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#15391 closed defect (limitation)

ArtiaX/pandas vs. numpy

Reported by:	chimerax-bug-report@…	Owned by:	Utz Ermel
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> set bgColor #ffffff00

Log from Wed Jun 5 23:00:51 2024UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/session.cxs

Log from Wed Jun 5 18:53:19 2024 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\Users\andrea.graziadei\Documents\Training\EMBO_tutorial\EMBO_tutorial\pdbfiles\state-3_fit-
> chains.pdb format pdb

Chain information for state-3_fit-chains.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> close

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/pdbfiles/state-2_fit-
> chains.pdb

Chain information for state-2_fit-chains.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/pdbfiles/state-3_fit-
> chains.pdb

Chain information for state-3_fit-chains.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/pdbfiles/state-4_fit-
> chains.pdb

Chain information for state-4_fit-chains.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/pdbfiles/fold_cullin_samhd1_alphafold3_model_0.cif

Chain information for fold_cullin_samhd1_alphafold3_model_0.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
F | .  
  

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/pdbfiles/state-3_fit-
> chains.pdb

Chain information for state-3_fit-chains.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/pdbfiles/state-4_fit-
> chains.pdb

Chain information for state-4_fit-chains.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/pdbfiles/fold_cullin_samhd1_alphafold3_model_0.cif

Chain information for fold_cullin_samhd1_alphafold3_model_0.cif #7  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
E | .  
F | .  
  

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/pdbfiles/state-2_fit-
> chains.pdb

Chain information for state-2_fit-chains.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
G | No description available  
  

> hide atoms

> show cartoons

> close #7#5-6,8

> ui tool show Matchmaker

> matchmaker #4#!1,3 to #2/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker state-3_fit-chains.pdb, chain B (#2) with
fold_cullin_samhd1_alphafold3_model_0.cif, chain B (#4), sequence alignment
score = 1618.2  
RMSD between 322 pruned atom pairs is 0.673 angstroms; (across all 331 pairs:
0.829)  
  
Matchmaker state-3_fit-chains.pdb, chain B (#2) with state-2_fit-chains.pdb,
chain B (#1), sequence alignment score = 1730.4  
RMSD between 331 pruned atom pairs is 0.001 angstroms; (across all 331 pairs:
0.001)  
  
Matchmaker state-3_fit-chains.pdb, chain B (#2) with state-4_fit-chains.pdb,
chain B (#3), sequence alignment score = 1730.4  
RMSD between 331 pruned atom pairs is 0.001 angstroms; (across all 331 pairs:
0.001)  
  

> matchmaker #4#!1,3 to #2/B pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker state-3_fit-chains.pdb, chain B (#2) with
fold_cullin_samhd1_alphafold3_model_0.cif, chain B (#4), sequence alignment
score = 1618.2  
RMSD between 322 pruned atom pairs is 0.673 angstroms; (across all 331 pairs:
0.829)  
  
Matchmaker state-3_fit-chains.pdb, chain B (#2) with state-2_fit-chains.pdb,
chain B (#1), sequence alignment score = 1730.4  
RMSD between 331 pruned atom pairs is 0.001 angstroms; (across all 331 pairs:
0.001)  
  
Matchmaker state-3_fit-chains.pdb, chain B (#2) with state-4_fit-chains.pdb,
chain B (#3), sequence alignment score = 1730.4  
RMSD between 331 pruned atom pairs is 0.001 angstroms; (across all 331 pairs:
0.001)  
  

> hide #4 models

> hide #!3 models

> hide #!2 models

> color /B blue

> color /A salmon

> color /C teal

> color /D wheat

> color /E forestgreen

> color /G forestgreen

> set bgColor white

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> hide #!1 models

> show #!2 models

> show #4 models

> hide #!2 models

> color #4/A forestgreen

> color #4/C salmon

> color #4/F teal

> color #4/E goldenrod

> hide #4 models

> show #!2 models

> save
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/session.cxs

——— End of log from Wed Jun 5 18:53:19 2024 ———

opened ChimeraX session  

> open
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/pdbfiles/SAMHD1_peptide.pdb

Chain information for SAMHD1_peptide.pdb #5  
---  
Chain | Description  
B | No description available  
  

> hide #5 models

> show #5 models

> color #5 goldenrod

> show #5 atoms

> hide #5#!2 atoms

> show #5#!2 atoms

> hide #5#!2 atoms

> show #5 atoms

> style #5#!2 sphere

Changed 19354 atom styles  

> select add #5

729 atoms, 736 bonds, 44 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,146.55,0,1,0,-119.32,0,0,1,200.06

> view matrix models #5,1,0,0,236.14,0,1,0,-3.343,0,0,1,235.77

> select subtract #5

Nothing selected  

> hide #5 models

> save
> C:/Users/andrea.graziadei/Documents/Training/EMBO_tutorial/EMBO_tutorial/session.cxs

——— End of log from Wed Jun 5 23:00:51 2024 ———

opened ChimeraX session  

> show #!1 models

> hide #!2 models

> show #!3 models

> ui tool show XMAS

Traceback (most recent call last):  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\\__init__.py", line 54, in <module>  
from pandas.compat import (  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\compat\\__init__.py", line 26, in <module>  
from pandas.compat.numpy import is_numpy_dev  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\compat\numpy\\__init__.py", line 21, in <module>  
raise ImportError(  
ImportError: this version of pandas is incompatible with numpy < 1.22.4  
your numpy version is 1.22.1.  
Please upgrade numpy to >= 1.22.4 to use this pandas version  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 559, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1325, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\\__init__.py", line 42, in start_tool  
from . import tool  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 16, in <module>  
from .info_file import InfoFile  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\info_file.py", line 16, in <module>  
import pandas as pd  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\\__init__.py", line 59, in <module>  
raise ImportError(  
ImportError: C extension: None not built. If you want to import pandas from
the source directory, you may need to run 'python setup.py build_ext' to build
the C extensions first.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 1685, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\cmd.py",
line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show XMAS

Traceback (most recent call last):  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\\__init__.py", line 54, in <module>  
from pandas.compat import (  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\compat\\__init__.py", line 26, in <module>  
from pandas.compat.numpy import is_numpy_dev  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\compat\numpy\\__init__.py", line 21, in <module>  
raise ImportError(  
ImportError: this version of pandas is incompatible with numpy < 1.22.4  
your numpy version is 1.22.1.  
Please upgrade numpy to >= 1.22.4 to use this pandas version  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 559, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1325, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\\__init__.py", line 42, in start_tool  
from . import tool  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\tool.py", line 16, in <module>  
from .info_file import InfoFile  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\chimerax\xmas\info_file.py", line 16, in <module>  
import pandas as pd  
File "C:\Users\mpk02\AppData\Local\UCSF\ChimeraX\1.4\site-
packages\pandas\\__init__.py", line 59, in <module>  
raise ImportError(  
ImportError: C extension: None not built. If you want to import pandas from
the source directory, you may need to run 'python setup.py build_ext' to build
the C extensions first.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\gui.py",
line 1685, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-packages\chimerax\ui\cmd.py",
line 219, in ui_tool_show  
bi.start_tool(session, name)  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool XMAS in
bundle ChimeraX-XMAS:  
C extension: None not built. If you want to import pandas from the source
directory, you may need to run 'python setup.py build_ext' to build the C
extensions first.  
  
File "C:\Program Files\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 564, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 31.0.101.4502
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_IN.cp1252
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows

Manufacturer: LENOVO
Model: 82RK
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 16,890,978,304
MaxProcessMemory: 137,438,953,344
CPU: 12 12th Gen Intel(R) Core(TM) i7-1255U
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-XMAS: 1.1.2
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    et-xmlfile: 1.1.0
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.26.4
    openpyxl: 3.1.3
    openvr: 1.16.802
    packaging: 21.3
    pandas: 2.2.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pywin32: 303
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    QtRangeSlider: 0.1.5
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    seaborn: 0.13.2
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    tzdata: 2024.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 18 months ago

Component:	Unassigned → Third Party
Owner:	set to Utz Ermel
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → ArtiaX/pandas vs. numpy

comment:2 by Eric Pettersen, 18 months ago

Resolution:	→ limitation
Status:	assigned → closed

User needs to upgrade version of ChimeraX

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