Opened 19 months ago

Last modified 5 days ago

#15035 assigned enhancement

Revert Greek/special characters to plain text on output

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

Description (last modified by Eric Pettersen)

I just downloaded a pdb file from AlphaFold DB (AF-P69905-F1-model_v4.pdb). After modifying it with ChimeraX (version 1.6.1 (2023-05-09)) I've saved the modified atomic structure as a cif file. The original pdb file contains this line:

COMPND 2 MOLECULE: HEMOGLOBIN SUBUNIT ALPHA;

After saving the file as cif format ALPHA is not longer a string but a GREEK character:

_entity.pdbx_description "hemoglobin subunit α"

Change History (2)

comment:1 by Eric Pettersen, 19 months ago

Description: modified (diff)

comment:2 by Eric Pettersen, 5 days ago

Cc: Eric Pettersen added; Greg Couch removed
Owner: changed from Eric Pettersen to Greg Couch
Type: defect → enhancement

The mmCIF writer doesn't convert greek letters into their PDB ASCII equivalents. It would be nice if it did. Would probably not be too hard if you reversed the chimerax.pdb.pdb.greek_letters dictionary (upcasing the values).

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