ChargeError during dockprep

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7.dev202305102306 (2023-05-10 23:06:58 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7.dev202305102306 (2023-05-10)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "E:\Research\Tomato\Alphafold\3D without SS1.pdb" format pdb

Chain information for 3D without SS1.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open C:/Users/zawar/Downloads/4802.mol

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> ui tool show "Build Structure"

> select ::name="UNL"

75 atoms, 78 bonds, 1 residue, 1 model selected  

> ui tool show "Build Structure"

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
3D without SS1.pdb #1/A SER 302: phi -83.2, psi none trans  
Applying SER rotamer (chi angles: 65.3) to 3D without SS1.pdb #1/A SER 302  
Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Termini for 3D without SS1.pdb (#1) chain A determined from SEQRES
records  
Chain-initial residues that are actual N termini: 3D without SS1.pdb #1/A GLU
1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: 3D without SS1.pdb #1/A SER
302  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue 3D without SS1.pdb #1/A SER 302  
288 hydrogen bonds  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
0 hydrogen bonds  
2245 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue UNL (net charge +0) with am1-bcc method  
Running ANTECHAMBER command: C:/Program
Files/ChimeraX/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\zawar\AppData\Local\Temp\tmp2ztdg6i9\ante.in.mol2 -fi mol2 -o
C:\Users\zawar\AppData\Local\Temp\tmp2ztdg6i9\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(UNL) ``  
(UNL) `Welcome to antechamber 20.0: molecular input file processor.`  
(UNL) ``  
(UNL) `Info: Finished reading file
(C:\Users\zawar\AppData\Local\Temp\tmp2ztdg6i9\ante.in.mol2); atoms read (76),
bonds read (80).`  
(UNL) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/bondtype" -j part
-i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) ``  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
(UNL) `Info: Total number of electrons: 298; net charge: 0`  
(UNL) ``  
(UNL) `Running: "C:/Program Files/ChimeraX/bin/amber20/bin/sqm" -O -i sqm.in
-o sqm.out`  
(UNL) `bash.exe: warning: could not find /tmp, please create!`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =107
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-07 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-05
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      202
    | QMMM:    diag iterations used for timing =        4
    | QMMM:
    | QMMM:              Internal diag routine = 0.058927 seconds
    | QMMM:                 Dspev diag routine = 0.038570 seconds
    | QMMM:                Dspevd diag routine = 0.033331 seconds
    | QMMM:                Dspevx diag routine = 0.145253 seconds
    | QMMM:                 Dsyev diag routine = 0.050358 seconds
    | QMMM:                Dsyevd diag routine = 0.033006 seconds
    | QMMM:                Dsyevr diag routine = 0.037558 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.024401 seconds
    | QMMM:
    | QMMM: Using dsyevd routine (diag_routine=6).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      C        2.9820   -3.8740    0.0150
      QMMM:     2        2      N        4.2720   -3.7190    0.0550
      QMMM:     3        3      C        4.4840   -2.3650    0.0650
      QMMM:     4        4      C        3.1840   -1.7000    0.0330
      QMMM:     5        5      C        2.2060   -2.6200    0.0060
      QMMM:     6        6      N        7.1510   -3.6790    0.0830
      QMMM:     7        7      C        8.4770   -3.8710    0.0500
      QMMM:     8        8      C        9.1770   -2.6550    0.0470
      QMMM:     9        9      C        8.1820   -1.6330    0.0740
      QMMM:    10       10      C        6.9730   -2.3480    0.0840
      QMMM:    11       11      N        4.2550   -6.5900    0.0300
      QMMM:    12       12      C        2.9220   -6.3350   -0.0010
      QMMM:    13       13      C        2.2270   -7.6150   -0.0130
      QMMM:    14       14      C        3.1550   -8.5870    0.0020
      QMMM:    15       15      C        4.4680   -7.9320    0.0260
      QMMM:    16       16      C        8.4460   -6.3770   -0.0210
      QMMM:    17       17      N        7.0950   -6.6040    0.0370
      QMMM:    18       18      C        6.9410   -7.9000    0.0260
      QMMM:    19       19      C        8.2030   -8.6720   -0.0370
      QMMM:    20       20      C        9.1020   -7.6760   -0.1200
      QMMM:    21       21      C        5.6700   -1.7370    0.0820
      QMMM:    22       22      C        2.2540   -5.1650   -0.0190
      QMMM:    23       23      C        9.0710   -5.1860   -0.0070
      QMMM:    24       24      C        2.9250   -0.2790    0.0340
      QMMM:    25       25      C        8.3830   -0.1590    0.0650
      QMMM:    26       26      C        2.9120    0.4550   -1.0840
      QMMM:    27       27      C        2.9080  -10.0660   -0.0300
      QMMM:    28       28      C        2.5810  -10.6710    1.3350
      QMMM:    29       29      C        3.7480  -10.6370    2.2860
      QMMM:    30       30      O        3.8740   -9.8440    3.2060
      QMMM:    31       31      O        4.6330  -11.6270    2.0120
      QMMM:    32       32      C        8.3940  -10.1520   -0.0970
      QMMM:    33       33      C        9.4610  -10.6860    0.8680
      QMMM:    34       34      C        8.9330  -11.8260    1.6980
      QMMM:    35       35      O        8.7670  -12.9660    1.2900
      QMMM:    36       36      O        8.6970  -11.4340    2.9750
      QMMM:    37       37      C        0.7300   -2.4960   -0.0150
      QMMM:    38       38      C       10.5870   -2.4670    0.0100
      QMMM:    39       39      C       11.2960   -2.3820   -1.1220
      QMMM:    40       40      C       10.5750   -7.8290   -0.3090
      QMMM:    41       41      C        0.7400   -7.7360   -0.0310
      QMMM:    42       42      C        5.6320   -8.6150    0.0320
      QMMM:    43       43      H        1.1720   -5.1270   -0.0580
      QMMM:    44       44      H        5.6650   -0.6480    0.0800
      QMMM:    45       45      H        2.7470    0.1880    0.9980
      QMMM:    46       46      H        0.2940   -2.9970    0.8560
      QMMM:    47       47      H        0.4050   -1.4520    0.0110
      QMMM:    48       48      H        0.3150   -2.9500   -0.9210
      QMMM:    49       49      H       10.1580   -5.1920   -0.0410
      QMMM:    50       50      H       11.1020   -2.3470    0.9600
      QMMM:    51       51      H        9.4450    0.1060    0.0530
      QMMM:    52       52      H        7.9200    0.2840   -0.8230
      QMMM:    53       53      H        7.9370    0.2970    0.9550
      QMMM:    54       54      H        0.3040   -7.2200    0.8320
      QMMM:    55       55      H        0.3280   -7.2890   -0.9420
      QMMM:    56       56      H        0.4030   -8.7740    0.0100
      QMMM:    57       57      H        2.0590  -10.2650   -0.6970
      QMMM:    58       58      H        3.7420  -10.6040   -0.4900
      QMMM:    59       59      H        5.6470   -9.6940    0.0260
      QMMM:    60       60      H        7.4520  -10.6740    0.0880
      QMMM:    61       61      H        8.6770  -10.4190   -1.1230
      QMMM:    62       62      H       10.9540   -7.1310   -1.0620
      QMMM:    63       63      H       11.1040   -7.6500    0.6330
      QMMM:    64       64      H       10.8430   -8.8300   -0.6600
      QMMM:    65       65      H        3.0910    0.0110   -2.0590
      QMMM:    66       66      H        2.7240    1.5220   -1.0380
      QMMM:    67       67      H        1.7400  -10.1470    1.8040
      QMMM:    68       68      H        2.2710  -11.7160    1.2120
      QMMM:    69       69      H        5.0400  -11.9890    2.8270
      QMMM:    70       70      H       10.3150  -11.0720    0.2980
      QMMM:    71       71      H        9.8480   -9.9110    1.5380
      QMMM:    72       72      H        7.8720  -10.9100    3.0590
      QMMM:    73       73      H       10.8280   -2.4760   -2.0960
      QMMM:    74       74      H       12.3660   -2.2070   -1.0870
      QMMM:    75       75      H        6.4330   -4.3900    0.1040
      QMMM:    76       76      H        4.9800   -5.8870    0.0540
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10       47.8732 kcal/mol        4.3009 kcal/(mol*A)
    xmin    20       44.8747 kcal/mol        0.9465 kcal/(mol*A)
    xmin    30       44.4266 kcal/mol        0.8495 kcal/(mol*A)
    xmin    40       43.6409 kcal/mol        1.4202 kcal/(mol*A)
    xmin    50       42.5844 kcal/mol        0.3768 kcal/(mol*A)
    xmin    60       42.1693 kcal/mol        0.2849 kcal/(mol*A)
    xmin    70       41.9279 kcal/mol        0.8590 kcal/(mol*A)
    xmin    80       41.7151 kcal/mol        0.6714 kcal/(mol*A)
    xmin    90       41.4603 kcal/mol        0.3718 kcal/(mol*A)
    xmin   100       41.2071 kcal/mol        0.4804 kcal/(mol*A)
    xmin   110       40.6994 kcal/mol        0.9720 kcal/(mol*A)
    xmin   120       39.8778 kcal/mol        1.0044 kcal/(mol*A)
    

  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\tool.py", line 263, in add_charges  
add_nonstandard_res_charges(self.session, residues, charge, method=method)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 319, in
add_nonstandard_res_charges  
nonstd_charge(session, tautomer_residues, net_charge, method, status=status)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 618, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
chimerax.add_charge.charge.ChargeError: Failure running ANTECHAMBER for
residue UNL  
Check reply log for details  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\add_charge\charge.py", line 618, in nonstd_charge  
raise ChargeError(ante_failure_msg)  
  
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_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: HP
Model: HP Laptop 15-dw3xxx
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 16,907,886,592
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.11
    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: 1.45.5
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.2
    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: 1.7.dev202305102306
    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: 1.1.2
    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: 1.2
    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: 2.1
    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: 1.10.2
    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: 1.11.1
    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: 1.2.2
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.1
    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
    comtypes: 1.1.14
    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: 4.39.4
    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
    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: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    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
    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
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    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
    WMI: 1.5.1
    zipp: 3.15.0