[Chimera-users] [chimera-dev] Suggestion: define selection name for startup chimera

Jean Didier Pie Marechal JeanDidier.Marechal at uab.cat
Wed Sep 9 12:12:58 PDT 2009

Hi Eric,

"binding site" was an idea more than anything else but I realize from your e-mail that we don't really need. Strangely, though using @/display frequently I never thought about using it for selecting. 

Think I can do without the shortcut...


Dr. Jean-Didier Maréchal
Computational Biotechnological Chemistry @ Transmet
Unitat de Química Física
Departament de Química
Universitat Autònoma de Barcelona
Edifici C.n.
08193 Cerdanyola (Barcelona)
Tel: +34.935814936
e-mail: JeanDidier.Marechal at uab.es

----- Missatge original -----
De: Eric Pettersen <pett at cgl.ucsf.edu>
Data: Dimecres, Setembre 9, 2009 8:46 pm
Assumpte: Re: [chimera-dev] Suggestion: define selection name for startup	chimera

> On Sep 8, 2009, at 10:31 AM, Jean Didier Pie Marechal wrote:
> > In the new builts of chimera, you have change the initial  
> > representation of the protein so that binding sites immediately  
> > appear and the rest of the protein is in ribbon (which is a 
> great  
> > idea by the way). That means that you have a automatic analysis 
> of  
> > binding site recognition. I wonder if you couldn't include a  
> > selection named "binding site" (or something similar), that 
> would  
> > appear as a named selection and that we could call at the early  
> > beginning of the session.
> Hi JD,
> 	I could.  I definitely wouldn't want to call it "binding site" 
> since  
> it includes waters and residues not necessarily involved in 
> binding,  
> not to mention the entire structure for small-molecule structures. 
> It's also a misleading name for structures without ligand present -
> -  
> since their binding sites won't be selected by it.  FInally, it's 
> also  
> somewhat confusing as to what should happen if you open multiple  
> structures over the course of a session.
> 	So it could be called "smart display atoms" I suppose.  If some 
> other  
> users thought it'd be useful I'd do that (anyone?).  In the 
> interim,  
> you can pretty easily create the selection yourself with these  
> commands after opening the structure:
> 	sel @/display; namesel smart atoms; ~sel
> You could alias that to something snappier. :-)
> --Eric

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