>From a practical point of view, a solution for documenting grouped occupancy refinement should at minimum allow
(a) easy & automatic harvesting from the respective refinement log files, and (b) equally easy extraction from the PDB/cif format to replicate the same refinement (c) not mess up legacy code/format or use undocumented 'features' How this is best implemented is probably not trivial (except the REMARK kludge) and needs the data base/integrity/validation experts. Best, BR From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of dusan turk Sent: Donnerstag, 24. Juli 2014 05:32 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? Hello, A solution exists also for PDB records: As a consequence of a discussion with George which took place years ago, I have taken the liberty to extend the PDB record length of 80 characters and use additional characters to specify the group ID and their members list number and provided an interface to manipulate them. Thereby the PDB limitations were extended to adopt the SHELX philosophy of treating combined groups of any composition. ATOM 1 N GLY A 1 -31.334 -24.247 23.250 0.54 34.05 1A N 1 0 ATOM 2477 N GLY A 1 -29.650 -24.643 23.839 0.46 41.88 1B N 1 1 The records with our the group extension are not members of groups with partial occupancy. These two records shown are members of group ID 1, the atom in the first record belongs to group ID 1 members list number 0 and the second to group ID 1 and members list no 1. (The members lists begin with 0.) On Jul 24, 2014, at 1:02 AM, CCP4BB automatic digest system <lists...@jiscmail.ac.uk> wrote: Von: CCP4 bulletin board [ <mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Frances C. Bernstein Gesendet: Mittwoch, 23. Juli 2014 17:20 An: <mailto:CCP4BB@JISCMAIL.AC.UK> 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 Dr. Dusan Turk, Prof. Head of Structural Biology Group http://bio.ijs.si/sbl/ Head of Centre for Protein and Structure Production Centre of excellence for Integrated Approaches in Chemistry and Biology of Proteins, Scientific Director http://www.cipkebip.org/ Professor of Structural Biology at IPS "Jozef Stefan" e-mail: dusan.t...@ijs.si phone: +386 1 477 3857 Dept. of Biochem.& Mol.& Struct. Biol. fax: +386 1 477 3984 Jozef Stefan Institute Jamova 39, 1 000 Ljubljana,Slovenia Skype: dusan.turk (voice over internet: www.skype.com <http://www.skype.com/>
