Hmmm..so can I interpret this as a subtle hint to start abandoning the PDB format and
saving myself various kinds of grief by submitting nmCIF coordinate files instead? If so, a maybe not so subtle hint on the deposition page might be in order for the common good.. or at least for the fossils still vi-ing PDB files. Thx, BR From: John Berrisford [mailto:j...@ebi.ac.uk] Sent: Sunday, December 10, 2017 11:59 AM To: b...@hofkristallamt.org; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] LINK vs LINKR Dear Bernhard When we convert from PDB to mmCIF we do indeed ignore LINKR records as these are also present between unmodelled residues in the PDB file (or were when we tested). However, if you output an mmCIF file directly from refmac then the link records are correctly written out into _struct_conn records (mmCIF equivalent of LINK records) which are correctly handled by the deposition system. To do this simply add the keyword "pdbout format mmcif" to your refmac commands and it will output an mmCIF file ready for deposition. I hope this helps John PDBe On 09/12/2017 20:34, Bernhard Rupp wrote: Dear Developers, the TER issue in REFMAC seems to be fixed, but is really necessary that REFMAC places LINKR records instead of LINK records in the PDB header? The PDB does not recognize those, and although it's only a minor nuisance to fix them in an editor, one tends to forget this between revisions.or the PDB could simply ignore the 'R'.. Best, BR ------------------------------------------------------ Bernhard Rupp http://www.hofkristallamt.org/ b...@hofkristallamt.org <mailto:b...@hofkristallamt.org> +1 925 209 7429 +43 767 571 0536 ------------------------------------------------------ Many plausible ideas vanish at the presence of thought ------------------------------------------------------ -- John Berrisford PDBe European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UK Tel: +44 1223 492529 http://www.pdbe.org http://www.facebook.com/proteindatabank http://twitter.com/PDBeurope
