Opened 3 years ago

Closed 3 years ago

#7704 closed defect (fixed)

chain.from_seqres not set from PDB file

Reported by: Greg Couch Owned by: Eric Pettersen
Priority: moderate Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

After "open 3fx2 format pdb", if you start the shell and do:

m = session.models[0]
c = m.chains[0]
c.from_seqres

You will see that c.from_seqres is False even though 3fx2 has SEQRES records. That causes the mmCIF writer to omit the sequence information and emit "Not saving entity_poly_seq for non-authoritative sequences" (eg., from "save foo.cif").

c.from_seqres is True in ChimeraX 1.2, but False in 1.3, 1.4, and the daily build.

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Sequence
Priority: critical → moderate
Status: assigned → accepted

comment:2 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: accepted → closed

Bug was side effect of PDB 2-character chain ID support -- the sequence info passed into the atomic layer mistakenly did not strip a leading space.

Fix: ​https://github.com/RBVI/ChimeraX/commit/0b6bcf190859684c0b7b171cfdb05581ae25ebfc

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