Opened 3 years ago

Closed 3 years ago

#7904 closed defect (fixed)

RCSB biological unit: PDBx/mmCIF styling lost

Reported by: pett Owned by: Greg Couch
Priority: moderate Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

Opening the attached biological unit downloaded from the RCSB results in "mmCIF parsing error: PDBx/mmCIF styling lost near line 5956" and no structure

Attachments (1)

2CSE.cif​ (81.9 MB ) - added by pett 3 years ago.

Change History (6)

by pett, 3 years ago

Attachment: 2CSE.cif​ added

comment:1 by pett, 3 years ago

From the "Export Models" link on this page: ​https://www.rcsb.org/3d-view/2CSE/1

comment:2 by Greg Couch, 3 years ago

Asked info@… if this is intentional. The problem is that our heuristic to detect PDBx/mmCIF styling (fixed width columns) fails in this case. We don't want to give up using PDBx/mmCIF styling because it gives up an almost 3X speed improvement when reading mmCIF files. If this intentional, we will need to figure out a different heuristic. But there are only two differences between the good and bad files. The bad file has "audit_conform.dict_version 5.3180000000000005" vs. "audit_conform.dict_version 5.318", and the bad one has "pdbx_database_status.SG_entry n".

comment:3 by Greg Couch, 3 years ago

TODO: when a ""PDBx/mmCIF styling lost" exception is seen, reparse the mmCIF file with styling turned off. Will need to figure out an API to disable using styling.

comment:4 by Greg Couch, 3 years ago

Status: assigned → accepted

comment:5 by Greg Couch, 3 years ago

Resolution: → fixed
Status: accepted → closed

Done for #8484.

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