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#20329 accepted defect

Problems minimizing 9XHR

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Structure Editing	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.26200
ChimeraX Version: 1.12rc202605110632 (2026-05-11 06:32:03 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.12rc202605110632 (2026-05-11)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/PRANAV KARTHICK . T/OneDrive/Desktop/drug
> docking/9XHR.pdb.gz"

9XHR.pdb.gz title:  
Crystal structure of human cathepsin B with A D-peptide substrate [more
info...]  
  
Chain information for 9XHR.pdb.gz #1  
---  
Chain | Description | UniProt  
A | cathepsin B | CATB_HUMAN 0-254  
C | ace-dar-dly-dty-dty-gly-0QE |   
  
Non-standard residues in 9XHR.pdb.gz #1  
---  
0QE — chloromethane (chloro methyl group)  
ACE — acetyl group  
DAR — D-arginine  
DLY — D-lysine  
DTY — D-tyrosine  
  

> select ::name="0QE"

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select ::name="ACE"

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select ::name="DAR"

11 atoms, 10 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select ::name="DLY"

9 atoms, 8 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select ::name="DTY"

24 atoms, 25 bonds, 2 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select ::name="HOH"

261 atoms, 261 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Add Charges"

> addh

Summary of feedback from adding hydrogens to 9XHR.pdb.gz #1  
---  
notes | Termini for 9XHR.pdb.gz (#1) chain A determined from SEQRES records  
Termini for 9XHR.pdb.gz (#1) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /A LYS 0  
Chain-initial residues that are not actual N termini: /C GLY 6  
Chain-final residues that are actual C termini: /A ASP 254  
Chain-final residues that are not actual C termini: /C GLY 6  
Missing OXT added to C-terminal residue /A ASP 254  
229 hydrogen bonds  
Adding 'H' to /C GLY 6  
/C GLY 6 is not terminus, removing H atom from 'C'  
1813 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues 5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  

> ui tool show "Add Hydrogens"

> addh

Summary of feedback from adding hydrogens to 9XHR.pdb.gz #1  
---  
notes | Termini for 9XHR.pdb.gz (#1) chain A determined from SEQRES records  
Termini for 9XHR.pdb.gz (#1) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /A LYS 0  
Chain-initial residues that are not actual N termini: /C GLY 6  
Chain-final residues that are actual C termini: /A ASP 254  
Chain-final residues that are not actual C termini: /C GLY 6  
219 hydrogen bonds  
/C GLY 6 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

> 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  
Summary of feedback from adding hydrogens to 9XHR.pdb.gz #1  
---  
notes | Termini for 9XHR.pdb.gz (#1) chain A determined from SEQRES records  
Termini for 9XHR.pdb.gz (#1) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /A LYS 0  
Chain-initial residues that are not actual N termini: /C GLY 6  
Chain-final residues that are actual C termini: /A ASP 254  
Chain-final residues that are not actual C termini: /C GLY 6  
219 hydrogen bonds  
/C GLY 6 is not terminus, removing H atom from 'C'  
0 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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\minimize\tool.py", line 116, in minimize  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.12rc202605110632\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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 132, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 131, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 203, in _minimize  
cx_atom = name_lookup[cx_res][omm_atom.name]  
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
KeyError: 'H1'  
  
KeyError: 'H1'  
  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 203, in _minimize  
cx_atom = name_lookup[cx_res][omm_atom.name]  
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Add Hydrogens"

> addh

Summary of feedback from adding hydrogens to 9XHR.pdb.gz #1  
---  
notes | Termini for 9XHR.pdb.gz (#1) chain A determined from SEQRES records  
Termini for 9XHR.pdb.gz (#1) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /A LYS 0  
Chain-initial residues that are not actual N termini: /C GLY 6  
Chain-final residues that are actual C termini: /A ASP 254  
Chain-final residues that are not actual C termini: /C GLY 6  
219 hydrogen bonds  
/C GLY 6 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

> 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  
Summary of feedback from adding hydrogens to 9XHR.pdb.gz #1  
---  
notes | Termini for 9XHR.pdb.gz (#1) chain A determined from SEQRES records  
Termini for 9XHR.pdb.gz (#1) chain C determined from SEQRES records  
Chain-initial residues that are actual N termini: /A LYS 0  
Chain-initial residues that are not actual N termini: /C GLY 6  
Chain-final residues that are actual C termini: /A ASP 254  
Chain-final residues that are not actual C termini: /C GLY 6  
219 hydrogen bonds  
/C GLY 6 is not terminus, removing H atom from 'C'  
0 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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\minimize\tool.py", line 116, in minimize  
run(self.session, cmd)  
File "C:\Program Files\ChimeraX 1.12rc202605110632\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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 132, in prep  
callback(session, state, structures)  
File "C:\Program Files\ChimeraX 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\dock_prep\cmd.py", line 156, in run_steps  
callback()  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\dock_prep\prep.py", line 131, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File "C:\Program Files\ChimeraX 1.12rc202605110632\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 1.12rc202605110632\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 203, in _minimize  
cx_atom = name_lookup[cx_res][omm_atom.name]  
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
KeyError: 'H1'  
  
KeyError: 'H1'  
  
File "C:\Program Files\ChimeraX 1.12rc202605110632\bin\Lib\site-
packages\chimerax\minimize\cmd.py", line 203, in _minimize  
cx_atom = name_lookup[cx_res][omm_atom.name]  
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 32.0.101.7076
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.11.9
Locale: en_IN.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: windows

Manufacturer: LENOVO
Model: 83EM
OS: Microsoft Windows 11 Home Single Language (Build 26200.8246)
Memory: 16,857,817,088
MaxProcessMemory: 137,438,953,344
CPU: 16 13th Gen Intel(R) Core(TM) i7-13620H
OSLanguage: en-US

Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.2.0
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2026.4.22
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12rc202605110632
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.2.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchAlign: 1.1
    ChimeraX-MatchMaker: 2.4
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.8
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0.1
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.6
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.3
    colorama: 0.4.6
    comm: 0.2.3
    comtypes: 1.4.11
    contourpy: 1.3.3
    coverage: 7.14.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.20
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.62.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.14
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.21.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    nvidia-nvjitlink-cu12: 12.9.86
    OpenMM: 8.4.0
    OpenMM-CUDA-12: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.9.6
    plotly: 6.7.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    psutil: 7.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.17.1
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.1
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.28
    pywin32: 311
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    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: 3.4.3
    stack-data: 0.6.3
    starlette: 1.0.0
    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: 6.5.5
    tqdm: 4.67.3
    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: 0.46.0
    wcwidth: 0.7.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    WMI: 1.5.1
    yarl: 1.23.0

Change History (1)

comment:1 by Eric Pettersen, 2 hours ago

Component:	Unassigned → Structure Editing
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Problems minimizing 9XHR

Regardless of whether the non-standard residues are deleted (different errors though)

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