Bad IDATM typing

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-11-10.0.26200-SP0
ChimeraX Version: 1.13.dev202608021548 (2026-08-02 15:48:26 UTC)
Description
New `idatm_type` assignment failure: in COD 2214833, the planar N=CH2 is typed as N3+ - C3

Log:
> clipper init

> cofr centerOfView showPivot true

> camera ortho

> lighting simple

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.13.dev202608021548 (2026-08-02)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2214833 fromDatabase cod

2214833 title:  
diethylmethyleneammonium chloride [more info...]  
  
7 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> label #1 atoms text {0.idatm_type} height 0.3




OpenGL version: 3.3.0 NVIDIA 610.62
OpenGL renderer: NVIDIA GeForce RTX 5070 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.14.6
Locale: en_GB.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows

Manufacturer: LENOVO
Model: 83LU
OS: Microsoft Windows 11 Pro (Build 26200.8875)
Memory: 33,752,997,888
MaxProcessMemory: 137,438,953,344
CPU: 24 Intel(R) Core(TM) Ultra 9 275HX
OSLanguage: en-US

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[Tristan Croll]

More generally: I've been steadily whittling down the COD to a core corpus
of high-quality structures to use for force field training. It's been
proving fruitful ground for finding new edge cases where
`estimate_net_charge` gets the wrong answer... while some are damn near
impossible to infer from the model alone, quite a few are salvageable (and
the nice thing is, most entries come with `_chemical_formula_iupac` and
`_chemical_formula_moiety` entries which provide ground truth net charges
(well... most of them, anyway - people always find ways to mangle things).
For now I've been having Claude work on an expanded set of
charge-assignment rules to catch as much as possible, and fall back to the
ground-truth values when all else fails... if you're interested, I could
share that code - or just a set of example cases.

On Tue, Aug 4, 2026 at 10:02 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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