Opened 20 months ago
Last modified 20 months ago
#14720 assigned defect
ISOLDE: failure registering 'isolde' command
Reported by: | Owned by: | Tristan Croll | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Third Party | Version: | |
Keywords: | Cc: | Greg Couch | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-5.15.0-97-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > toolshed show Downloading bundle ChimeraX_PhenixUI-1.2.2-py3-none-any.whl Installed ChimeraX-PhenixUI (1.2.2) Downloading bundle MolecularDynamicsViewer-1.4-py3-none-any.whl Installed MolecularDynamicsViewer (1.4) Downloading bundle ChimeraX_TugLigands-1.1-py3-none-any.whl Installed ChimeraX-TugLigands (1.1) Downloading bundle ChimeraX_PDBImages-1.2-py3-none-any.whl Installed ChimeraX-PDBImages (1.2) > open > /home/ricardo/aakz211/alphafold/prediction/aakz211_alphafold_relaxed.pdb_0015.pdb Summary of feedback from opening /home/ricardo/aakz211/alphafold/prediction/aakz211_alphafold_relaxed.pdb_0015.pdb --- warnings | Ignored bad PDB record found on line 1026 # All scores below are weighted scores, not raw scores. Ignored bad PDB record found on line 1027 #BEGIN_POSE_ENERGIES_TABLE aakz211_alphafold_relaxed.pdb_0015.pdb Ignored bad PDB record found on line 1028 label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 coordinate_constraint omega fa_dun p_aa_pp yhh_planarity ref rama_prepro total Ignored bad PDB record found on line 1029 weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.5 0.4 0.7 0.6 0.625 1 0.45 NA Ignored bad PDB record found on line 1030 pose -276.16 49.5133 196.04 0.58039 9.86906 -6.8243 -71.2564 5.26504 -12.2395 -10.6681 -14.7577 -3.95274 -2.44072 58.1571 30.0705 73.8135 -4.72605 0.00131 17.9771 32.4543 70.7171 73 messages similar to the above omitted Chain information for aakz211_alphafold_relaxed.pdb_0015.pdb #1 --- Chain | Description A | No description available > show atoms > hide atoms > show cartoons > show atoms > show cartoons > style sphere Changed 1021 atom styles > style sphere Changed 1021 atom styles > hide atoms > hide cartoons > show atoms > color byhetero > hide surfaces > show surfaces > hide surfaces > hide atoms > show atoms > style sphere Changed 1021 atom styles > style stick Changed 1021 atom styles > hide atoms > show atoms > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for aakz211_alphafold_relaxed.pdb_0015.pdb_A SES surface #1.1: minimum, -9.93, mean 1.50, maximum 12.36 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface "aakz211_alphafold_relaxed.pdb_0015.pdb_A SES surface": minimum -27.07, mean -4.717, maximum 21.14 To also show corresponding color key, enter the above mlp command and add key true > coulombic Coulombic values for aakz211_alphafold_relaxed.pdb_0015.pdb_A SES surface #1.1: minimum, -9.93, mean 1.50, maximum 12.36 To also show corresponding color key, enter the above coulombic command and add key true > color byhetero > color bychain > color bypolymer > rainbow > coulombic Coulombic values for aakz211_alphafold_relaxed.pdb_0015.pdb_A SES surface #1.1: minimum, -9.93, mean 1.50, maximum 12.36 To also show corresponding color key, enter the above coulombic command and add key true Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 330, in _register_cmd api._api_caller.register_command(api, self, ci, logger) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1286, in register_command return cls._get_func(api, "register_command")(ci.name, logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/__init__.py", line 170, in register_command cmd.register_isolde(logger) File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/cmd/cmd.py", line 478, in register_isolde from chimerax.isolde.manipulations.cmd import register_manip_commands File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/manipulations/__init__.py", line 12, in <module> from .register_shift import ProteinRegisterShifter File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/manipulations/register_shift.py", line 15, in <module> from scipy import interpolate File "<frozen importlib._bootstrap>", line 1231, in _handle_fromlist File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/scipy/__init__.py", line 189, in __getattr__ return _importlib.import_module(f'scipy.{name}') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/importlib/__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/interpolate/__init__.py", line 167, in <module> from ._interpolate import * File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/interpolate/_interpolate.py", line 12, in <module> from . import _fitpack_py File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/interpolate/_fitpack_py.py", line 10, in <module> from ._bsplines import BSpline File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/interpolate/_bsplines.py", line 9, in <module> from scipy.optimize import minimize_scalar File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/__init__.py", line 410, in <module> from ._minimize import * File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/_minimize.py", line 27, in <module> from ._trustregion_constr import _minimize_trustregion_constr File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/_trustregion_constr/__init__.py", line 4, in <module> from .minimize_trustregion_constr import _minimize_trustregion_constr File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py", line 5, in <module> from .._constraints import ( File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/_constraints.py", line 8, in <module> from numpy.testing import suppress_warnings File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/testing/__init__.py", line 11, in <module> from ._private.utils import * File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/testing/_private/utils.py", line 1253, in <module> _SUPPORTS_SVE = check_support_sve() ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/testing/_private/utils.py", line 1247, in check_support_sve output = subprocess.run(cmd, capture_output=True, text=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 550, in run stdout, stderr = process.communicate(input, timeout=timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 1207, in communicate stdout, stderr = self._communicate(input, endtime, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 2097, in _communicate stdout = self._translate_newlines(stdout, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 1084, in _translate_newlines data = data.decode(encoding, errors) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 422: ordinal not in range(128) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2227, in lazy_register deferred.call() File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2158, in call return self.proxy() ^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 320, in cb s._register_cmd(ci, logger) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd raise ToolshedError( chimerax.core.toolshed.ToolshedError: register_command() failed for command isolde in bundle ChimeraX-ISOLDE: 'ascii' codec can't decode byte 0xc3 in position 422: ordinal not in range(128) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/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/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 1302, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/__init__.py", line 183, in run_provider toolbar_command(session, name) File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/toolbar.py", line 19, in toolbar_command run(session, 'isolde start') 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 2843, in run self._find_command_name(final, used_aliases=_used_aliases) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2579, in _find_command_name what.lazy_register(cmd_name) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2229, in lazy_register raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e)) RuntimeError: delayed command registration for 'isolde' failed (register_command() failed for command isolde in bundle ChimeraX-ISOLDE: 'ascii' codec can't decode byte 0xc3 in position 422: ordinal not in range(128)) RuntimeError: delayed command registration for 'isolde' failed (register_command() failed for command isolde in bundle ChimeraX-ISOLDE: 'ascii' codec can't decode byte 0xc3 in position 422: ordinal not in range(128)) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2229, in lazy_register raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e)) See log for complete Python traceback. FYI: command is replacing existing command: "isolde start" FYI: command is replacing existing command: "isolde set" FYI: command is replacing existing command: "isolde select" FYI: command is replacing existing command: "isolde sim" FYI: command is replacing existing command: "isolde report" FYI: command is replacing existing command: "isolde ignore" FYI: command is replacing existing command: "isolde ~ignore" FYI: command is replacing existing command: "isolde tutorial" FYI: command is replacing existing command: "isolde demo" FYI: command is replacing existing command: "isolde stepto" FYI: command is replacing existing command: "isolde jumpto" FYI: command is replacing existing command: "isolde adjust bfactors" FYI: command is replacing existing command: "isolde shorthand" FYI: command is replacing existing command: "isolde remote xmlrpc" FYI: command is replacing existing command: "isolde remote rest start" FYI: command is replacing existing command: "isolde remote rest info" FYI: command is replacing existing command: "isolde remote rest stop" FYI: command is replacing existing command: "isolde restrain distances" FYI: command is replacing existing command: "isolde restrain single distance" FYI: command is replacing existing command: "isolde release distances" FYI: command is replacing existing command: "isolde restrain basepairs" FYI: command is replacing existing command: "isolde adjust distances" FYI: command is replacing existing command: "isolde restrain ligands" FYI: command is replacing existing command: "isolde restrain torsions" FYI: command is replacing existing command: "isolde adjust torsions" FYI: command is replacing existing command: "isolde release torsions" FYI: command is replacing existing command: "isolde restrain talosNMR" Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 330, in _register_cmd api._api_caller.register_command(api, self, ci, logger) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1286, in register_command return cls._get_func(api, "register_command")(ci.name, logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/__init__.py", line 170, in register_command cmd.register_isolde(logger) File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/cmd/cmd.py", line 478, in register_isolde from chimerax.isolde.manipulations.cmd import register_manip_commands File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/manipulations/__init__.py", line 12, in <module> from .register_shift import ProteinRegisterShifter File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/manipulations/register_shift.py", line 15, in <module> from scipy import interpolate File "<frozen importlib._bootstrap>", line 1231, in _handle_fromlist File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/scipy/__init__.py", line 189, in __getattr__ return _importlib.import_module(f'scipy.{name}') ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/importlib/__init__.py", line 126, in import_module return _bootstrap._gcd_import(name[level:], package, level) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/interpolate/__init__.py", line 167, in <module> from ._interpolate import * File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/interpolate/_interpolate.py", line 12, in <module> from . import _fitpack_py File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/interpolate/_fitpack_py.py", line 10, in <module> from ._bsplines import BSpline File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/interpolate/_bsplines.py", line 9, in <module> from scipy.optimize import minimize_scalar File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/__init__.py", line 410, in <module> from ._minimize import * File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/_minimize.py", line 27, in <module> from ._trustregion_constr import _minimize_trustregion_constr File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/_trustregion_constr/__init__.py", line 4, in <module> from .minimize_trustregion_constr import _minimize_trustregion_constr File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/_trustregion_constr/minimize_trustregion_constr.py", line 5, in <module> from .._constraints import ( File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/scipy/optimize/_constraints.py", line 8, in <module> from numpy.testing import suppress_warnings File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/testing/__init__.py", line 11, in <module> from ._private.utils import * File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/testing/_private/utils.py", line 1253, in <module> _SUPPORTS_SVE = check_support_sve() ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/numpy/testing/_private/utils.py", line 1247, in check_support_sve output = subprocess.run(cmd, capture_output=True, text=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 550, in run stdout, stderr = process.communicate(input, timeout=timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 1207, in communicate stdout, stderr = self._communicate(input, endtime, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 2097, in _communicate stdout = self._translate_newlines(stdout, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 1084, in _translate_newlines data = data.decode(encoding, errors) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 422: ordinal not in range(128) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2227, in lazy_register deferred.call() File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2158, in call return self.proxy() ^^^^^^^^^^^^ File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 320, in cb s._register_cmd(ci, logger) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 332, in _register_cmd raise ToolshedError( chimerax.core.toolshed.ToolshedError: register_command() failed for command isolde in bundle ChimeraX-ISOLDE: 'ascii' codec can't decode byte 0xc3 in position 422: ordinal not in range(128) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/lib/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/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 1302, in run_provider return cls._get_func(api, "run_provider")(session, name, mgr, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/__init__.py", line 183, in run_provider toolbar_command(session, name) File "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site- packages/chimerax/isolde/toolbar.py", line 19, in toolbar_command run(session, 'isolde start') 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 2843, in run self._find_command_name(final, used_aliases=_used_aliases) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2579, in _find_command_name what.lazy_register(cmd_name) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2229, in lazy_register raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e)) RuntimeError: delayed command registration for 'isolde' failed (register_command() failed for command isolde in bundle ChimeraX-ISOLDE: 'ascii' codec can't decode byte 0xc3 in position 422: ordinal not in range(128)) RuntimeError: delayed command registration for 'isolde' failed (register_command() failed for command isolde in bundle ChimeraX-ISOLDE: 'ascii' codec can't decode byte 0xc3 in position 422: ordinal not in range(128)) File "/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2229, in lazy_register raise RuntimeError("delayed command registration for %r failed (%s)" % (cmd_name, e)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 535.161.07 OpenGL renderer: NVIDIA GeForce GTX 1060/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: pt_BR.UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=cinnamon XDG_SESSION_DESKTOP=cinnamon XDG_CURRENT_DESKTOP=X-Cinnamon DISPLAY=:0 Manufacturer: LENOVO Model: 81CQ OS: Linux Mint 21.3 Virginia Architecture: 64bit ELF Virtual Machine: none CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz Cache Size: 6144 KB Memory: total used free shared buff/cache available Mem: 15Gi 4.6Gi 455Mi 587Mi 10Gi 9.9Gi Swap: 2.8Gi 0B 2.8Gi Graphics: 00:02.0 VGA compatible controller [0300]: Intel Corporation HD Graphics 630 [8086:591b] (rev 04) Subsystem: Lenovo HD Graphics 630 [17aa:38e1] Kernel driver in use: i915 Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 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: 2.10.5 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: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.4 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: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 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 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: 1.7.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 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: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBImages: 1.2 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.2.2 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StarMap: 1.2.15 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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-TugLigands: 1.1 ChimeraX-UI: 1.33.2 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-XMAS: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 distro: 1.7.0 docutils: 0.19 et-xmlfile: 1.1.0 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 MolecularDynamicsViewer: 1.4 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openpyxl: 3.1.2 openvr: 1.23.701 packaging: 23.2 pandas: 2.2.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 pyqtgraph: 0.13.3 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 seaborn: 0.13.2 Send2Trash: 1.8.2 SEQCROW: 1.8.7 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9
Change History (1)
comment:1 by , 20 months ago
Cc: | added |
---|---|
Component: | Unassigned → Third Party |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → ISOLDE: failure registering 'isolde' command |
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Reported by Ricardo Torquato