[Chimera-users] select by residue type or category

Francesco Malatesta francesco.malatesta at fastwebnet.it
Tue Mar 19 11:49:59 PDT 2013


Thank you very much Elaine
Francesco

Il giorno 19/mar/2013, alle ore 19:45, Elaine Meng ha scritto:

> 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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