-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Bernhard,
do you refer to the PDB who, according to Martyn, remove the altloc indicator? That's certainly a serious bug that should be fixed as quickly as possible. Within refmac the preservation is fine and as you would expect it to be: altA only sees atoms in altA and those witout altLoc, etc, which makes sure you PDB file is interpreted correctly by refmac5. That's how I refmac works. Best, Tim On 07/23/2014 03:26 PM, Bernhard Rupp wrote: >> 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/ > > ----------------------------------------------------------------------- > > > > > > > - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTz7qjUxlJ7aRr7hoRAs9cAKD4LFul9cmKYgsV5n6o3LZqTgHI6wCfZ4fS 2CdyyS0zWMjryhZrwgA2mZk= =iogi -----END PGP SIGNATURE-----
