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... Sorry! Cheers JD Dr. Jean-Didier Maréchal Lecturer 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@uab.es ----- Missatge original ----- De: Eric Pettersen <pett@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