>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: CCP4BB@JISCMAIL.AC.UK 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 b...@ruppweb.org b...@hofkristallamt.org http://www.ruppweb.org/ -----------------------------------------------------------------------
