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An additional problem is existence of alternative conformations close to rotational axis that violate crystal symmetry. If we want to describe such correlated alternative configurations, we need to describe also how they transform by such rotational axis. This problems may also exists also for other packing contacts; however, for conformations close to rotational axis, symmetry operator cannot preserve conformer ID, and this issue cannot be avoided. Zbyszek Otwinowski >>I would probably make the two waters alternates of each other. > > > > Quite possible, but the group definition, i.e. to which alt conf. side > chain they belong, > > would need to be preserved, too. > > > > BR > > > > > > Cheers, > Robbie > > Sent from my Windows Phone > > _____ > > Van: Bernhard Rupp > Verzonden: 23-7-2014 10:19 > Aan: [log in to unmask] > Onderwerp: [ccp4bb] correlated alternate confs - validation? > > Hi Fellows, > > > > something that may eventually become an issue for validation and reporting > in PDB headers: > > > > using the Refmac grouped occupancy keyword I was able to form and refine > various networks of correlated > > alternate conformations - it seems to works really well at least in a 1.6 > and 1.2 A case I tried. > > Both occupancy and B-factors refine to reasonable values as > expected/guessed from e-density and environment. > > Respect & thanks for implementing this probably underutilized secret. > > > > This opens a question for validation: Instead of pretty much ignoring any > atoms below occupancy of 1, one > > can now validate each of the network groups’ geometry and density fit > separately just as any other > > set of coordinates. I think with increasing data quality, resolution, and > user education such refinements will become more > > frequent (and make a lot more sense than arbitrarily setting guessed > independent hard occupancies/Bs > > that are not validated). Maybe some common format for (annotating) such > correlated occupancy groups might > > eventually become necessary. > > > > Best, BR > > > > PS: Simple example shown below: two alternate confs of residue 338 which > correlate with one > > water atom each in chain B, with corresponding partial occupancy (grp1: > A338A-B5 ~0.6, grp2: A338B-B16 ~0.4). > > > > occupancy group id 1 chain A residue 338 alt A > > occupancy group id 1 chain B residue 5 > > occupancy group id 2 chain A residue 338 alt B > > occupancy group id 2 chain B residue 16 > > occupancy group alts complete 1 2 > > . more similar… > > occupancy refine > > > > AfaIct this does what I want. True? > > > > ---------------------------------------------------------------------------------------- > > Bernhard Rupp > > k.-k. Hofkristallamt > > 001 (925) 209-7429 > > [log in to unmask] > > [log in to unmask] > > http://www.ruppweb.org/ > > ----------------------------------------------------------------------- > > > > > > Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353