Coulombic failure with UNK chains

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/niu/Downloads/5lc5.pdb

5lc5.pdb title:  
Structure of mammalian respiratory complex I, CLASS2 [more info...]  
  
Chain information for 5lc5.pdb #1  
---  
Chain | Description | UniProt  
A | NADH dehydrogenase subunit 3 | NU3M_BOVIN  
B | nadh dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial |
NDUS7_BOVIN  
C | nadh dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial |
NDUS3_BOVIN  
D | nadh dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial |
NDUS2_BOVIN  
E | nadh dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial |
NDUV2_BOVIN  
F | nadh dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial |
NDUV1_BOVIN  
G | nadh-ubiquinone oxidoreductase 75 kda subunit, mitochondrial,nadh-
ubiquinone oxidoreductase 75 kda subunit, mitochondrial,nadh-ubiquinone
oxidoreductase 75 kda subunit, mitochondrial,nadh-ubiquinone oxidoreductase 75
kda subunit, NDUFS1 | NDUS1_BOVIN  
H | NADH dehydrogenase subunit 1 | NU1M_BOVIN  
I | nadh dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial |
NDUS8_BOVIN  
J | NADH dehydrogenase subunit 6 | NU6M_BOVIN  
K | NADH dehydrogenase subunit 4L | NU4LM_BOVIN  
L | NADH dehydrogenase subunit 5 | NU5M_BOVIN  
M | NADH dehydrogenase subunit 4 | NU4M_BOVIN  
N | NADH dehydrogenase subunit 2 | NU2M_BOVIN  
O | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, NDUFA10,nadh
dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial,nadh
dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial,nadh
dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial |
NDUAA_BOVIN  
P | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial |  
Q | nadh dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial |  
R | nadh dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,nadh
dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,nadh
dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial,nadh
dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial | NDUS6_BOVIN  
S | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 2 | NDUA2_BOVIN  
T | acyl carrier protein, mitochondrial | ACPM_BOVIN  
U | acyl carrier protein, mitochondrial | ACPM_BOVIN  
V | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 5 | NDUA5_BOVIN  
W | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 6 | NDUA6_BOVIN  
X | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 8,nadh
dehydrogenase [ubiquinone] 1 α subcomplex subunit 8,nadh dehydrogenase
[ubiquinone] 1 α subcomplex subunit 8,nadh dehydrogenase [ubiquinone] 1 α
subcomplex subunit 8 | NDUA8_BOVIN  
Y | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 11 | NDUAB_BOVIN  
Z | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 13,nadh
dehydrogenase [ubiquinone] 1 α subcomplex subunit 13,nadh dehydrogenase
[ubiquinone] 1 α subcomplex subunit 13,nadh dehydrogenase [ubiquinone] 1 α
subcomplex subunit 13,nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit
13,nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 13,nadh
dehydrogenase [ubiquinone] 1 α subcomplex subunit 13 | NDUAD_BOVIN  
a | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 1 | NDUA1_BOVIN  
b | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 3,nadh
dehydrogenase [ubiquinone] 1 α subcomplex subunit 3,nadh dehydrogenase
[ubiquinone] 1 α subcomplex subunit 3 | NDUA3_BOVIN  
c | nadh dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial | NDUC1_BOVIN  
d | nadh dehydrogenase [ubiquinone] 1 subunit C2,nadh dehydrogenase
[ubiquinone] 1 subunit C2,nadh dehydrogenase [ubiquinone] 1 subunit C2,nadh
dehydrogenase [ubiquinone] 1 subunit C2,nadh dehydrogenase [ubiquinone] 1
subunit C2,nadh dehydrogenase [ubiquinone] 1 subunit C2,nadh dehydrogenase
[ubiquinone] 1 subunit C2 | NDUC2_BOVIN  
e | nadh dehydrogenase [ubiquinone] iron-sulfur protein 5 | NDUS5_BOVIN  
f | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 1 | NDUB1_BOVIN  
g | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial |
NDUBB_BOVIN  
h | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 5,
mitochondrial,nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 5,
mitochondrial,nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 5,
mitochondrial,nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 5,
mitochondrial | NDUB5_BOVIN  
i | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 6,nadh
dehydrogenase [ubiquinone] 1 β subcomplex subunit 6,nadh dehydrogenase
[ubiquinone] 1 β subcomplex subunit 6,nadh dehydrogenase [ubiquinone] 1 β
subcomplex subunit 6 | NDUB6_BOVIN  
j | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, NDUFB2 |  
k | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 3, NDUFB3 |  
l | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, NDUFB8 |  
m | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 4,nadh
dehydrogenase [ubiquinone] 1 β subcomplex subunit 4,nadh dehydrogenase
[ubiquinone] 1 β subcomplex subunit 4,nadh dehydrogenase [ubiquinone] 1 β
subcomplex subunit 4 | NDUB4_BOVIN  
n | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 9,nadh
dehydrogenase [ubiquinone] 1 β subcomplex subunit 9,nadh dehydrogenase
[ubiquinone] 1 β subcomplex subunit 9,nadh dehydrogenase [ubiquinone] 1 β
subcomplex subunit 9 | NDUB9_BOVIN  
o | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 7 | NDUB7_BOVIN  
p | nadh dehydrogenase [ubiquinone] 1 β subcomplex subunit 10, NDUFB10,nadh
dehydrogenase [ubiquinone] 1 β subcomplex subunit 10,nadh dehydrogenase
[ubiquinone] 1 β subcomplex subunit 10, NDUFB10 | NDUBA_BOVIN  
q | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 12 | NDUAC_BOVIN  
r | nadh dehydrogenase [ubiquinone] 1 α subcomplex subunit 7, NDUFA7 |  
s | nadh dehydrogenase [ubiquinone] flavoprotein 3, NDUFV3 |  
  
Non-standard residues in 5lc5.pdb #1  
---  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> surface

> hide target a

> ui tool show "Color Actions"

> set bgColor white

> ui tool show "Color Actions"

> color bychain

> color bypolymer

> color byhetero

[Repeated 1 time(s)]

> color byelement

> color byhetero

> color bynucleotide

> color bychain

> color bypolymer

> ui tool show "Color Actions"

> save /Users/niu/Downloads/5lc5.tif width 2000 height 1704 supersample 3

> rainbow

> save /Users/niu/Downloads/5lc5-1.tif width 2000 height 1704 supersample 3
> transparentBackground true

> save /Users/niu/Downloads/5lc5-1.tif width 797 height 679 supersample 3

> color byhetero

[Repeated 1 time(s)]

> color bychain

> save /Users/niu/Downloads/5lc5-2.tif width 797 height 679 supersample 3

> save /Users/niu/Downloads/5lc5-2.tif width 2000 height 1704 supersample 4
> transparentBackground true

> color bypolymer

> save /Users/niu/Downloads/5lc5.tif width 2000 height 1704 supersample 3
> transparentBackground true

> color byhetero

> color bychain

> rainbow

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/toolbar/tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 381, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1284, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/__init__.py", line 52, in run_provider  
shortcuts.run_provider(session, name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 1334, in run_provider  
keyboard_shortcuts(session).try_shortcut(name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 390, in try_shortcut  
self.run_shortcut(keys)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 408, in run_shortcut  
sc.run(self.session, status = self._enabled)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 327, in run  
f(s)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 61, in func_plus_tip  
func(cmd + " %s")(session)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 569, in run_expanded_command  
run(session, cmd)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/shortcuts/shortcuts.py", line 512, in run  
run_command(session, command, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/coulombic/coulombic.py", line 99, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 23, in add_charges  
uncharged_res_types = add_standard_charges(session, residues, status=status,
query_user=query_user,  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 186, in add_standard_charges  
fr = FakeRes(connected)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 775, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
ValueError: Could not come up with unique atom name in mega-residue  
  
ValueError: Could not come up with unique atom name in mega-residue  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 775, in __init__  
raise ValueError("Could not come up with unique atom name in mega-residue")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 10
      L2 Cache: 20 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 1 day 20:11

Graphics/Displays:

    Apple G13X:

      Chipset Model: Apple G13X
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      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: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    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
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
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    imagesize: 1.3.0
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    lxml: 4.6.3
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    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
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    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
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    requests: 2.26.0
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    sfftk-rw: 0.7.1
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    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0