reading pdb, chain A twice

[Tamas Hegedus]

Hi,

I think there is a bug in the pdb reader.
If I read pdb files then segid A is present twice.

print(mda.__version__)
u = mda.Universe("/mnt/data/adat/pdb/6msm.pdb")
print(f"segments: {u.segments}")
print(u.segments[0] == u.segments[2])
print(u.segments[1] == u.segments[2])
print("a.a.0 from seg.0", u.select_atoms(f"name CA and segid
{u.segments[0].segid}")[0].position)
print("a.a.0 from seg.2", u.select_atoms(f"name CA and segid
{u.segments[2].segid}")[0].position)

2.0.0
segments: <SegmentGroup [<Segment A>, <Segment B>, <Segment A>]>
False
False
a.a.0 from seg.0 [134.21  175.727 137.933]
a.a.0 from seg.2 [134.21  175.727 137.933]

Bests,
Tamas

[biohe...@gmail.com]

I just realized that different entities (protein and small molecules) with the same chain ID gets different segments with the same segid.