Minimization failure: KeyError: 'N'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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 C:/Users/sdey6/Downloads/6LUB_PYMOL.cif

Summary of feedback from opening C:/Users/sdey6/Downloads/6LUB_PYMOL.cif  
---  
warnings | Unknown polymer entity '1' on line 36  
Missing or incorrect sequence information. Inferred polymer connectivity.  
  
  
Chain information for 6LUB_PYMOL.cif #1  
---  
Chain | Description  
A | No description available  
  
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> ui tool show "Add Hydrogens"

> addh #!1

Summary of feedback from adding hydrogens to 6LUB_PYMOL.cif #1  
---  
warnings | Not adding hydrogens to /A LYS 714 CD because it is missing heavy-atom bond partners  
Not adding hydrogens to /A LYS 716 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A GLU 734 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 737 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 754 CD because it is missing heavy-atom bond
partners  
11 messages similar to the above omitted  
notes | No usable SEQRES records for 6LUB_PYMOL.cif (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLY 696  
Chain-initial residues that are not actual N termini: /A THR 725, /A THR 751,
/A ASP 1006  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ILE 1018, /A GLY 721,
/A GLU 746, /A PRO 990  
267 hydrogen bonds  
Adding 'H' to /A THR 725  
Adding 'H' to /A THR 751  
Adding 'H' to /A ASP 1006  
/A ILE 1018 is not terminus, removing H atom from 'C'  
2333 hydrogens added  
  

> ui tool show "Add Charges"

Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  

> ui tool show "Minimize Structure"

> minimize #1

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Filling out missing side chains  
/A LYS 714: phi -74.5, psi 148.1 trans  
/A LYS 716: phi -165.7, psi 162.8 trans  
/A GLU 734: phi -44.3, psi 117.2 trans  
/A LYS 737: phi 56.3, psi 33.6 trans  
/A LYS 754: phi -78.9, psi -26.0 trans  
/A LYS 757: phi -60.4, psi -34.8 trans  
/A GLU 804: phi -69.7, psi -16.0 trans  
/A LYS 806: phi -35.0, psi -52.0 trans  
/A LYS 875: phi -76.3, psi 110.9 trans  
/A GLU 922: phi -74.3, psi -22.4 trans  
/A LYS 929: phi -68.9, psi -18.9 trans  
/A GLN 982: phi -68.1, psi 114.0 trans  
/A GLU 985: phi -71.7, psi 11.4 trans  
/A ARG 986: phi -108.5, psi -29.8 trans  
/A HIS 988: phi -163.7, psi 133.2 trans  
/A MET 1007: phi -151.7, psi 40.6 trans  
/A ILE 1018: phi 13.9, psi none trans  
Applying LYS rotamer (chi angles: -66.8 -178.8 -179.8 179.3) to /A LYS 714  
Applying LYS rotamer (chi angles: -172.5 71.1 81.2 -67.0) to /A LYS 716  
Applying GLU rotamer (chi angles: -66.2 -69.1 -22.9) to /A GLU 734  
Applying LYS rotamer (chi angles: -177.3 176.3 174.5 64.9) to /A LYS 737  
Applying LYS rotamer (chi angles: 68.7 -179.2 -177.2 -65.9) to /A LYS 754  
Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 757  
Applying GLU rotamer (chi angles: -67.8 179.4 -6.7) to /A GLU 804  
Applying LYS rotamer (chi angles: -71.1 -176.9 175.1 65.8) to /A LYS 806  
Applying LYS rotamer (chi angles: -179.5 70.3 178.4 68.4) to /A LYS 875  
Applying GLU rotamer (chi angles: -67.8 179.4 -6.7) to /A GLU 922  
Applying LYS rotamer (chi angles: -176.8 174.9 78.9 -74.5) to /A LYS 929  
Applying GLN rotamer (chi angles: -66.0 82.7 -17.4) to /A GLN 982  
Applying GLU rotamer (chi angles: 68.1 -85.3 18.3) to /A GLU 985  
Applying ARG rotamer (chi angles: -64.4 -74.5 82.1 -166.6) to /A ARG 986  
Applying HIS rotamer (chi angles: 63.3 34.0) to /A HIS 988  
Applying MET rotamer (chi angles: -64.9 177.9 69.6) to /A MET 1007  
Applying ILE rotamer (chi angles: -63.8 170.1) to /A ILE 1018  
Summary of feedback from adding hydrogens to 6LUB_PYMOL.cif #1  
---  
notes | No usable SEQRES records for 6LUB_PYMOL.cif (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A GLY 696  
Chain-initial residues that are not actual N termini: /A THR 725, /A THR 751,
/A ASP 1006  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ILE 1018, /A GLY 721,
/A GLU 746, /A PRO 990  
276 hydrogen bonds  
/A ILE 1018 is not terminus, removing H atom from 'C'  
143 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\tool.py", line 116, in minimize  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.12\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 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 43, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 150, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\addh\dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\add_charge\dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 149, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 45, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 232, in _minimize  
system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer,
constraints=HBonds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\openmm\app\forcefield.py", line 1279, in createSystem  
data.setAtomClasses(self)  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\openmm\app\forcefield.py", line 683, in setAtomClasses  
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\openmm\app\forcefield.py", line 683, in <listcomp>  
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^  
KeyError: 'N'  
  
KeyError: 'N'  
  
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\openmm\app\forcefield.py", line 683, in  
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 22.20.42.02.221103
OpenGL renderer: AMD Radeon (TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.9
Locale: en_US.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: Modern 15 B7M
OS: Microsoft Windows 11 Home Single Language (Build 22631.5039)
Memory: 16,516,427,776
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 7530U with Radeon Graphics         
OSLanguage: en-US

Installed Packages:
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    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
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    build: 1.3.0
    certifi: 2026.5.20
    cftime: 1.6.5
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    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
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    ChimeraX-Clashes: 2.4
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    ChimeraX-FunctionKey: 1.0.1
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    ChimeraX-gltf: 1.0
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    ChimeraX-Hbonds: 2.5.3
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    ChimeraX-IO: 1.0.4
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    rpds-py: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.4.4
    stack-data: 0.6.3
    starlette: 1.3.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.7
    tqdm: 4.68.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2026.2
    Unidecode: 1.4.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.8.1
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    WMI: 1.5.1
    yarl: 1.24.2

[Eric Pettersen]

Works fine with the regular 6LUB entry, so would need file to reproduce.