chirality command incorrectly says S atom of ligand SAM is non-chiral

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.11.dev202509171705 (2025-09-17 17:05:04 UTC)
Description
Seems the sulfur atom of CCD ligand SAM is chiral (S) but ChimeraX chirality command says it is not chiral.  Not sure how one decides with only 3 attached atoms that it is chiral.  I was reading a Boltz github issue about SAM sulfur atom being assigned the wrong chirality so I thought I'd see what ChimeraX says.

https://github.com/jwohlwend/boltz/issues/589


Log:
UCSF ChimeraX version: 1.11.dev202509171705 (2025-09-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open SAM fromDatabase ccd

SAM title:  
S-adenosylmethionine  
  
Opened CCD SAM  

> select /A:1@SD

1 atom, 1 residue, 1 model selected  

> chirality sel

There are no possible stereo centers in the specified atoms  

> chirality #1

/A SAM 1 C1' is R  
/A SAM 1 C2' is R  
/A SAM 1 C3' is S  
/A SAM 1 C4' is S  
/A SAM 1 C5' is not chiral  
/A SAM 1 CA is S  
/A SAM 1 CB is not chiral  
/A SAM 1 CE is not chiral  
/A SAM 1 CG is not chiral  
/A SAM 1 N is not chiral  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
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      Model Identifier: Mac14,14
      Model Number: Z1800003VLL/A
      Chip: Apple M2 Ultra
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      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

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      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
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[Eric Pettersen]

Strictly speaking, the CIP rules for determining chirality require four atoms to be bound to the chiral center. This is because in many cases there is a low barrier to inversion of the center if one of the "substituents" is only a lone pair. This is particularly true for nitrogen, which easily passes through a temporary sp2 state to invert the center. Nonetheless, for sulphur and phosphorus, this inversion is much harder to achieve and the CIP rules could be amended in such cases to treat them as actual chiral centers.