The following bug report has been submitted:
Platform: Linux-5.8.0-45-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Error occurs when I was following the ChimeraX webminar.
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3
Installed ChimeraX-AddH (2.1.3)
Installed ChimeraX-HKCage (1.3)
> open 7kkj
Summary of feedback from opening 7kkj fetched from pdb
---
notes | Fetching compressed mmCIF 7kkj from
http://files.rcsb.org/download/7kkj.cif
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif
7kkj title:
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]
Chain information for 7kkj #1
---
Chain | Description
A C | Synthetic nanobody mNb6
Non-standard residues in 7kkj #1
---
CL — chloride ion
SO4 — sulfate ion
7kkj mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> select /A:1-118
1762 atoms, 1781 bonds, 118 residues, 1 model selected
> select /C:1-119
1769 atoms, 1788 bonds, 119 residues, 1 model selected
> select :CL
1 atom, 1 residue, 1 model selected
> select :CL
1 atom, 1 residue, 1 model selected
> select :CL
1 atom, 1 residue, 1 model selected
> show sel atoms
> select :SO4
20 atoms, 16 bonds, 4 residues, 1 model selected
> sym #1 assembly 1
> view
> sym #1 assembly 2
> view
> close #2
> close #3
> show #1 models
> hide #1 models
> show #1 models
> show sel atoms
> select clear
> show atoms
> hide atoms
> style sphere
Changed 3683 atom styles
> show atoms
> lighting soft
> hide atoms
> lighting simple
> color yellow
> undo
> color bychain
> select clear
> color bychain
> rainbow
> hide atoms
> show cartoons
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> preset cartoons/nucleotides cylinders/stubs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> show surfaces
> lighting soft
> coulombic
Atoms with non-standard names found in standard residues: /A CYS 96 HG and /A
CYS 22 HG. Try deleting all hydrogens first.
> coulombic
Atoms with non-standard names found in standard residues: /A CYS 96 HG and /A
CYS 22 HG. Try deleting all hydrogens first.
> delete H
> coulombic
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics: /C SER 119 OG
> mlp
Map values for surface "7kkj_A SES surface": minimum -26.2, mean -6.039,
maximum 19.75
Map values for surface "7kkj_C SES surface": minimum -25.35, mean -5.999,
maximum 20.09
> color bfactor
1945 atoms, 373 residues, 2 surfaces, atom bfactor range 18.9 to 86.1
> hide surfaces
> show cartoons
> select /C:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /C:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /C:64
7 atoms, 6 bonds, 1 residue, 1 model selected
Drag select of 13 residues
> select /C:64
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /C:62
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:63
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
30 atoms, 29 bonds, 4 residues, 2 models selected
> mlp sel
Map values for surface "7kkj_C SES surface": minimum -25.35, mean -5.999,
maximum 20.09
> mlp sel
Map values for surface "7kkj_C SES surface": minimum -25.35, mean -5.999,
maximum 20.09
> color sel bychain
> hide sel surfaces
> show sel surfaces
> mlp sel
Map values for surface "7kkj_C SES surface": minimum -25.35, mean -5.999,
maximum 20.09
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> show sel surfaces
> hide sel cartoons
> hide sel atoms
> hide sel surfaces
> style sel sphere
Changed 62 atom styles
> preset "initial styles" "original look"
Preset implemented in Python; no expansion to individual ChimeraX commands
available.
> select up
98 atoms, 97 bonds, 15 residues, 2 models selected
> select up
974 atoms, 925 bonds, 186 residues, 2 models selected
> select down
98 atoms, 97 bonds, 15 residues, 2 models selected
> select up
974 atoms, 925 bonds, 186 residues, 2 models selected
> select down
98 atoms, 97 bonds, 15 residues, 2 models selected
> select up
974 atoms, 925 bonds, 186 residues, 2 models selected
> select down
98 atoms, 97 bonds, 15 residues, 2 models selected
> select up
974 atoms, 925 bonds, 186 residues, 2 models selected
> select up
1945 atoms, 1847 bonds, 373 residues, 2 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> log metadata #1
Metadata for 7kkj #1
---
Title | Structure of anti-SARS-CoV-2 Spike nanobody mNb6
Citation | Schoof, M., Faust, B., Saunders, R.A., Sangwan, S., Rezelj, V.,
Hoppe, N., Boone, M., Billesbolle, C.B., Puchades, C., Azumaya, C.M.,
Kratochvil, H.T., Zimanyi, M., Deshpande, I., Liang, J., Dickinson, S.,
Nguyen, H.C., Chio, C.M., Merz, G.E., Thompson, M.C., Diwanji, D., Schaefer,
K., Anand, A.A., Dobzinski, N., Zha, B.S., Simoneau, C.R., Leon, K., White,
K.M., Chio, U.S., Gupta, M., Jin, M., Li, F., Liu, Y., Zhang, K., Bulkley, D.,
Sun, M., Smith, A.M., Rizo, A.N., Moss, F., Brilot, A.F., Pourmal, S.,
Trenker, R., Pospiech, T., Gupta, S., Barsi-Rhyne, B., Belyy, V., Barile-Hill,
A.W., Nock, S., Liu, Y., Krogan, N.J., Ralston, C.Y., Swaney, D.L., Garcia-
Sastre, A., Ott, M., Vignuzzi, M., Walter, P., Manglik, A. (2020). An
ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive
Spike. Science, 370, 1473-1479. PMID: 33154106. DOI: 10.1126/science.abe3255
Non-standard residues | CL — chloride ion
SO4 — sulfate ion
Gene source | synthetic construct
Experimental method | X-ray diffraction
Resolution | 2.05Å
> open 7kkj fromDatabase eds
Summary of feedback from opening 7kkj fetched from eds
---
note | Fetching map 7kkj from
http://www.ebi.ac.uk/pdbe/coordinates/files/7kkj.ccp4
Opened 7kkj.ccp4, grid size 118,103,128, pixel 0.619,0.594,0.611, shown at
level 1.16, step 1, values float32
> color sel byhetero
> volume showOutlineBox true
> volume zone #2 nearAtoms #1
> volume showOutlineBox false
> volume #2 level 0.7315
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting simple
> ui mousemode right clip
> ui mousemode right clip
Drag select of 79 atoms, 177 residues, 67 bonds, 2 eds 7kkj
> help volume zone
> show sel atoms
> hide sel cartoons
> hide sel surfaces
> close
> open 7kkl
Summary of feedback from opening 7kkl fetched from pdb
---
notes | Fetching compressed mmCIF 7kkl from
http://files.rcsb.org/download/7kkl.cif
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif
7kkl title:
SARS-CoV-2 Spike in complex with neutralizing nanobody mNb6 [more info...]
Chain information for 7kkl #1
---
Chain | Description
A C D | Spike glycoprotein
B E F | Synthetic nanobody mNb6
Non-standard residues in 7kkl #1
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> color yellow
> undo
> color /B,E,F gold
> set bgColor white
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> save /home/simeons/Desktop/image1.png supersample 3
> save spike.pdf width 1500
No known data format for file suffix '.pdf'
> open /home/simeons/Downloads/emd_22910_trimmed.mrc
Opened emd_22910_trimmed.mrc, grid size 109,109,151, pixel 1.67,1.67,1.67,
shown at level 3.56, step 1, values float32
> hide #!1 models
> open 6vxx
Summary of feedback from opening 6vxx fetched from pdb
---
note | Fetching compressed mmCIF 6vxx from
http://files.rcsb.org/download/6vxx.cif
6vxx title:
Structure of the SARS-CoV-2 spike glycoprotein (closed state) [more info...]
Chain information for 6vxx #3
---
Chain | Description
A B C | Spike glycoprotein
Non-standard residues in 6vxx #3
---
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
> hide #!3 cartoons
> show #!3 atoms
> style #!3 sphere
Changed 23694 atom styles
> select #3/B:557@O
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> select #3/C:125@CG
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> lighting simple
> set bgColor black
> select clear
> select #3/C:213@CB
1 atom, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "translate selected models"
> select clear
> ui mousemode right "translate selected models"
> ui tool show "Fit in Map"
Fit molecule 6vxx (#3) to map emd_22910_trimmed.mrc (#2) using 23694 atoms
average map value = 0.7506, steps = 216
shifted from previous position = 53.8
rotated from previous position = 3.54 degrees
atoms outside contour = 22045, contour level = 3.555
Position of 6vxx (#3) relative to emd_22910_trimmed.mrc (#2) coordinates:
Matrix rotation and translation
0.99894283 0.04136371 0.02005664 -53.66760554
-0.04050105 0.99831054 -0.04166214 -16.05251636
-0.02174605 0.04080578 0.99893043 -12.83615854
Axis 0.66779997 0.33850536 -0.66291577
Axis point 0.00000000 842.81828800 -153.27356834
Rotation angle (degrees) 3.54003564
Shift along axis -32.76379637
Fit molecule 6vxx (#3) to map emd_22910_trimmed.mrc (#2) using 23694 atoms
average map value = 0.7506, steps = 40
shifted from previous position = 0.00393
rotated from previous position = 0.00989 degrees
atoms outside contour = 22045, contour level = 3.555
Position of 6vxx (#3) relative to emd_22910_trimmed.mrc (#2) coordinates:
Matrix rotation and translation
0.99893541 0.04149569 0.02015347 -53.71162630
-0.04063012 0.99830745 -0.04161039 -16.03256607
-0.02184601 0.04074725 0.99893063 -12.80132871
Axis 0.66600958 0.33964131 -0.66413480
Axis point 0.00000000 843.39417278 -152.56660834
Rotation angle (degrees) 3.54481148
Shift along axis -32.71597132
> color #!3 bychain
> volume #2 level 1.174
> volume #2 level 3.325
> color zone #2 near #3
> hide #!3 models
> lighting soft
> color zone #2 near #3 distance 6
> open 7kkj
7kkj title:
Structure of anti-SARS-CoV-2 Spike nanobody mNb6 [more info...]
Chain information for 7kkj #4
---
Chain | Description
A C | Synthetic nanobody mNb6
Non-standard residues in 7kkj #4
---
CL — chloride ion
SO4 — sulfate ion
7kkj mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> volume #2 level 5.477
> volume #2 level 0.3128
> select #4/C
1841 atoms, 1792 bonds, 187 residues, 1 model selected
> volume #2 level 1.633
> hide sel atoms
> show sel cartoons
> hide sel atoms
> show sel cartoons
> delete atoms sel
> delete bonds sel
> show #!1 models
> hide #!2 models
> ui tool show Matchmaker
> matchmaker #4/A to #1/B pairing ss
Parameters
---
Chain pairing | ss
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 7kkl, chain B (#1) with 7kkj, chain A (#4), sequence alignment
score = 589.7
RMSD between 90 pruned atom pairs is 0.751 angstroms; (across all 117 pairs:
3.062)
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
> hide #4#!1 atoms
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
Error processing trigger "changes":
RuntimeError: wrapped C/C++ object of type ChainMenuButton has been deleted
File "/usr/lib/ucsf-chimerax/lib/python3.7/site-
packages/chimerax/ui/widgets/item_chooser.py", line 305, in _items_change
if not hasattr(self, '_recursion'):
See log for complete Python traceback.
OpenGL version: 4.5 (Core Profile) Mesa 20.2.6
OpenGL renderer: AMD OLAND (DRM 2.50.0, 5.8.0-45-generic, LLVM 11.0.0)
OpenGL vendor: X.Org
Manufacturer: Dell Inc.
Model: Precision Tower 7910
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
CPU: 40 Intel(R) Xeon(R) CPU E5-2650 v3 @ 2.30GHz
Cache Size: 25600 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 8.6Gi 30Gi 860Mi 23Gi 52Gi
Swap: 63Gi 0B 63Gi
Graphics:
03:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Oland GL [FirePro W2100] [1002:6608]
Subsystem: Dell Oland GL [FirePro W2100] [1028:2120]
Kernel driver in use: radeon
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
ptyprocess: 0.6.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Hi Saw,
--Eric