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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Bernhard Rupp
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+43 767 571 0536
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John Berrisford
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
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