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Opened 12 months ago
Last modified 12 months ago
#16172 assigned defect
ISOLDE: structure contains 'LP' (lone pair) element
| Reported by: | Owned by: | Tristan Croll | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Third Party | Version: | |
| Keywords: | Cc: | Eric Pettersen | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-6.6.52-gentoo-x86_64-AMD_Ryzen_9_6900HX_with_Radeon_Graphics-with-glibc2.39
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/pauline/Desktop/P47_maps/J142/Autosharpen_15/sharpened_map.ccp4
> format ccp4
Opened sharpened_map.ccp4 as #1, grid size 560,560,560, pixel 0.97, shown at
level 4, step 4, values float32
> volume #1 step 1
> surface dust #1 size 9.7
> open /home/pauline/Desktop/P47_maps/J142/coot_fits/phenix15/working-
> coot-1.cif format mmcif
Summary of feedback from opening
/home/pauline/Desktop/P47_maps/J142/coot_fits/phenix15/working-coot-1.cif
---
warnings | Unknown polymer entity '1' on line 85
Atom . is not in the residue template for ILE /A:456
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for working-coot-1.cif #2
---
Chain | Description
A | No description available
> transparency 50
> hide #!1 models
> ui mousemode right select
> select clear
> select /A:359
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> volume #1 level 4.802
> hide #!1 models
> select /A:356
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> select /A:358
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /A:359
21 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:360
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> select clear
> select /A:364
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> select /A:361
19 atoms, 18 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> select /A:355
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:356
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /A:355
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide sel atoms
> hide #!1 models
> select /A:354
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> hide sel atoms
> select /A:353
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> select clear
> select /A:327
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:366
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:367
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /A:327
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:326
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:354
20 atoms, 20 bonds, 1 residue, 1 model selected
> select clear
> select /A:326
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:327
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /A:326
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:328
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:325
21 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select /A:354
20 atoms, 20 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> volume #1 level 6.14
> volume #1 level 7.21
> hide #!1 models
> select /A:328
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /A:327
24 atoms, 23 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> select add #1
24 atoms, 23 bonds, 1 residue, 3 models selected
> select subtract #1
24 atoms, 23 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> select /A:172
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:171
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide #!1 models
> select clear
> select /A:168
12 atoms, 11 bonds, 1 residue, 1 model selected
> select /A:167
17 atoms, 16 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
Drag select of 1 sharpened_map.ccp4 , 3 atoms, 3 bonds
> select clear
Drag select of 1 sharpened_map.ccp4 , 1 atoms, 1 bonds
Drag select of 1 sharpened_map.ccp4
> select clear
> hide #!1 models
> select /A:244
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:243
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
> hide sel atoms
> hide #!1 models
> select /A:244
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:245
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:243
24 atoms, 25 bonds, 1 residue, 1 model selected
> select /A:245
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /A:243
24 atoms, 25 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!1 models
Drag select of 1 sharpened_map.ccp4
> select #1
2 models selected
> hide #!1 models
> show #!1 models
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 6 residues in model #2 to IUPAC-IUB
standards.
Chain information for working-coot-1.cif
---
Chain | Description
2.2/A | No description available
ISOLDE: created disulfide bonds between the following residues:
A343-A352; A373-A382; A80-A93; A308-A317; A183-A205; A427-A436; A121-A154;
A345-A370; A385-A403; A72-A96; A320-A340; A289-A306; A287-A296; A439-A453;
A43-A53
> clipper associate #1 toModel #2
Opened sharpened_map.ccp4 as #2.1.1.1, grid size 560,560,560, pixel 0.97,
shown at step 1, values float32
s1:
TAQPDPCYDEHGLPRRCIPDFVNSAFGKEVKVSSTCGKPPSRYCVVTEKGEEQVRSCHLCNASDPKRAHPPSFLTDLNNPHNLTCWQSDSYVQYPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGKTWVPFQFYSTQCRKMYNKPSRAAITKQNEQEAICTDSHTDVRPLSGGLIAFSTLDGRPTAHDFDNSPVLQDWVTATDIKVTFSRLHTFGDENEDDSRDSYFYAVSDLQVGGRCKCNGHASRCVRDRDDNLVCDCKHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDLSKPISHRKACKECDCHPVGAAGQTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKI
s2:
TAQPDPCYDEHGLPRRCIPDFVNSAFGKEVKVSSTCGKPPSRYCVVTEKGEEQVRSCHLCNASDPKRAHPPSFLTDLNNPHNLTCWQSDSYVQYPHNVTLTLSLGKKFEVTYVSLQFCSPRPESMAIYKSMDYGKTWVPFQFYSTQCRKMYNKPSRAAITKQNEQEAICTDSHTDVRPLSGGLIAFSTLDGRPTAHDFDNSPVLQDWVTATDIKVTFSRLHTFGDENEDDSRDSYFYAVSDLQVGGRCKCNGHASRCVRDRDDNLVCDCKHNTAGPECDRCKPFHYDRPWQRATAREANECVACNCNLHARRCRFNMELYKLSGRKSGGVCLNCRHNTAGRHCHYCKEGFYRDLSKPISHRKACKECDCHPVGAAGQTCNQTTGQCPCKDGVTGITCNRCAKGYQQSRSPIAPCIKI
> isolde sim start /A
Sim termination reason: None
ISOLDE: stopped sim
Traceback (most recent call last):
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/lib64/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/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1306, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 184, in run_provider
toolbar_command(session, name)
File "/home/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 21, in toolbar_command
run(session, f'isolde sim start {_current_residue_sel_string(session)}')
File "/usr/lib64/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/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim
isolde.start_sim()
File "/home/pauline/.local/share/ChimeraX/1.8/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/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 343, in __init__
raise e
File "/home/pauline/.local/share/ChimeraX/1.8/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/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1078, in __init__
top, residue_templates = create_openmm_topology(atoms, template_dict)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 2965, in
create_openmm_topology
element = Element.getBySymbol(ename)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/element.py", line 103, in getBySymbol
return Element._elements_by_symbol[s]
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
KeyError: 'LP'
KeyError: 'LP'
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/element.py", line 103, in getBySymbol
return Element._elements_by_symbol[s]
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
See log for complete Python traceback.
> isolde sim start /A
Sim termination reason: None
ISOLDE: stopped sim
Traceback (most recent call last):
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 205, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/lib64/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/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1306, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/__init__.py", line 184, in run_provider
toolbar_command(session, name)
File "/home/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/toolbar.py", line 21, in toolbar_command
run(session, f'isolde sim start {_current_residue_sel_string(session)}')
File "/usr/lib64/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/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/cmd/cmd.py", line 122, in isolde_sim
isolde.start_sim()
File "/home/pauline/.local/share/ChimeraX/1.8/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/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 343, in __init__
raise e
File "/home/pauline/.local/share/ChimeraX/1.8/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/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1078, in __init__
top, residue_templates = create_openmm_topology(atoms, template_dict)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/pauline/.local/share/ChimeraX/1.8/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 2965, in
create_openmm_topology
element = Element.getBySymbol(ename)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/element.py", line 103, in getBySymbol
return Element._elements_by_symbol[s]
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
KeyError: 'LP'
KeyError: 'LP'
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/openmm/app/element.py", line 103, in getBySymbol
return Element._elements_by_symbol[s]
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 470.256.02
OpenGL renderer: NVIDIA GeForce RTX 3070 Ti Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.4
Locale: en_CA.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=XFCE
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Strix G513RW_G513RW
OS: Gentoo 2.15 n/a
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 9 6900HX with Radeon Graphics
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 3.3Gi 51Gi 25Mi 8.3Gi 58Gi
Swap: 63Gi 0B 63Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [Geforce RTX 3070 Ti Laptop GPU] [10de:24a0] (rev a1)
Subsystem: ASUSTeK Computer Inc. Device [1043:1cb2]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
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: 1.2.4
ChimeraX-DiffPlot: 1.0
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-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
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: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.7
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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: 3.0.15
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: 1.16.5
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
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
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: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
distro: 1.9.0
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
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: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
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: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
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: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (1)
comment:1 by , 12 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Third Party |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → ISOLDE: structure contains 'LP' (lone pair) element |
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