SEQCROW: numpy error testing file readers

[andreapellegrini6698@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Can't visualise the normal mode.

Log:
> setattr a radius 1

Assigning radius attribute to 0 items  
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  
Successfully installed 'SEQCROW==1.8'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Collecting SEQCROW==1.8  
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/seqcrow/releases/1.8/SEQCROW-1.8-py3-none-
any.whl (3.3 MB)  
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.3/3.3 MB 1.4 MB/s eta 0:00:00  
Requirement already satisfied: scipy in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.8) (1.9.3)  
Requirement already satisfied: Send2Trash in /Users/andrea/Library/Application
Support/ChimeraX/1.6/site-packages (from SEQCROW==1.8) (1.8.0)  
Requirement already satisfied: jinja2 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.8) (3.1.2)  
Requirement already satisfied: ChimeraX-Core<=1.7,>=1.3 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.8) (1.6.1)  
Requirement already satisfied: psutil in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from SEQCROW==1.8) (5.9.4)  
Requirement already satisfied: MarkupSafe>=2.0 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from jinja2->SEQCROW==1.8) (2.1.2)  
Requirement already satisfied: numpy<1.26.0,>=1.18.5 in
/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from scipy->SEQCROW==1.8) (1.23.5)  
Installing collected packages: SEQCROW  
Attempting uninstall: SEQCROW  
Found existing installation: SEQCROW 1.7.3  
Uninstalling SEQCROW-1.7.3:  
Successfully uninstalled SEQCROW-1.7.3  
Successfully installed SEQCROW-1.8  
  

  
[notice] A new release of pip is available: 23.0 -> 23.2.1  
[notice] To update, run:
/Applications/ChimeraX-1.6.1.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip  
  

> open /Users/andrea/Desktop/scratch/berny_ts3.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/berny_ts3.out  
---  
notes | berny_ts3.out has 1 imaginary harmonic vibrational mode  
359.32i  
  
  
Opened berny_ts3.out as an ORCA output file  

> save /Users/andrea/Desktop/scratch/pre.xyz models #1

> save /Users/andrea/Desktop/scratch/post.xyz models #1

> open /Users/andrea/Desktop/scratch/post_ts1b.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/post_ts1b.out  
---  
notes | post_ts1b.out has 1 imaginary harmonic vibrational mode  
17.66i  
  
  
Opened post_ts1b.out as an ORCA output file  

> close #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
Error processing trigger "AaronTools file closed":  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
  
See log for complete Python traceback.  
  

> save /Users/andrea/Desktop/scratch/guess.xyz models #2

> close

> open /Users/andrea/Desktop/scratch/post_sn2.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/post_sn2.out  
---  
notes | post_sn2.out has 1 imaginary harmonic vibrational mode  
10.88i  
  
  
Opened post_sn2.out as an ORCA output file  

> save /Users/andrea/Desktop/scratch/guess.xyz models #1

> open /Users/andrea/Desktop/scratch/optf_ts4.out

Summary of feedback from opening /Users/andrea/Desktop/scratch/optf_ts4.out  
---  
notes | optf_ts4.out has 1 imaginary harmonic vibrational mode  
50.44i  
  
  
Opened optf_ts4.out as an ORCA output file  

> close #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
Error processing trigger "AaronTools file closed":  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
  
See log for complete Python traceback.  
  

> open /Users/andrea/Desktop/scratch/post_ts1b.out

Opened post_ts1b.out as an ORCA output file  

> close #2

> close

> open /Users/andrea/Desktop/scratch/post_ts1b.out format out

Opened post_ts1b.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/post_ts.2_post_sn2.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/post_ts.2_post_sn2.out  
---  
notes | post_ts.2_post_sn2.out has 1 imaginary harmonic vibrational mode  
11.09i  
  
  
Opened post_ts.2_post_sn2.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/post_ts.1_post_ts3.out

Opened post_ts.1_post_ts3.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/post_ts.2_post_ts1b.out

Opened post_ts.2_post_ts1b.out as an ORCA output file  

> close

> open /Users/andrea/Desktop/scratch/berny_ts.1_berny_ts4.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/berny_ts.1_berny_ts4.out  
---  
notes | berny_ts.1_berny_ts4.out has 2 imaginary harmonic vibrational modes  
66.28i  
1.53i  
  
  
Opened berny_ts.1_berny_ts4.out as an ORCA output file  

> save /Users/andrea/Desktop/scratch/guess.xyz models #1

> open /Users/andrea/Desktop/scratch/post_ts_post_ts3.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/post_ts_post_ts3.out  
---  
notes | post_ts_post_ts3.out has 1 imaginary harmonic vibrational mode  
9.53i  
  
  
Opened post_ts_post_ts3.out as an ORCA output file  

> close #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
Error processing trigger "AaronTools file closed":  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
  
See log for complete Python traceback.  
  

> close

> open /Users/andrea/Desktop/scratch/post_ts_post_ts3.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/post_ts_post_ts3.out  
---  
notes | post_ts_post_ts3.out has 1 imaginary harmonic vibrational mode  
9.53i  
  
  
Opened post_ts_post_ts3.out as an ORCA output file  

> save /Users/andrea/Desktop/scratch/guess.xyz models #1

> open /Users/andrea/Desktop/scratch/post_ts.3_post_sn2.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/post_ts.3_post_sn2.out  
---  
notes | post_ts.3_post_sn2.out has 1 imaginary harmonic vibrational mode  
11.16i  
  
  
Opened post_ts.3_post_sn2.out as an ORCA output file  

> close

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
Error processing trigger "AaronTools file closed":  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
  
See log for complete Python traceback.  
  

> open /Users/andrea/Desktop/scratch/post_ts.3_post_sn2.out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/post_ts.3_post_sn2.out  
---  
notes | post_ts.3_post_sn2.out has 1 imaginary harmonic vibrational mode  
11.16i  
  
  
Opened post_ts.3_post_sn2.out as an ORCA output file  
Traceback (most recent call last):  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/tools/normal_modes.py", line 693, in show_anim  
model.add_coordsets(coordsets, replace=True)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1662, in add_coordsets  
cs_size = self.coordset_size  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/tools/normal_modes.py", line 693, in show_anim  
model.add_coordsets(coordsets, replace=True)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1662, in add_coordsets  
cs_size = self.coordset_size  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
AttributeError: 'AtomicStructure' object has no attribute '_c_pointer_ref'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 95, in get_prop  
cget(self._c_pointer_ref, 1, v_ref)  
  
See log for complete Python traceback.  
  

> close

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
Error processing trigger "AaronTools file closed":  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
  
See log for complete Python traceback.  
  

> open /Users/andrea/Desktop/scratch/post_ts.3_post_sn2.out format out

Summary of feedback from opening
/Users/andrea/Desktop/scratch/post_ts.3_post_sn2.out  
---  
notes | post_ts.3_post_sn2.out has 1 imaginary harmonic vibrational mode  
11.16i  
  
  
Opened post_ts.3_post_sn2.out as an ORCA output file  

> close

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
Error processing trigger "AaronTools file closed":  
ValueError: The truth value of an array with more than one element is
ambiguous. Use a.any() or a.all()  
  
File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site-
packages/SEQCROW/widgets/comboboxes.py", line 162, in _del_filereaders  
if fr in filereaders:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: MKGP3T/A
      Chip: Unknown
      Total Number of Cores: 8 (6 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A5337a)
      Kernel Version: Darwin 23.0.0
      Time since boot: 5 days, 21 hours, 24 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL P2312H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60.00Hz
          Mirror: Off
          Online: Yes


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    argcomplete: 3.0.5
    asttokens: 2.2.1
    attrs: 22.2.0
    Babel: 2.12.1
    backcall: 0.2.0
    basis-set-exchange: 0.9
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jsonschema: 4.17.3
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    pyrsistent: 0.19.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    regex: 2023.3.23
    requests: 2.28.2
    scipy: 1.9.3
    Send2Trash: 1.8.0
    SEQCROW: 1.8
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Tony Schaefer]

Sorry about the delay, I've been a bit busy lately. I just uploaded a fix
for this to the toolshed.

On Thu, Sep 7, 2023 at 7:10 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

>
>
>