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