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#18121 closed defect (can't reproduce)

UnicodeDecodeError when numpy check SVE support

Reported by:	chimerax-bug-report@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Core	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-6.5.0-41-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/student/Downloads/4udx-CO2-dimer.pdb

Summary of feedback from opening /home/student/Downloads/4udx-CO2-dimer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP X 10
GLY X 24 1 15  
Start residue of secondary structure not found: HELIX 2 2 THR X 27 LYS X 36 1
10  
Start residue of secondary structure not found: HELIX 3 3 CYS X 39 GLY X 45 1
7  
Start residue of secondary structure not found: HELIX 4 4 THR X 73 GLN X 109 1
37  
Start residue of secondary structure not found: HELIX 5 5 ASP X 119 GLY X 131
1 13  
43 messages similar to the above omitted  
notes | Combining 2 symmetry atoms into HOH /A:2091 O  
Combining 2 symmetry atoms into HOH /A:2396 O  
Combining 2 symmetry atoms into HOH /A:2339 O  
  
4udx-CO2-dimer.pdb title:  
CO2 bound to cluster C of Ni,Fe-Co dehydrogenase At true-atomic resolution
[more info...]  
  
Chain information for 4udx-CO2-dimer.pdb #1  
---  
Chain | Description | UniProt  
A | No description available | COOS2_CARHZ 1-636  
B | No description available |  
  
Non-standard residues in 4udx-CO2-dimer.pdb #1  
---  
CO2 — carbon dioxide  
FE2 — Fe (II) ion  
FES — FE2/S2 (inorganic) cluster  
SF4 — iron/sulfur cluster  
WCC — Fe(3)-Ni(1)-S(4) cluster (C cluster cubane)  
  

> select add #1

20159 atoms, 18716 bonds, 82 pseudobonds, 2056 residues, 2 models selected  

> select /A

10856 atoms, 9358 bonds, 49 pseudobonds, 1417 residues, 2 models selected  

> color (#!1 & sel) hot pink

> select /B

9303 atoms, 9358 bonds, 33 pseudobonds, 639 residues, 2 models selected  

> color (#!1 & sel) lime

> select ::name="FES"

8 atoms, 8 bonds, 2 pseudobonds, 2 residues, 2 models selected  

> color (#!1 & sel) red

> select add #1

20159 atoms, 18716 bonds, 82 pseudobonds, 2056 residues, 2 models selected  

> lighting shadows true

> lighting flat

[Repeated 1 time(s)]

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting flat

> lighting soft

> select ::name="CO2"

6 atoms, 4 bonds, 2 residues, 1 model selected  

> color sel forest green

> select ::name="HOH"

1555 atoms, 780 residues, 1 model selected  

> color sel blue

> select ::name="SF4"

16 atoms, 36 pseudobonds, 2 residues, 2 models selected  

> color (#!1 & sel) orange

> select ::name="WCC"

16 atoms, 4 bonds, 26 pseudobonds, 2 residues, 2 models selected  

> color (#!1 & sel) cyan

> select ::name="FE2"

2 atoms, 2 residues, 1 model selected  

> color sel orange

> select add #1

20159 atoms, 18716 bonds, 82 pseudobonds, 2056 residues, 2 models selected  

> style sel stick

Changed 20159 atom styles  

> style sel stick

Changed 20159 atom styles  

> style sel sphere

Changed 20159 atom styles  

> style sel stick

Changed 20159 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> select /A:1004@FE

1 atom, 1 residue, 1 model selected  

> style sel sphere

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> select add #1

20159 atoms, 18716 bonds, 82 pseudobonds, 2056 residues, 2 models selected  

> color sel byhetero

> hbonds sel reveal true

5690 hydrogen bonds found  

> hbonds sel reveal true

5690 hydrogen bonds found  

> hbonds sel reveal true

5690 hydrogen bonds found  

> undo

[Repeated 4 time(s)]

> ~hbonds

> undo

[Repeated 4 time(s)]

> redo

[Repeated 3 time(s)]

> hide sel atoms

> show sel atoms

> show sel cartoons

> show sel surfaces

> undo

[Repeated 7 time(s)]

> hide sel cartoons

> hide sel surfaces

> show sel cartoons

> hide sel atoms

> select add #1

20159 atoms, 18716 bonds, 82 pseudobonds, 2056 residues, 4 models selected  

> show sel atoms

> show sel cartoons

> hide sel atoms

> show sel atoms

> style sel sphere

Changed 20159 atom styles  

> style sel stick

Changed 20159 atom styles  

> select /A:2699@@serial_number=10920

1 atom, 1 residue, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select add #1

20159 atoms, 18716 bonds, 82 pseudobonds, 2056 residues, 2 models selected  

> hide sel atoms

> open /home/student/Downloads/4udx-CO2-dimer.pdb

Summary of feedback from opening /home/student/Downloads/4udx-CO2-dimer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP X 10
GLY X 24 1 15  
Start residue of secondary structure not found: HELIX 2 2 THR X 27 LYS X 36 1
10  
Start residue of secondary structure not found: HELIX 3 3 CYS X 39 GLY X 45 1
7  
Start residue of secondary structure not found: HELIX 4 4 THR X 73 GLN X 109 1
37  
Start residue of secondary structure not found: HELIX 5 5 ASP X 119 GLY X 131
1 13  
43 messages similar to the above omitted  
notes | Combining 2 symmetry atoms into HOH /A:2091 O  
Combining 2 symmetry atoms into HOH /A:2396 O  
Combining 2 symmetry atoms into HOH /A:2339 O  
  
4udx-CO2-dimer.pdb title:  
CO2 bound to cluster C of Ni,Fe-Co dehydrogenase At true-atomic resolution
[more info...]  
  
Chain information for 4udx-CO2-dimer.pdb #2  
---  
Chain | Description | UniProt  
A | No description available | COOS2_CARHZ 1-636  
B | No description available |  
  
Non-standard residues in 4udx-CO2-dimer.pdb #2  
---  
CO2 — carbon dioxide  
FE2 — Fe (II) ion  
FES — FE2/S2 (inorganic) cluster  
SF4 — iron/sulfur cluster  
WCC — Fe(3)-Ni(1)-S(4) cluster (C cluster cubane)  
  

> select #1/A#2/A

21712 atoms, 18716 bonds, 98 pseudobonds, 2834 residues, 4 models selected  

> color (#!1-2 & sel) orange

> ui tool show Distances

[Repeated 1 time(s)]Drag select of 12 residues, 16 atoms, 12 bonds  

> ui tool show Distances

> select clear

> ui tool show Distances

> select #2/B:1005@O1

1 atom, 1 residue, 1 model selected  

> select #2/B:93@NE2

1 atom, 1 residue, 1 model selected  

> select #2/B:1005@O1

1 atom, 1 residue, 1 model selected  

> ui tool show Distances

> select #2/B:93@NE2

1 atom, 1 residue, 1 model selected  

> select #2/B:1005@O1

1 atom, 1 residue, 1 model selected  

> select #2/B:93@NE2

1 atom, 1 residue, 1 model selected  

> select #2/B:1005@O1

1 atom, 1 residue, 1 model selected  

> hbonds sel reveal true

8 hydrogen bonds found  
Drag select of 12 residues, 20 atoms, 4 pseudobonds, 17 bonds  

> select #1/B:235

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #2/B:235

7 atoms, 6 bonds, 1 residue, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select #1/B:299

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select add #2

20174 atoms, 18730 bonds, 86 pseudobonds, 2057 residues, 5 models selected  

> hbonds sel reveal true

20172 hydrogen bonds found  

> style sel stick

Changed 20174 atom styles  

> ~hbonds

> hbonds sel reveal true

20172 hydrogen bonds found  

> undo

[Repeated 1 time(s)]Undo failed, probably because structures have been
modified.  

> open /home/student/Downloads/4udx-CO2-dimer.pdb

Summary of feedback from opening /home/student/Downloads/4udx-CO2-dimer.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ASP X 10
GLY X 24 1 15  
Start residue of secondary structure not found: HELIX 2 2 THR X 27 LYS X 36 1
10  
Start residue of secondary structure not found: HELIX 3 3 CYS X 39 GLY X 45 1
7  
Start residue of secondary structure not found: HELIX 4 4 THR X 73 GLN X 109 1
37  
Start residue of secondary structure not found: HELIX 5 5 ASP X 119 GLY X 131
1 13  
43 messages similar to the above omitted  
notes | Combining 2 symmetry atoms into HOH /A:2091 O  
Combining 2 symmetry atoms into HOH /A:2396 O  
Combining 2 symmetry atoms into HOH /A:2339 O  
  
4udx-CO2-dimer.pdb title:  
CO2 bound to cluster C of Ni,Fe-Co dehydrogenase At true-atomic resolution
[more info...]  
  
Chain information for 4udx-CO2-dimer.pdb #4  
---  
Chain | Description | UniProt  
A | No description available | COOS2_CARHZ 1-636  
B | No description available |  
  
Non-standard residues in 4udx-CO2-dimer.pdb #4  
---  
CO2 — carbon dioxide  
FE2 — Fe (II) ion  
FES — FE2/S2 (inorganic) cluster  
SF4 — iron/sulfur cluster  
WCC — Fe(3)-Ni(1)-S(4) cluster (C cluster cubane)  
  

> hide #!1 models

> hide #!2 models

> hide #3 models

> hide #!4 models

> show #!4 models

> select ::name="HIS"

1938 atoms, 1938 bonds, 114 residues, 3 models selected  

> style sel & #!4 stick

Changed 646 atom styles  

> color sel & #!4 byhetero

[Repeated 1 time(s)]

> show sel & #!4 cartoons

> show sel & #!4 atoms

[Repeated 1 time(s)]

> hide sel & #!4 atoms

> show sel & #!4 atoms

> select ::name="HOH"

4665 atoms, 11170 pseudobonds, 2340 residues, 4 models selected  

> show sel & #!4 atoms

> hide sel & #!4 atoms

> select #1/A#2/A#4/A

32568 atoms, 28074 bonds, 15740 pseudobonds, 4251 residues, 7 models selected  

> hide sel & #!4 cartoons

> hide sel & #!4 atoms

> open /home/student/Schreibtisch/MB28-PR/Ni-Fe-CODH/7zxc-chainB.pdb

Summary of feedback from opening /home/student/Schreibtisch/MB28-PR/Ni-Fe-
CODH/7zxc-chainB.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 AA1 ARG X 3
LYS X 7 5 5  
Start residue of secondary structure not found: HELIX 2 AA2 ASP X 10 GLY X 24
1 15  
Start residue of secondary structure not found: HELIX 3 AA3 THR X 27 LYS X 36
1 10  
Start residue of secondary structure not found: HELIX 4 AA4 CYS X 39 GLY X 45
1 7  
Start residue of secondary structure not found: HELIX 5 AA5 THR X 73 GLN X 109
1 37  
44 messages similar to the above omitted  
  
7zxc-chainB.pdb title:  
H96D mutant of recombinant codh-II [more info...]  
  
Chain information for 7zxc-chainB.pdb #5  
---  
Chain | Description | UniProt  
B | No description available | COOS2_CARHZ 4-636  
  
Non-standard residues in 7zxc-chainB.pdb #5  
---  
FE — Fe (III) ion  
FES — FE2/S2 (inorganic) cluster  
SF4 — iron/sulfur cluster  
WCC — Fe(3)-Ni(1)-S(4) cluster (C cluster cubane)  
  

> select add #5

37977 atoms, 32819 bonds, 15788 pseudobonds, 5610 residues, 10 models selected  

> close #5

> open /home/student/Schreibtisch/MB28-PR/Ni-Fe-CODH/7zxc-chainA.pdb

Summary of feedback from opening /home/student/Schreibtisch/MB28-PR/Ni-Fe-
CODH/7zxc-chainA.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 AA1 ARG X 3
LYS X 7 5 5  
Start residue of secondary structure not found: HELIX 2 AA2 ASP X 10 GLY X 24
1 15  
Start residue of secondary structure not found: HELIX 3 AA3 THR X 27 LYS X 36
1 10  
Start residue of secondary structure not found: HELIX 4 AA4 CYS X 39 GLY X 45
1 7  
Start residue of secondary structure not found: HELIX 5 AA5 THR X 73 GLN X 109
1 37  
44 messages similar to the above omitted  
  
7zxc-chainA.pdb title:  
H96D mutant of recombinant codh-II [more info...]  
  
Chain information for 7zxc-chainA.pdb #5  
---  
Chain | Description | UniProt  
A | No description available | COOS2_CARHZ 4-636  
  
Non-standard residues in 7zxc-chainA.pdb #5  
---  
FE — Fe (III) ion  
FES — FE2/S2 (inorganic) cluster  
SF4 — iron/sulfur cluster  
WCC — Fe(3)-Ni(1)-S(4) cluster (C cluster cubane)  
  

> hide #!5 models

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> set bgColor gray

> set bgColor #80808000

> set bgColor white

> set bgColor #ffffff00

> lighting flat

> cartoon style (#!4 & sel) modeHelix tube sides 20

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1891, in
_update_graphics_if_needed  
s[i].update_graphics_if_needed()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 357, in update_graphics_if_needed  
self._create_ribbon_graphics()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 667, in _create_ribbon_graphics  
ribbons_drawing.compute_ribbons(self)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 600, in compute_ribbons  
_make_ribbon_graphics(structure, self)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 141, in _make_ribbon_graphics  
centers = _arc_helix_geometry(coords, xs_mgr, displays, start, end, geometry)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 980, in _arc_helix_geometry  
hc = HelixCylinder(coords[start:end])  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 198, in __init__  
self._try_curved()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 403, in _try_curved  
self._curved_optimize(c_center, c_axis, c_radius)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 447, in _curved_optimize  
opt = OptArc(self.coords, center, axis, major_radius)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 96, in __init__  
from scipy.optimize import minimize  
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 102:
ordinal not in range(128)  
  
Error processing trigger "graphics update":  
UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 102:
ordinal not in range(128)  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/subprocess.py", line 1084, in
_translate_newlines  
data = data.decode(encoding, errors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) UHD Graphics 770 (ADL-S GT1)
OpenGL vendor: Intel

Python: 3.11.2
Locale: de_DE.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
GNOME_SETUP_DISPLAY=:3
DISPLAY=:2
WAYLAND_DISPLAY=wayland-0
Manufacturer: Dell Inc.
Model: OptiPlex SFF 7010
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 13th Gen Intel(R) Core(TM) i5-13500
Cache Size: 24576 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi       3.2Gi       3.1Gi       429Mi       9.0Gi        11Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	0000:03:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Device [1002:743f] (rev c3)	
	Subsystem: Dell Device [1028:0041]	
	Kernel driver in use: amdgpu

Installed Packages:
    alabaster: 0.7.16
    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: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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-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: 1.7.1
    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-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: 2.6.1
    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: 1.5.14
    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-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    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-StdCommands: 1.12.4
    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-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    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
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    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: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    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
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    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: 1.0.8
    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: 0.5.0
    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: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 4 months ago

Component:	Unassigned → Core
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → UnicodeDecodeError when numpy check SVE support

comment:2 by Eric Pettersen, 4 months ago

Resolution:	→ can't reproduce
Status:	accepted → closed

Not using that version of numpy anymore.

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