Changes between Initial Version and Version 5 of Ticket #3676


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Timestamp:
Nov 17, 2025, 4:20:57 PM (2 weeks ago)
Author:
Greg Couch
Comment:

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  • Ticket #3676

    • Property Component Unassigned → Input/Output
    • Property Owner set to Greg Couch
    • Property Platform → all
    • Property Project → ChimeraX
    • Property Status new → closed
    • Property Summary ChimeraX bug report submission → Out-of-date mmCIF templates
    • Property Resolution → fixed

  • Ticket #3676 – Description

    initial v5  
    44ChimeraX Version: 1.1rc202008312018 (2020-08-31 20:18:51 UTC)
    55Description
     6}}}
    67I take it you're now bundling the mmCIF templates for some common residues into the ChimeraX distribution? Unfortunately, at least some of these are out of date - using PDB V2 atom names rather than the current V3. For instance, the LYS template uses the V2 name "HN2" for the "extra" hydrogen attached to the N, while the SER template uses the up-to-date "H2".
    78
    89If it's useful, I have a .cif file containing templates for all residues covered by the "core" AMBER forcefield bundled with ISOLDE (protein including protonation variants, nucleic acid, sugars), composed directly from templates fetched from ligand-expo.
    9 
     10{{{
    1011OpenGL version: 3.3.0 NVIDIA 450.51.06
    1112OpenGL renderer: TITAN Xp/PCIe/SSE2