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I was hoping to get some help on PDBfixer's findMissingResidues() functionality. 3ODU has missing residues at both the N and C terminal regions of the PDB strucuture but for some reaosn PDBfixer does not detect them and the fixer.missingResidues dict is empty.
The first two chains of 466 and 456 amino acids should correspond to the seqres lengths of 502 and 502 and although they don't match, PDBfixer doesn't find those missing residues.
Would really appreciate any help I could get on this because I am quite clueless on how to sort this out.
The text was updated successfully, but these errors were encountered:
There's something very strange in that file. The residue numbers abruptly jump from 229 to 900.
ATOM 1653 CB SER A 229 0.030 -10.221 29.843 1.00 53.91 C
ANISOU 1653 CB SER A 229 6936 7452 6093 58 -855 -128 C
ATOM 1654 OG SER A 229 -0.628 -9.302 30.696 1.00 64.08 O
ANISOU 1654 OG SER A 229 8162 8736 7451 59 -856 -70 O
ATOM 1655 N GLY A 900 1.252 -10.057 27.133 1.00 45.01 N
ANISOU 1655 N GLY A 900 5535 5672 5897 -368 299 -198 N
ATOM 1656 CA GLY A 900 2.208 -10.415 26.106 1.00 44.83 C
ANISOU 1656 CA GLY A 900 5512 5648 5874 -367 298 -197 C
PDBFixer interprets that as meaning there are hundreds of missing residues in the middle of the chain. Since there are no corresponding residues in the SEQRES section, it isn't able to match them up and figure out what the sequence ought to be. Any idea why the numbering is like that?
Thanks for pointing this out, I don't know why the numbering turned out like this but it makes sense that this won't be able to be matched against the SEQRES section.
Hi developers of PDBfixer,
I was hoping to get some help on PDBfixer's
findMissingResidues()
functionality.3ODU has missing residues at both the N and C terminal regions of the PDB strucuture but for some reaosn PDBfixer does not detect them and the
fixer.missingResidues
dict is empty.The first two chains of
466
and456
amino acids should correspond to the seqres lengths of502
and502
and although they don't match, PDBfixer doesn't find those missing residues.Would really appreciate any help I could get on this because I am quite clueless on how to sort this out.
The text was updated successfully, but these errors were encountered: