Dear John - sorry for my ignorance but does mmCIF provide a proper LINKR replacement?
Surely there is just as likely to be redundant LINK records as LINKR? It is easy enough to get rid of a residue and forgetting to leave useless CISPEP SSBOND LNK etc lines in the header... Eleanor On 10 December 2017 at 19:59, John Berrisford <j...@ebi.ac.uk> wrote: > 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 > > +1 925 209 7429 <(925)%20209-7429> > > +43 767 571 0536 <+43%207675%20710536> > > ------------------------------------------------------ > > 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 <+44%201223%20492529> > http://www.pdbe.orghttp://www.facebook.com/proteindatabankhttp://twitter.com/PDBeurope > >
