Not sure why this qualifies as a flame or who you want to flame - seems reasonable but needs to be done so that the data items are extracted consistently from all programs and can be interpreted again by the refinement (or validation) programs independently of which program they came from. Insular kludges probably won't do.
BR -----Original Message----- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Donnerstag, 24. Juli 2014 12:10 To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Betreff: Re: [ccp4bb] correlated alternate confs - validation? -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 [flame] It's all there in the shelx format. If someone would write a wrapper to translate it into mmCIF, everybody would be happy with the least necessary effort [/flame] ;-) Cheers, Tim On 07/24/2014 10:46 AM, Bernhard Rupp wrote: > 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/> > > > > > > > > > > > > > > > > > > > > - -- - -- 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/ iD8DBQFT0NuIUxlJ7aRr7hoRAuorAKDaX42345ovf1SIrVIPzAuO1g1UkwCglBsF NoX6cxLs99wWwd0KZyaZ9XE= =buQc -----END PGP SIGNATURE-----
