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Opened 70 minutes ago
#20781 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-15.4.1-arm64-arm-64bit-Mach-O
ChimeraX Version: 1.13.dev202607201743 (2026-07-20 17:43:16 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.13.dev202607201743 (2026-07-20)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/reyyverie/Downloads/pdb4kxq.ent
pdb4kxq.ent title:
Structure of nad-dependent protein deacetylase sirtuin-1 (closed state, 1.85
A) [more info...]
Chain information for pdb4kxq.ent #1
---
Chain | Description | UniProt
A | nad-dependent protein deacetylase sirtuin-1 | SIR1_HUMAN 234-510
B | nad-dependent protein deacetylase sirtuin-1 | SIR1_HUMAN 641-663
Non-standard residues in pdb4kxq.ent #1
---
APR — adenosine-5-diphosphoribose
BME — β-mercaptoethanol
GOL — glycerol (glycerin; propane-1,2,3-triol)
ZN — zinc ion
127 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/reyyverie/Downloads/pdb4kxq.ent
pdb4kxq.ent title:
Structure of nad-dependent protein deacetylase sirtuin-1 (closed state, 1.85
A) [more info...]
Chain information for pdb4kxq.ent #2
---
Chain | Description | UniProt
A | nad-dependent protein deacetylase sirtuin-1 | SIR1_HUMAN 234-510
B | nad-dependent protein deacetylase sirtuin-1 | SIR1_HUMAN 641-663
Non-standard residues in pdb4kxq.ent #2
---
APR — adenosine-5-diphosphoribose
BME — β-mercaptoethanol
GOL — glycerol (glycerin; propane-1,2,3-triol)
ZN — zinc ion
127 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close
> open /Users/reyyverie/SIRT1_clean.pdb
Chain information for SIRT1_clean.pdb #1
---
Chain | Description
A | No description available
B | No description available
254 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
Computing secondary structure
> ui tool show "Dock Prep"
Populating font family aliases took 113 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
/A HIS 232: phi none, psi 101.8 trans
/A SER 275: phi -78.9, psi 171.4 trans
/A ARG 282: phi -65.3, psi -37.3 trans
/A CYS 326: phi -60.3, psi -47.1 trans
/A LYS 377: phi -116.3, psi 137.3 trans
/A ARG 384: phi -60.0, psi -44.7 trans
/A LYS 430: phi -51.9, psi -45.4 trans
/A ILE 510: phi -63.5, psi none trans
/B GLN 641: phi -102.9, psi 149.9 trans
/B ASP 660: phi -114.2, psi none trans
/A SER 275 OG has bad number of bonds (3)
donor: /A SER 1 N acceptor: /A SER 275 O
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/tool.py", line 168, in dock_prep
self.dock_prep_info['callback'](self.structures, tool_settings=params)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/tool.py", line 27, in callback
dock_prep_caller(session, structures, _from_tool=True, **tool_settings)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/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'],
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
structures, kw_dict)
^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/prep.py", line 139, in prep
swap_aa(session, targets, "same", rot_lib=style)
~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/swap_res/swap_res.py", line 122, in swap_aa
process_hbonds(session, res, by_alt_loc, False, None, None, hbond_relax,
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
hbond_dist_slop, hbond_angle_slop, False, None, ignore_other_models,
cache_da=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/swap_res/swap_res.py", line 807, in process_hbonds
hbonds = { hb: color for hb in find_hbonds(session, target_models,
intra_model=False,
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
dist_slop=dist_slop, angle_slop=angle_slop, cache_da=cache_da, status=False) }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
/A HIS 232: phi none, psi 101.8 trans
/A SER 275: phi -78.9, psi 171.4 trans
/A ARG 282: phi -65.3, psi -37.3 trans
/A CYS 326: phi -60.3, psi -47.1 trans
/A LYS 377: phi -116.3, psi 137.3 trans
/A ARG 384: phi -60.0, psi -44.7 trans
/A LYS 430: phi -51.9, psi -45.4 trans
/A ILE 510: phi -63.5, psi none trans
/B GLN 641: phi -102.9, psi 149.9 trans
/B ASP 660: phi -114.2, psi none trans
donor: /A SER 1 N acceptor: /A SER 275 O
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/tool.py", line 168, in dock_prep
self.dock_prep_info['callback'](self.structures, tool_settings=params)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/tool.py", line 27, in callback
dock_prep_caller(session, structures, _from_tool=True, **tool_settings)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/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'],
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
structures, kw_dict)
^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/prep.py", line 139, in prep
swap_aa(session, targets, "same", rot_lib=style)
~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/swap_res/swap_res.py", line 122, in swap_aa
process_hbonds(session, res, by_alt_loc, False, None, None, hbond_relax,
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
hbond_dist_slop, hbond_angle_slop, False, None, ignore_other_models,
cache_da=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/swap_res/swap_res.py", line 807, in process_hbonds
hbonds = { hb: color for hb in find_hbonds(session, target_models,
intra_model=False,
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
dist_slop=dist_slop, angle_slop=angle_slop, cache_da=cache_da, status=False) }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> ui tool show "Dock Prep"
Starting dock prep
Deleting solvent
Deleting non-metal-complex ions
Deleting non-current alt locs
Filling out missing side chains
/A HIS 232: phi none, psi 101.8 trans
/A SER 275: phi -78.9, psi 171.4 trans
/A ARG 282: phi -65.3, psi -37.3 trans
/A CYS 326: phi -60.3, psi -47.1 trans
/A LYS 377: phi -116.3, psi 137.3 trans
/A ARG 384: phi -60.0, psi -44.7 trans
/A LYS 430: phi -51.9, psi -45.4 trans
/A ILE 510: phi -63.5, psi none trans
/B GLN 641: phi -102.9, psi 149.9 trans
/B ASP 660: phi -114.2, psi none trans
donor: /A SER 1 N acceptor: /A SER 275 O
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/tool.py", line 168, in dock_prep
self.dock_prep_info['callback'](self.structures, tool_settings=params)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/tool.py", line 27, in callback
dock_prep_caller(session, structures, _from_tool=True, **tool_settings)
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller
run_steps(session, state, structures)
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/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'],
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
structures, kw_dict)
^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/dock_prep/prep.py", line 139, in prep
swap_aa(session, targets, "same", rot_lib=style)
~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/swap_res/swap_res.py", line 122, in swap_aa
process_hbonds(session, res, by_alt_loc, False, None, None, hbond_relax,
~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
hbond_dist_slop, hbond_angle_slop, False, None, ignore_other_models,
cache_da=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/swap_res/swap_res.py", line 807, in process_hbonds
hbonds = { hb: color for hb in find_hbonds(session, target_models,
intra_model=False,
~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
dist_slop=dist_slop, angle_slop=angle_slop, cache_da=cache_da, status=False) }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/site-
packages/chimerax/hbonds/hbond.py", line 615, in find_hbonds
if not geom_func(donor_atom, donor_hyds, *args):
~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple
Python: 3.14.6
Locale: C.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 Air
Model Identifier: Mac16,12
Model Number: MW0Y3HN/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.101.1
OS Loader Version: 11881.101.1
Software:
System Software Overview:
System Version: macOS 15.4.1 (24E263)
Kernel Version: Darwin 24.4.0
Time since boot: 49 days, 18 hours, 21 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.7.1
aiohttp: 3.11.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.14.2
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.2
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.9.1
build: 1.5.0
certifi: 2026.6.17
cffi: 2.1.0
cftime: 1.6.5
charset-normalizer: 3.4.9
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.3.1
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2.2
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: 1.70.2
ChimeraX-AtomicLibrary: 14.4.2
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: 1.13.dev202607201743
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.6
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.3
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
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: 2.5.4
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: 1.8.5
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: 1.2.1
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19.2
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.4.3
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.17
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.24
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-NMRSTAR: 1.0.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.16.2
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: 1.11
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.3
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: 1.5.3
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: 2.19.1
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: 1.20
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: 1.53.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.5
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: 8.4.2
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.15.2
cryptography: 49.0.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 1.0.1
glfw: 2.10.1
grako: 3.16.5
h11: 0.16.0
h2: 4.3.0
h5py: 3.16.0
hpack: 4.2.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
hyperframe: 6.1.0
idna: 3.18
ihm: 2.2
imagecodecs: 2026.6.26
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.3.0
ipython: 9.14.1
ipython_pygments_lexers: 1.1.1
jedi: 0.20.0
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.9.1
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.4.5
Markdown: 3.8.2
markdown-it-py: 4.2.0
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.28.1
mdurl: 0.1.2
msgpack: 1.1.1
multidict: 6.7.1
ndindex: 1.10.1
nest-asyncio2: 1.7.2
netCDF4: 1.7.4
networkx: 3.3
numexpr: 2.14.2
numpy: 2.4.6
OpenMM: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 12.3.0
pip: 26.1.2
pkginfo: 1.12.1.2
platformdirs: 4.10.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pycparser: 3.0
pydantic: 2.13.4
pydantic-settings: 2.14.2
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.20.0
Pygments: 2.18.0
PyJWT: 2.13.0
pynmrstar: 3.5.1
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: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.1.1
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.2
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
rich: 15.0.0
roman-numerals: 4.1.0
rpds-py: 2026.6.3
scipy: 1.18.0
setuptools: 82.0.1
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.9
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: 3.4.6
stack-data: 0.6.3
starlette: 1.3.1
superqt: 0.7.6
tables: 3.11.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.69.0
traitlets: 5.15.1
typing-inspection: 0.4.2
typing_extensions: 4.16.0
urllib3: 2.7.0
uv: 0.11.26
uvicorn: 0.51.0
wcwidth: 0.8.2
webcolors: 24.11.1
wheel: 0.47.0
wheel-filename: 1.4.2
yarl: 1.24.5
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