Hi Paul.
An increasing number of entries do not have PDB files, instead only being
available in mmCIF format.
The number of entries affected by this will likely increase rapidly soon as
we do not make a PDB file for an entry when it doesn't fit exactly into the
format.
Multi-letter chain IDs are one reason for not producing a PDB file for an
entry and this is the default when using mmCIF format as an output from refmac.
mmCIF format is now mandatory for deposition so we are seeing lots of
entries which we will not be able to make PDB files for.
Maybe this would be a good opportunity for coot to switch to downloading
mmCIF format?
John
On 21 October 2019 00:02:02 Paul Emsley <[email protected]> wrote:
On 18/10/2019 20:54, Robert A Grant wrote:
Recently I noticed that my installation of COOT can no longer fetch PDB files.
The program reports the following error:
PDB Accession Code: dps
(get-ebi-pdb "dps")
DEBUG:: in get-url-str: "dps"
"http://www.ebi.ac.uk/pdbe-srv/view/files/dps.ent"; pdb
(handle-read-draw-molecule-with-recentre "coot-download/dps.pdb.ent" 1)
INFO:: Reading coordinate file: coot-download/dps.pdb.ent
WARNING:: Error reading small-molecule cif "coot-download/dps.pdb.ent"
There was an error reading coot-download/dps.pdb.ent.
ERROR 44 READ: Non-existent or empty file.
There was a coordinates read error
This would appear to be because the //www.ebi.ac.uk/pdbe-srv site no longer
supports this feature.
Is there a way to fix this?
It's related to https. A fix is in the works, I think - I am not sure where
it has percolated to - and it's
related to the curlew failure. Debugging network issues on other people's
computers is tricky.
I think that 0.8.9.3-pre from my site works - maybe not curlew though.
Regards,
Paul.
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