I am having trouble loading biological assemblies for PDB 4OPJ. The
structure is unusual in that it contains 2 single stranded DNA molecules
together with 2 protein chains in the asymmetric unit. The double stranded
DNA comes only when reconstructing the biological unit from the symmetry
operators.
Using Jmol 14.4.0_2015.11.13, if I do:
load /my/dir/4OPJ.cif filter "assembly 1"
what I get is a protein chain and a single stranded DNA chain that don't
even contact each other. What I should get instead is a double stranded DNA
that contacts 1 of the protein chains.
I've looked into it and the issue seems to be confusion between asym_id
(internal chain identifiers in mmCIF files) and author_id (a.k.a.
pdb_strand_id, the classic chain identifiers as used in PDB files). For
this particular file the mapping happens to be a bit unusual:
asym_id -> author_id
A -> B
B -> D
C -> A
D -> C
The issue is that in mmCIF files, the biological assembly is specified as a
list of operators to apply to a list of chains, *identified by asym_ids*.
For 4OPJ biological unit 1, it is:
loop_
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
_pdbx_struct_assembly_gen.asym_id_list
1 1 B
1 2 C,A
So operator 1 needs to be applied to asym_id B (corresponding to author_id
D) and operator 2 to asym_id C,A (corresponding to author_ids A,B).
It seems that Jmol is getting the chain ids mixed up, thus ending up with
molecules in the wrong places and no double stranded DNA.
Is this a bug, or am I doing something wrong?
Thanks
Jose
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