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Opened 5 weeks ago
Last modified 5 weeks ago
#19058 assigned defect
isolde sim start: Residue has multiple bonds to neighbor
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-83-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/home/mahb3/Desktop/Pietro model
> /cryosparc_P14_J126_007_volume_map_sharp.mrc"
Opened cryosparc_P14_J126_007_volume_map_sharp.mrc as #1, grid size
180,180,180, pixel 1.67, shown at level 0.106, step 1, values float32
> transparency 50
> open "/home/mahb3/Desktop/Pietro model /GFP removed pietro.pdb"
Chain information for GFP removed pietro.pdb #2
---
Chain | Description
A | No description available
B | No description available
Computing secondary structure
> isolde start
> set selectionWidth 4
Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 11.2 - if installed, please make sure this is
on your library path before starting ChimeraX.
> clipper associate #2 toModel #1
Invalid "toModel" argument: must specify 1 structure, got 0 for "#1"
> clipper associate #1 toModel #2
Opened cryosparc_P14_J126_007_volume_map_sharp.mrc as #1.1.1.1, grid size
180,180,180, pixel 1.67, shown at level 0.375, step 1, values float32
Chain information for GFP removed pietro.pdb
---
Chain | Description
1.2/A | No description available
1.2/B | No description available
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 96 residues in model #1.2 to IUPAC-IUB
standards.
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 11.2 - if installed, please make sure this is
on your library path before starting ChimeraX.
> addh
Summary of feedback from adding hydrogens to GFP removed pietro.pdb #1.2
---
warning | Unknown hybridization for atom (O5) of residue type NAG; not adding hydrogens to it
notes | No usable SEQRES records for GFP removed pietro.pdb (#1.2) chain A; guessing termini instead
No usable SEQRES records for GFP removed pietro.pdb (#1.2) chain B; guessing
termini instead
Chain-initial residues that are actual N termini: /A SER 620, /B LYS 345
Chain-initial residues that are not actual N termini: /A ALA 744, /A VAL 660
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A SER 743, /A SER 659, /A
LYS 619, /B ILE 344
1002 hydrogen bonds
Adding 'H' to /A ALA 744
Adding 'H' to /A VAL 660
/A SER 743 is not terminus, removing H atom from 'C'
/B ILE 344 is not terminus, removing H atom from 'C'
11540 hydrogens added
> liganda #1
Unknown command: isolde restrain liganda #1
> isolde restrain ligands #1
> isolde restrain ligands #2
Must specify at least one atomic structure!
> isolde sim start /A-B
Sim termination reason: None
ISOLDE: stopped sim
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 166, in run_provider
toolbar_command(session, name)
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 23, in toolbar_command
run(session, f'isolde sim start {_current_residue_sel_string(session)}')
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 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim
isolde.start_sim()
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/isolde.py", line 876, in start_sim
sm = self._sim_manager = SimManager(self, self.selected_model, main_sel,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 343, in __init__
raise e
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 321, in __init__
sh = self.sim_handler = SimHandler(session, sim_params, sc,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1077, in __init__
template_dict = find_residue_templates(sim_construct.all_residues, ff,
ligand_db=ligand_db, logger=session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3010, in
find_residue_templates
tname, prot_res = find_glycan_template_name_and_link(sugar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 249, in
find_glycan_template_name_and_link
raise RuntimeError('Residue {}{} has multiple bonds to neighbor {}{}'.format(
RuntimeError: Residue A1208 has multiple bonds to neighbor A390
RuntimeError: Residue A1208 has multiple bonds to neighbor A390
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 249, in
find_glycan_template_name_and_link
raise RuntimeError('Residue {}{} has multiple bonds to neighbor {}{}'.format(
See log for complete Python traceback.
> isolde sim start /A-B
Sim termination reason: None
ISOLDE: stopped sim
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1419, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 166, in run_provider
toolbar_command(session, name)
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 23, in toolbar_command
run(session, f'isolde sim start {_current_residue_sel_string(session)}')
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 3221, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim
isolde.start_sim()
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/isolde.py", line 876, in start_sim
sm = self._sim_manager = SimManager(self, self.selected_model, main_sel,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 343, in __init__
raise e
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 321, in __init__
sh = self.sim_handler = SimHandler(session, sim_params, sc,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1077, in __init__
template_dict = find_residue_templates(sim_construct.all_residues, ff,
ligand_db=ligand_db, logger=session.logger)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 3010, in
find_residue_templates
tname, prot_res = find_glycan_template_name_and_link(sugar)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 249, in
find_glycan_template_name_and_link
raise RuntimeError('Residue {}{} has multiple bonds to neighbor {}{}'.format(
RuntimeError: Residue A1208 has multiple bonds to neighbor A390
RuntimeError: Residue A1208 has multiple bonds to neighbor A390
File "/home/mahb3/.local/share/ChimeraX/1.10/lib/python3.11/site-
packages/chimerax/isolde/openmm/amberff/glycam.py", line 249, in
find_glycan_template_name_and_link
raise RuntimeError('Residue {}{} has multiple bonds to neighbor {}{}'.format(
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 25.0.7-0ubuntu0.24.04.2
OpenGL renderer: Mesa Intel(R) HD Graphics 530 (SKL GT2)
OpenGL vendor: Intel
Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=mate
XDG_SESSION_DESKTOP=mate
XDG_CURRENT_DESKTOP=MATE
DISPLAY=:0
Manufacturer: HP
Model: HP EliteDesk 800 G3 DM 65W
OS: Linux Mint 22
Architecture: 64bit ELF
Virtual Machine: none
CPU: 4 Intel(R) Core(TM) i5-6500 CPU @ 3.20GHz
Cache Size: 6144 KB
Memory:
total used free shared buff/cache available
Mem: 15Gi 3.7Gi 8.5Gi 675Mi 3.8Gi 11Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 530 [8086:1912] (rev 06)
DeviceName: Onboard IGD
Subsystem: Hewlett-Packard Company HD Graphics 530 [103c:829a]
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2025.7.14
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
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: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
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: 1.1.4
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: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
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-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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
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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
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-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
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
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (1)
comment:1 by , 5 weeks ago
| Component: | Unassigned → Third Party |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → isolde sim start: Residue has multiple bonds to neighbor |
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