Will try to check mmCIF, but how does one describe angles, chirality etvc for LINKs if there isnt a named dictionary definition to use.. Eleanor
On 10 December 2017 at 20:28, John Berrisford <j...@ebi.ac.uk> wrote: > Dear Eleanor > > mmCIF does not have a equivalent of LINKR records. > > If you define links during refinement then these are output as > _struct_conn in mmCIF files. The _struct_conn records are used during > deposition to determine if two atoms are linked, allowing using to validate > chirality (such as ASN to a NAG) and ignore these atoms in clashes. Any > _struct_conn records which are invalid due to one of the atoms missing will > not affect the analysis at deposition, they will just be ignored. > > Please try outputing an mmCIF file out of refmac and report any incorrect > or missing _struct_conn records to the refmac developers. > > John > > On 10/12/2017 20:04, Eleanor Dodson wrote: > > 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 <%28925%29%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 >> >> > > -- > 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 > >
