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#14721 closed defect (nonchimerax)

ISOLDE: error registering 'isolde' command

Reported by:	torquato@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:	Greg Couch, Eric Pettersen
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  

> open
> /home/ricardo/aakz211/alphafold/prediction/aakz211_alphafold_relaxed.pdb_0015.pdb
> format 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  
  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  
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 "/home/ricardo/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/ui/general_tab/sim_fidelity.py", line 63, in
_button_click_cb  
run(self.session, f'isolde set simFidelityMode "{b.text()}"')  
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.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1 to IUPAC-IUB
standards.  
Chain information for aakz211_alphafold_relaxed.pdb_0015.pdb  
---  
Chain | Description  
1.2/A | No description available  
  
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 21, 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 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 470.239.06
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       1.5Gi        12Gi       250Mi       1.5Gi        13Gi
	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
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    openvr: 1.23.701
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    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
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    platformdirs: 4.1.0
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    pure-eval: 0.2.2
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    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
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    python-dateutil: 2.8.2
    pytz: 2023.3.post1
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    QtPy: 2.4.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.31.0
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    Send2Trash: 1.8.2
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Change History (5)

comment:1 by Eric Pettersen, 20 months ago

Cc:	Greg Couch added
Component:	Unassigned → Third Party
Owner:	set to Tristan Croll
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ISOLDE: error registering 'isolde' command

Reported by Ricardo Torquato

comment:2 by Tristan Croll, 20 months ago

I don’t think this is ISOLDE’s doing as such, but I’m mystified as to why
it’s happening. The error is arising deep in the guts of numpy, triggered
by the innocuous line:

from scipy import interpolate

On Thu, 7 Mar 2024 at 21:19, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>
>

comment:3 by Tristan Croll, 20 months ago

Owner:	changed from Tristan Croll to Eric Pettersen

This looks like a Numpy bug. Reassigning to Eric to decide where to go from here. The cascade of imports ultimately leads to Numpy running check_support_sve() (line 1239 of numpy/testing/_private/utils.py):

def check_support_sve():
    """
    gh-22982
    """
    
    import subprocess
    cmd = 'lscpu'
    try:
        output = subprocess.run(cmd, capture_output=True, text=True)
        return 'sve' in output.stdout
    except OSError:
        return False

From the error, it looks like it's expecting the lscpu output to be pure ASCII but there are some extended Unicode characters in there (0xc3 is "Ã").

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)

comment:4 by Eric Pettersen, 20 months ago

Cc:	Eric Pettersen added
Owner:	changed from Eric Pettersen to Tom Goddard

numpy bug

comment:5 by Tom Goddard, 20 months ago

Resolution:	→ nonchimerax
Status:	assigned → closed

I agree it is a numpy bug. Looks like it was probably introduced into numpy source code on June 16, 2023 with this commit

https://github.com/numpy/numpy/commit/c52a0430b8463c7286cc878d2ad00517b8444243

It happens when importing numpy.testing which is being done by scipy.

I see only one mention of this bug online searching for numpy check_support_sve unicodedecodeerror

https://github.com/Acly/krita-ai-diffusion/issues/404

So I guess it effect almost no one. It apparently is caused by the lscpu unix command outputting non-ascii characters. That may have to do with the user's locale setting, or the actual CPU information on their system.

We are not going to revert to a very old numpy to fix this, unless many people are affected.

The reporter on this ticket can report a bug to the numpy github site and eventually it will probably be fixed by the numpy developers. Apparently it is so rare that it has not been reported.

ChimeraX 1.7 is using numpy version 1.25.1. The current ChimeraX daily build uses numpy version 1.26.4. The numpy check_support_sve() routine that has the problem has not changed (although possibly some code higher up the call stack catches the error). It might be worth trying the ChimeraX daily build. Probably ISOLDE does not work with the daily build. But "import numpy.testing" could be tried in the ChimeraX Python shell (menu Tools / General / Shell) to see if the bug still exists in numpy 1.26.4.

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