[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
"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
08193 Cerdanyola (Barcelona)
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
> > idea by the way). That means that you have a automatic analysis
> > binding site recognition. I wonder if you couldn't include a
> > selection named "binding site" (or something similar), that
> > 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"
> it includes waters and residues not necessarily involved in
> 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
> 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
> users thought it'd be useful I'd do that (anyone?). In the
> 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. :-)
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