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keitaroyam / servalcat

Structure refinement and validation for crystallography and single particle analysis
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poly.type not recognized by the wwPDB servers #19

Open daniel-s-d-larsson opened 2 hours ago

daniel-s-d-larsson commented 2 hours ago

I have a problem that the wwPDB deposition server and also the wwPDB validation server misidentifies my polymer chains as polyribonucleotide instead of polypeptide(L) when I upload the refined.mmcif file from refine_spa_norefmac. The poly.type is set correctly in the header, but the wwPDB staff says it is wrong on their side.

Example:

loop_
_entity_poly.entity_id
_entity_poly.type
_entity_poly.pdbx_strand_id
_entity_poly.pdbx_seq_one_letter_code
A polyribonucleotide A ?
B polypeptide(L)     B ?
C polypeptide(L)     C ?
D polypeptide(L)     D ?
E polypeptide(L)     E ?
...

This is a ribosome structure with both ribonucleic acids and many proteins. Strangely, only protein chains up til a specific point are identified as polyribonucleotide, which indicate to me that there is some corruption in the file. Could the lack of TER records cause this problem? In an earlier deposition, which used an older version of refine_spa, the polymer type records were not there.

wojdyr commented 2 hours ago

If you mean the lack of TER in mmCIF, it's fine, only PDB files have TER records.

The software used on the PDB servers discards and regenerates some information; it may easily happen that correct annotation is replaced with incorrect one. To investigate it, we'd need an example file that demonstrates the problem.