Corecif has metal coordination bonds only

[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

Picked up a new pathological case for corecif: for reasons known only to them, it's common for authors of organometallic crystal structures to *only* report the metal coordination bonds, not the covalent ones. This breaks corecif's geometry-based bonding perception - it skips adding new bonds for any atom that already has a bond defined in the cif, and metal-coordination bonds apparently count for that test. So every organic ligand in close contact with a metal ends up as just a point cloud of atoms.

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 7703621 fromDatabase cod

7703621 title:  
C106 H68 F24 Fe2 O14 P4 Ru6 S2 [more info...]  
  
158 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  




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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[Greg Couch]

I've changed the daily build to delay adding the metal bonds until after the small molecule is connected by distance. Please try tomorrow's daily build and let me that does what you expect.