-----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-----
