Bad model table in possible Boltz output

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
I opened a protein structure that i got from a generative model

Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> E:\\\Amy\\\boltz_run\\\kv1.3_run1\\\final_ranked_designs\\\final_100_designs\\\rank0001_run1_0076.cif

Chain information for rank0001_run1_0076.cif #1  
---  
Chain | Description  
A | No description available  
B C D E | No description available  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\\__main__.py", line 1023, in init  
commands.run(sess, "open %s" % StringArg.unparse(arg))  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 132, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\open_command\cmd.py", line 297, in provider_open  
session.models.add(opened_models)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\core\models.py", line 827, in add  
m.added_to_session(session)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1409, in added_to_session  
self._report_model_info(session)  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1757, in _report_model_info  
res = chain.residues[int(seq_id)-1]  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "C:\Program Files\ChimeraX 1.11.1\bin\Lib\site-
packages\chimerax\atomic\structure.py", line 1757, in _report_model_info  
res = chain.residues[int(seq_id)-1]  
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 591.74
OpenGL renderer: NVIDIA GeForce RTX 3080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: windows

Manufacturer: Supermicro
Model: Super Server
OS: Microsoft Windows 10 Enterprise (Build 19045)
Memory: 274,470,658,048
MaxProcessMemory: 137,438,953,344
CPU: 24 Intel(R) Xeon(R) Gold 5317 CPU @ 3.00GHz
OSLanguage: en-US

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[Tom Goddard]

This error is in code that assigns a residue attribute for mmCIF table ma_qa_metric_local. Apparently the seq_id in the mmCIF table is out of range. The structure was produced by BoltzGen. Maybe our code should check that the sequence ids are in range as this will make Model.added_to_session() raise an exception.

[Eric Pettersen]

This seems like a bug in the output that BoltzGen is creating. I'm going to sit on it for now on the assumption that they will fix the problem with their output. If reports keep coming in, I might change my mind and put in this shouldn't-be-needed check.

[Tom Goddard]

Sounds reasonable to ignore for now. They probably aren't going to fix BoltzGen since the MIT developers have disappeared into their startup company. But probably also BoltzGen will see declining use. And I used BoltzGen and never saw this error so you have to do something special to get it.