ISOLDLE: validation tab refers to deleted residue

[john.heumann@…]

The following bug report has been submitted:
Platform:        macOS-15.7.7-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Rebuild residue to template MC_3PE (for all residues of this name) for 3PE.

Log:
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/heumannj/Complex1Models/combined_phenix2Map.mrc format mrc

Opened combined_phenix2Map.mrc as #1, grid size 400,400,400, pixel 0.911,
shown at level 2.36, step 2, values float32  

> volume #1 level 11.78

> volume #1 step 1

> volume #1 level 9.087

> volume #1 level 8.259

> open /Users/heumannj/Complex1Models/v5_inProgress.cif

Summary of feedback from opening
/Users/heumannj/Complex1Models/v5_inProgress.cif  
---  
warnings | Unknown polymer entity '1' on line 275  
Unknown polymer entity '2' on line 5426  
Unknown polymer entity '3' on line 11016  
Unknown polymer entity '4' on line 18489  
Unknown polymer entity '5' on line 28243  
40 messages similar to the above omitted  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for v5_inProgress.cif #2  
---  
Chain | Description  
AAa | No description available  
ABa | No description available  
ACa | No description available  
ADa | No description available  
AEb | No description available  
AFa | No description available  
AGa | No description available  
AHa | No description available  
AIa | No description available  
AJa | No description available  
AKa | No description available  
ALa | No description available  
AMa | No description available  
ANa | No description available  
AOa | No description available  
AOb | No description available  
AQa | No description available  
ARa | No description available  
ASa | No description available  
Aa | No description available  
Ba | No description available  
Ca | No description available  
Da | No description available  
Ea | No description available  
Fa | No description available  
Ga | No description available  
Hb | No description available  
Ia | No description available  
Ja | No description available  
Ka | No description available  
La | No description available  
Ma | No description available  
Nb | No description available  
Oa | No description available  
Pa | No description available  
Qa | No description available  
Ra | No description available  
Sa | No description available  
Ta | No description available  
Ua | No description available  
Va | No description available  
Wa | No description available  
Xa | No description available  
Ya | No description available  
Za | No description available  
  

> hide atoms

> show cartoons

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for v5_inProgress.cif #2.2  
---  
Chain | Description  
AAa | No description available  
ABa | No description available  
ACa | No description available  
ADa | No description available  
AEb | No description available  
AFa | No description available  
AGa | No description available  
AHa | No description available  
AIa | No description available  
AJa | No description available  
AKa | No description available  
ALa | No description available  
AMa | No description available  
ANa | No description available  
AOa | No description available  
AOb | No description available  
AQa | No description available  
ARa | No description available  
ASa | No description available  
Aa | No description available  
Ba | No description available  
Ca | No description available  
Da | No description available  
Ea | No description available  
Fa | No description available  
Ga | No description available  
Hb | No description available  
Ia | No description available  
Ja | No description available  
Ka | No description available  
La | No description available  
Ma | No description available  
Nb | No description available  
Oa | No description available  
Pa | No description available  
Qa | No description available  
Ra | No description available  
Sa | No description available  
Ta | No description available  
Ua | No description available  
Va | No description available  
Wa | No description available  
Xa | No description available  
Ya | No description available  
Za | No description available  
  

> clipper associate #1 toModel #2

Opened combined_phenix2Map.mrc as #2.1.1.1, grid size 400,400,400, pixel
0.911, shown at step 1, values float32  

> ~select

Nothing selected  
Loading residue template for 3PE from internal database  
Loading residue template for DGT from internal database  
Loading residue template for FMN from internal database  
Loading residue template for PC1 from internal database  
Loading residue template for ZMP from internal database  

> delete :UQ

Traceback (most recent call last):  
File "/Users/heumannj/Library/Application
Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 184, in
_fix_button_clicked_cb  
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/Users/heumannj/Library/Application
Support/ChimeraX/1.12/lib/python/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 184, in
<listcomp>  
indices = [i for i in range(table.rowCount()) if table.item(i,
0).data(USER_ROLE)[0].name == residue.name]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "atomic_cpp/cymol.pyx", line 1267, in
chimerax.atomic.cymol.CyResidue.name.__get__  
RuntimeError: Residue already deleted  
  
RuntimeError: Residue already deleted  
  
File "atomic_cpp/cymol.pyx", line 1267, in
chimerax.atomic.cymol.CyResidue.name.__get__  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGQ3LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: mBoot-18000.120.36
      OS Loader Version: 11881.140.96.701.1

Software:

    System Software Overview:

      System Version: macOS 15.7.7 (24G720)
      Kernel Version: Darwin 24.6.0
      Time since boot: 5 hours, 46 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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