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