chirality command

[Tristan Croll]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.13.dev202606240437 (2026-06-24 04:37:46 UTC)
Description
Feeling like this is something I should ask for permission on first... to complement ISOLDE's existing `rama` and `rota` commands (adding the live Ramachandran and rotamer validators to a model), I'd like to add a `chirality` command (adding a similar live chiral-outlier markup, plus optional R/S flags on each chiral centre). Just want to make sure if I do so I wouldn't be shadowing any planned ChimeraX command. If you prefer I move them all subordinate to the "isolde" command (leaving "rama" and "rota" in place for a while with a deprecation warning). 

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.dev202606240437 (2026-06-24)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\tcroll\Downloads\ChimeraX\AlphaFold\AF-P62942-F1-model_v6.cif
> format mmcif

Chain information for AF-P62942-F1-model_v6.cif #1  
---  
Chain | Description | UniProt  
A | Peptidyl-prolyl cis-trans isomerase FKBP1A | FKB1A_HUMAN 1-108  
  
Color AF-P62942-F1-model_v6.cif by residue attribute pLDDT_score  




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

Python: 3.11.9
Locale: en_GB.cp1252
Qt version: PyQt6 6.11.0, Qt 6.11.0
Qt runtime version: 6.11.1
Qt platform: windows

Manufacturer: LENOVO
Model: 83LU
OS: Microsoft Windows 11 Pro (Build 26200.8655)
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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[Eric Pettersen]

Hi Tristan,

Well, since there is an existing 'chirality' command (​https://www.cgl.ucsf.edu/chimerax/docs/user/commands/chirality.html), adding your own would indeed be problematic. If your version carries out the full set of Cahn-Ingold-Prelog rules, I would be happy to substitute your implementation for mine (see the caveats in chirality's help page). Otherwise, perhaps you could leverage the existing implementation?

--Eric