One could check if the alternate conformations are part of a continuous alternate zone or if they make contact (no contact, no association). However, I think it is time to abandon the PDB format and move to cif or some other format.
My 2 cents, Herman -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] correlated alternate confs - validation? I agree that it would be excellent to be able to associate alternate conformations (beyond the individual residue) but when we defined the "PDB" format we had an 80-column limitation per atom and so only one column was allowed for alternate conformations. In an ASCII world only 36 characters were available to define alternate conformations. This is inadequate to allow for many residues with independent alternate conformations - one residue with three conformations would use up 3 of the 36 characters. Thus there was no way to say that alternate conformation A in one residue is or is not associated with alternate conformation A in another residue. Frances ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Wed, 23 Jul 2014, Tim Gruene wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi Bernhard, > > That's right, the definition is not in the PDB, but REFMAC sensibly > handles it this way. It is certainly a short-coming if not bug in the > PDB (definition). > > Best, > Tim > > On 07/23/2014 04:49 PM, Bernhard Rupp wrote: >> ?? Refmac knows because of the group definition, otherwise I cannot >> force grouped occupancy refinement. There is no definition in PDB >> that eg ALTLOC A (of whatever residue) belongs to ALTLOC A of >> (whatever) residue/water. >> >> BR >> >> -----Original Message----- From: Tim Gruene >> [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Mittwoch, 23. Juli 2014 >> 15:38 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: >> [ccp4bb] correlated alternate confs - validation? >> >> 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/ > > iD8DBQFTz85KUxlJ7aRr7hoRAoeqAKCGBTg8nowXCCFfbp9kfZsCYr2fHgCgoJhp > CPPMzM1r6DEZv2DJi4vwXmI= > =bMXr > -----END PGP SIGNATURE----- >
