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
<mailto: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
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+43 767 571 0536 <tel:+43%207675%20710536>
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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 <tel:+44%201223%20492529>
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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
