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

Eric Pettersen pett at cgl.ucsf.edu
Wed Sep 9 11:46:10 PDT 2009

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. :-)


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