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Chris Oldfield wrote:
I recently ran the mmCIFParser object over all of PDB's mmCIF files and found a large number of files failed to parse correctly (a short script at the end to demonstrate). Of ~50k mmCIF files, 3891 files failed to parse and another 1980 were missing fields in the mmCIF dictionary.
1alw, 1det, and 1tmy still fail using this script.
Redmine issue: https://redmine.open-bio.org/issues/2626
Chris Oldfield wrote:
I recently ran the mmCIFParser object over all of PDB's mmCIF files and found a large number of files failed to parse correctly (a short script at the end to demonstrate). Of ~50k mmCIF files, 3891 files failed to parse and another 1980 were missing fields in the mmCIF dictionary.
A few examples of files that failed to parse:
http://www.rcsb.org/pdb/files/1alw.cif.gz
http://www.rcsb.org/pdb/files/1det.cif.gz
http://www.rcsb.org/pdb/files/1tmy.cif.gz
A few with missing fields:
http://www.rcsb.org/pdb/files/1mfl.cif.gz
http://www.rcsb.org/pdb/files/1tfj.cif.gz
http://www.rcsb.org/pdb/files/1zn8.cif.gz
The problem seems to be that an error in one mmCIF table, like an extra field, seems to propogate through the rest of the parse.
x86_64 gentoo linux 2008, src BioPython install
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