Opened 7 years ago

Closed 7 years ago

#1274 closed defect (fixed)

PDB HELIX record format

Reported by: Tristan Croll Owned by: Eric Pettersen
Priority: moderate Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

If I submit a PDB file written by ChimeraX to PHENIX for refinement, the HELIX records are stripped from the final output with messages like:

Bad HELIX record, was skipped:
HELIX    1   1 ASP A   98  HIS A  102  1

I've confirmed that it can be fixed by adding the length record in columns 72-76 as per ​http://www.bmsc.washington.edu/CrystaLinks/man/pdb/part_42.html.

Change History (2)

comment:1 by Eric Pettersen, 7 years ago

Status: assigned → accepted

Early versions of the HELIX record (circa 1992) did not have those columns defined. I'm surprised they're required by any program, but nonetheless I will work on adding them.

--Eric

comment:2 by Eric Pettersen, 7 years ago

Resolution: → fixed
Status: accepted → closed

Easier than I though since the formatting code already supported that field -- it just wasn't being set.

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