GroEL-GroES complex (pdb 1aon) how do you select, for example, hydrophobic or acidic residues or both  in the say  J chain?
> thank you very much
> Francesco Malatesta




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