Minimize 6i4q: KeyError: 'N'

[paul.brodersen@…]

The following bug report has been submitted:
Platform:        Linux-6.17.0-29-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.12rc202606020412 (2026-06-02 04:12:41 UTC)
Description
1. Fetch PDB 6i4q
2. del :btb :so4 :hoh
3. Tools > Structure Editing > Minimize Structure

Possibly related to (though the error trace is different):
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/19923

Thanks for making ChimeraX!

Log:
Startup Messages  
---  
warning | No presets found in custom preset folder /home/paul/config/chimerax  
  

> alias cls close session

UCSF ChimeraX version: 1.12rc202606020412 (2026-06-02)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6i4q format mmcif fromDatabase pdbe_bio

Summary of feedback from opening 6i4q fetched from pdbe_bio  
---  
warnings | Missing or incorrect sequence information. Inferred polymer connectivity.  
Atom H is not in the residue template for VAL /B:-6  
  
6i4q bioassembly 1 title:  
Crystal structure of the human dihydrolipoamide dehydrogenase at 1.75 Angstrom
resolution [more info...]  
  
Chain information for 6i4q bioassembly 1 #1  
---  
Chain | Description  
A | Dihydrolipoyl dehydrogenase, mitochondrial  
B | Dihydrolipoyl dehydrogenase, mitochondrial  
  
Non-standard residues in 6i4q bioassembly 1 #1  
---  
BTB — (BTB)  
FAD — (FAD)  
SO4 — (SO4)  
  
249 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  
Opened 1 biological assemblies for 6i4q  

> delete :btb

> delete :so4

> delete :hoh

> ui tool show "Minimize Structure"

> minimize #1 logEnergy true

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Summary of feedback from adding hydrogens to 6i4q bioassembly 1 #1  
---  
notes | No usable SEQRES records for 6i4q bioassembly 1 (#1) chain A; guessing termini instead  
No usable SEQRES records for 6i4q bioassembly 1 (#1) chain B; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLN 3  
Chain-initial residues that are not actual N termini: /B VAL -6  
Chain-final residues that are actual C termini: /A PHE 474, /B PHE 474  
Chain-final residues that are not actual C termini:  
905 hydrogen bonds  
5 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue FAD (net charge -1) with am1-bcc method  
Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmp4jydjonb/ante.in.mol2 -fi mol2 -o /tmp/tmp4jydjonb/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n  
(FAD) ``  
(FAD) `Welcome to antechamber 20.0: molecular input file processor.`  
(FAD) ``  
(FAD) `Info: Finished reading file (/tmp/tmp4jydjonb/ante.in.mol2); atoms read
(85), bonds read (90).`  
(FAD) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(FAD) ``  
(FAD) ``  
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(FAD) `Info: Total number of electrons: 408; net charge: -1`  
(FAD) ``  
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(FAD) ``  
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  
(FAD) ``  
(FAD) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(FAD) ``  
Charges for residue FAD determined  
Dock prep finished  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 116, in minimize  
run(self.session, cmd)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 132, in prep  
callback(session, state, structures)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps  
callback()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 131, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 45, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 232, in _minimize  
system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer,
constraints=HBonds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 1279, in createSystem  
data.setAtomClasses(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 683, in setAtomClasses  
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/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 "/usr/lib/ucsf-chimerax/lib/python3.11/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: 4.6 (Core Profile) Mesa 25.2.8-0ubuntu0.24.04.1
OpenGL renderer: Mesa Intel(R) HD Graphics 630 (KBL GT2)
OpenGL vendor: Intel

Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu-wayland
XDG_SESSION_DESKTOP=ubuntu-wayland
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:2
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 15 9560
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
Cache Size: 6144 KB
Memory:
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	Mem:            31Gi       7.9Gi        11Gi       1.9Gi        12Gi        23Gi
	Swap:          8.0Gi       4.0Ki       8.0Gi

Graphics:
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    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
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    starlette: 1.2.1
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    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.15.0
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    tqdm: 4.67.3
    traitlets: 5.14.3
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    typing_extensions: 4.15.0
    Unidecode: 1.4.0
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    wcwidth: 0.7.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.24.2