Crash in event loop

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-28-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8.dev202404062101 (2024-04-06 21:01:47 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Current thread 0x0000700846513b80 (most recent call first):
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 54)
===== Log before crash start =====
UCSF ChimeraX version: 1.8.dev202404062101 (2024-04-06)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/mmg-2/Desktop/tubulin/maytansine_site/4tv8.pdb

Chain information for 4tv8.pdb #1  
---  
Chain | Description  
C | No description available  
D | No description available  
  
56 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> select ::name="3GT"

48 atoms, 51 bonds, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-current alt locs  
Filling out missing side chains  
/C VAL 440: phi -86.5, psi none trans  
/D ASP 441: phi -70.2, psi none trans  
Applying VAL rotamer (chi angles: 175.9) to /C VAL 440  
Applying ASP rotamer (chi angles: 62.5 1.3) to /D ASP 441  
Summary of feedback from adding hydrogens to 4tv8.pdb #1  
---  
notes | No usable SEQRES records for 4tv8.pdb (#1) chain C; guessing termini instead  
No usable SEQRES records for 4tv8.pdb (#1) chain D; guessing termini instead  
Chain-initial residues that are actual N termini: /C MET 1, /D MET 1  
Chain-initial residues that are not actual N termini: /D LEU 286  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /C VAL 440, /D ASP 441, /D
THR 276  
944 hydrogen bonds  
Adding 'H' to /D LEU 286  
/C VAL 440 is not terminus, removing H atom from 'C'  
/D ASP 441 is not terminus, removing H atom from 'C'  
6582 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 129, in add_standard_charges  
h.charge, h.gaff_type = hyd_charge_type_data[(h.residue.amber_name,
heavy.name.lower())]  
~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
KeyError: ('GTP', 'n3')  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 146, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 131, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
chimerax.add_charge.charge.ChargeError: Hydrogen /C GTP 501 H3 bonded to atom
that should not have hydrogens (/C GTP 501 N3)  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /C GTP 501 H3 bonded to atom
that should not have hydrogens (/C GTP 501 N3)  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 131, in add_standard_charges  
raise ChargeError("Hydrogen %s bonded to atom that should not have hydrogens
(%s)"  
  
See log for complete Python traceback.  
  

> delete :501@H3

> ui tool show "Add Charges"

Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue MG (net charge +2) with am1-bcc method  
Assigning partial charges to residue GOL (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpru2ooioq/ante.in.mol2 -fi mol2 -o /tmp/tmpru2ooioq/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(GOL) ``  
(GOL) `Welcome to antechamber 20.0: molecular input file processor.`  
(GOL) ``  
(GOL) `Info: Finished reading file (/tmp/tmpru2ooioq/ante.in.mol2); atoms read
(14), bonds read (13).`  
(GOL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(GOL) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(GOL) ``  
(GOL) ``  
(GOL) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(GOL) `Info: Total number of electrons: 50; net charge: 0`  
(GOL) ``  
(GOL) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/sqm -O -i sqm.in
-o sqm.out`  
(GOL) ``  
(GOL) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax-daily/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  
(GOL) ``  
(GOL) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(GOL) ``  
Charges for residue GOL determined  
Assigning partial charges to residue CA (net charge +2) with am1-bcc method  
Dock prep finished  

> save /home/mmg-2/Desktop/tubulin/maytansine_site/2dock/rec_charged.mol2

> select H

6580 atoms, 865 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> save /home/mmg-2/Desktop/tubulin/maytansine_site/2dock/rec_noH.pdb relModel
> #1

> close

> open /home/mmg-2/Desktop/tubulin/maytansine_site/autodock/3gt/3gt.pdb

> 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  
Assigning partial charges to residue 3GT (net charge +0) with gasteiger method  
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -i /tmp/tmp69gbjrff/ante.in.mol2 -fi mol2 -o
/tmp/tmp69gbjrff/ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n  
(3GT) ``  
(3GT) `Welcome to antechamber 20.0: molecular input file processor.`  
(3GT) ``  
(3GT) `Info: Finished reading file (/tmp/tmp69gbjrff/ante.in.mol2); atoms read
(94), bonds read (97).`  
(3GT) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(3GT) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(3GT) ``  
(3GT) ``  
(3GT) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(3GT) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /usr/lib/ucsf-chimerax-
daily/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF`  
(3GT) ``  
(3GT) `Warning: The net charge of the molecule (0 ) does not equal the total
formal charge (1.00 ) according to the Gasteiger atom types.`  
(3GT) ``  
Charges for residue 3GT determined  

> save /home/mmg-2/Desktop/tubulin/maytansine_site/2dock/3gt_charged.mol2

> close

> open /home/mmg-2/Desktop/tubulin/maytansine_site/autodock/3h4/3h4.pdb

> 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  
Assigning partial charges to residue 3H4 (net charge +0) with gasteiger method  
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -i /tmp/tmplkscdya4/ante.in.mol2 -fi mol2 -o
/tmp/tmplkscdya4/ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n  
(3H4) ``  
(3H4) `Welcome to antechamber 20.0: molecular input file processor.`  
(3H4) ``  
(3H4) `Info: Finished reading file (/tmp/tmplkscdya4/ante.in.mol2); atoms read
(86), bonds read (86).`  
(3H4) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(3H4) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(3H4) ``  
(3H4) ``  
(3H4) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(3H4) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /usr/lib/ucsf-chimerax-
daily/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF`  
(3H4) ``  
Charges for residue 3H4 determined  

> save /home/mmg-2/Desktop/tubulin/maytansine_site/2dock/3h4_charged.mol2

> close

> open /home/mmg-2/Desktop/tubulin/maytansine_site/autodock/36l/36l.pdb

> 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  
Assigning partial charges to residue 36L (net charge +0) with gasteiger method  
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -i /tmp/tmpddxg8y54/ante.in.mol2 -fi mol2 -o
/tmp/tmpddxg8y54/ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n  
(36L) ``  
(36L) `Welcome to antechamber 20.0: molecular input file processor.`  
(36L) ``  
(36L) `Info: Finished reading file (/tmp/tmpddxg8y54/ante.in.mol2); atoms read
(91), bonds read (94).`  
(36L) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(36L) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(36L) ``  
(36L) ``  
(36L) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(36L) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /usr/lib/ucsf-chimerax-
daily/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF`  
(36L) ``  
Charges for residue 36L determined  

> save /home/mmg-2/Desktop/tubulin/maytansine_site/2dock/36l_charged.mol2

> close

> open /home/mmg-2/Desktop/tubulin/maytansine_site/autodock/dkn/dkn.pdb

> 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  
Assigning partial charges to residue DKN (net charge +0) with gasteiger method  
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -i /tmp/tmph9m19jq3/ante.in.mol2 -fi mol2 -o
/tmp/tmph9m19jq3/ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n  
(DKN) ``  
(DKN) `Welcome to antechamber 20.0: molecular input file processor.`  
(DKN) ``  
(DKN) `Info: Finished reading file (/tmp/tmph9m19jq3/ante.in.mol2); atoms read
(100), bonds read (102).`  
(DKN) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(DKN) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(DKN) ``  
(DKN) ``  
(DKN) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(DKN) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /usr/lib/ucsf-chimerax-
daily/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF`  
(DKN) ``  
Charges for residue DKN determined  

> save /home/mmg-2/Desktop/tubulin/maytansine_site/2dock/dkn_charged.mol2

> close

> open /home/mmg-2/Desktop/tubulin/maytansine_site/vina/sg9.pdb

> 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  
Assigning partial charges to residue SG9 (net charge +0) with gasteiger method  
Running ANTECHAMBER command: /usr/lib/ucsf-chimerax-
daily/bin/amber20/bin/antechamber -i /tmp/tmppmaakhgp/ante.in.mol2 -fi mol2 -o
/tmp/tmppmaakhgp/ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n  
(SG9) ``  
(SG9) `Welcome to antechamber 20.0: molecular input file processor.`  
(SG9) ``  
(SG9) `Info: Finished reading file (/tmp/tmppmaakhgp/ante.in.mol2); atoms read
(180), bonds read (186).`  
(SG9) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(SG9) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/bondtype -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(SG9) ``  
(SG9) ``  
(SG9) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(SG9) `Running: /usr/lib/ucsf-chimerax-daily/bin/amber20/bin/atomtype -i
ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /usr/lib/ucsf-chimerax-
daily/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF`  
(SG9) ``  
Charges for residue SG9 determined  

> save /home/mmg-2/Desktop/tubulin/maytansine_site/2dock/sg9_charged.mol2

> close


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.8.dev202404062101 (2024-04-06)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.3 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: NV106
OpenGL vendor: Mesa

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: HP
Model: 550-107nl
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 AMD A10-8750 Radeon R7, 12 Compute Cores 4C+8G
Cache Size: 2048 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.7Gi       1.8Gi       521Mi       179Mi       5.4Gi       5.4Gi
	Swap:          2.0Gi       1.0Mi       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK208B [GeForce GT 730] [10de:1287] (rev a1)	
	DeviceName:  Onboard LAN	
	Subsystem: Micro-Star International Co., Ltd. [MSI] GK208B [GeForce GT 730] [1462:292a]

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.6.2
    build: 1.1.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56.1
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202404062101
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    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: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.9.2
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10