Comments (3)
rdk
commented on June 4, 2024
Prediction on mmCIF files saved by PyMOL fails with BioJava parsing error
org.rcsb.cif.EmptyColumnException: column auth_seq_id is undefined.
The problem is that PyMOL does not include column _atom_site.auth_seq_id even if the original file contained it.
auth_seq_id is optional according to the mmCIF spec but present in all PDB entries https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_atom_site.auth_seq_id.html .
The fact that BioJava fails to parse such files is a known long standing issue biojava/biojava#775 (currently moved to milestone version 6.1.0 but it was moved to the next version many times over last few years).
Details:
Current BioJava version used by P2Rank: 6.0.5 (latest)
Tested with PyMOL 2.3.4 (problem also reported with PyMOL 1.8.x and 2.5.x)
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rdk
commented on June 4, 2024
I have asked about the current status on biojava/biojava#775
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rdk
commented on June 4, 2024
In the meantime this has been solved on develop branch by using custom fork of biojava (biojava-structure-6.1.0-rdk1).
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