Accessing deleted widget

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 6733 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this.  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/andre/Jupyter/TRANSFFERRIN/TfR/TfR1_onechain.pdb

Chain information for TfR1_onechain.pdb #1  
---  
Chain | Description  
B | No description available  
  
7 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> ui tool show "Dock Prep"

QWindowsWindow::setGeometry: Unable to set geometry 779x857+1148+482 (frame:
801x913+1137+437) on QWidgetWindow/"QWidgetClassWindow" on "LQ145N1".
Resulting geometry: 775x848+1150+489 (frame: 797x904+1139+444) margins: 11,
45, 11, 11 minimum size: 519x545 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=801, y=874)))  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/B ARG 120: phi none, psi 115.4 trans  
/B ARG 121: phi -64.9, psi -39.5 trans  
/B ASP 204: phi -75.7, psi -176.3 trans  
/B LYS 205: phi -65.5, psi -26.5 trans  
/B ASN 206: phi -94.7, psi 4.3 trans  
/B ARG 208: phi -69.1, psi 149.7 trans  
/B LYS 241: phi -64.7, psi -38.7 trans  
/B GLU 244: phi -64.8, psi -42.3 trans  
/B ASP 245: phi -87.4, psi 24.3 trans  
/B TYR 247: phi -68.1, psi -48.5 trans  
/B ASP 356: phi -61.4, psi -31.6 trans  
/B LYS 358: phi -73.4, psi 70.9 trans  
/B GLU 369: phi -66.9, psi -16.7 trans  
/B ASP 560: phi -73.6, psi -16.3 trans  
/B GLU 578: phi -74.8, psi -42.8 trans  
/B GLU 582: phi 58.8, psi 41.7 trans  
/B GLU 606: phi -102.9, psi 150.3 trans  
/B GLU 664: phi -77.3, psi 131.6 trans  
/B GLU 714: phi -64.7, psi -42.4 trans  
/B LYS 720: phi -61.4, psi -42.3 trans  
/B GLN 721: phi -71.6, psi -11.5 trans  
/B ASN 722: phi 56.5, psi 37.1 trans  
/B ASN 723: phi -75.9, psi -15.9 trans  
/B ASN 758: phi -142.9, psi none trans  
Applying ARG rotamer (chi angles: -64.3 -80.3 78.7 -165.9) to /B ARG 120  
Applying ARG rotamer (chi angles: -178.3 -179.8 63.4 80.1) to /B ARG 121  
Applying ASP rotamer (chi angles: 68.3 15.8) to /B ASP 204  
Applying LYS rotamer (chi angles: -65.2 -62.0 -71.6 -176.1) to /B LYS 205  
Applying ASN rotamer (chi angles: 65.2 -4.5) to /B ASN 206  
Applying ARG rotamer (chi angles: -87.2 79.2 -84.3 -75.1) to /B ARG 208  
Applying LYS rotamer (chi angles: 179.8 -96.2 -71.1 178.0) to /B LYS 241  
Applying GLU rotamer (chi angles: -69.9 176.8 -8.7) to /B GLU 244  
Applying ASP rotamer (chi angles: 63.4 -3.8) to /B ASP 245  
Applying TYR rotamer (chi angles: 179.6 77.9) to /B TYR 247  
Applying ASP rotamer (chi angles: -71.8 -14.7) to /B ASP 356  
Applying LYS rotamer (chi angles: -83.7 68.8 178.6 177.8) to /B LYS 358  
Applying GLU rotamer (chi angles: 66.6 -85.0 17.8) to /B GLU 369  
Applying ASP rotamer (chi angles: -70.7 -16.3) to /B ASP 560  
Applying GLU rotamer (chi angles: -68.9 177.5 -9.2) to /B GLU 578  
Applying GLU rotamer (chi angles: -61.3 -176.5 -37.7) to /B GLU 582  
Applying GLU rotamer (chi angles: -64.5 -179.6 -7.3) to /B GLU 606  
Applying GLU rotamer (chi angles: -176.4 178.6 88.5) to /B GLU 664  
Applying GLU rotamer (chi angles: -178.0 65.6 20.3) to /B GLU 714  
Applying LYS rotamer (chi angles: -146.7 -61.9 97.2 56.3) to /B LYS 720  
Applying GLN rotamer (chi angles: -67.2 178.6 66.2) to /B GLN 721  
Applying ASN rotamer (chi angles: -64.1 164.7) to /B ASN 722  
Applying ASN rotamer (chi angles: -169.1 173.6) to /B ASN 723  
Applying ASN rotamer (chi angles: 68.9 101.9) to /B ASN 758  

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> ui tool show "Dock Prep"

QWindowsWindow::setGeometry: Unable to set geometry 779x857+1148+482 (frame:
801x913+1137+437) on QWidgetWindow/"QWidgetClassWindow" on "LQ145N1".
Resulting geometry: 775x848+1150+489 (frame: 797x904+1139+444) margins: 11,
45, 11, 11 minimum size: 519x545 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=801, y=874)))  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/B ASN 758: phi -142.9, psi none trans  
Applying ASN rotamer (chi angles: 68.9 101.9) to /B ASN 758  

QWindowsWindow::setGeometry: Unable to set geometry 533x384+1271+717 (frame:
555x440+1260+672) on QWidgetWindow/"QWidgetClassWindow" on "LQ145N1".
Resulting geometry: 529x375+1273+724 (frame: 551x431+1262+679) margins: 11,
45, 11, 11 minimum size: 338x230 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=529, y=401)))  

Summary of feedback from adding hydrogens to TfR1_onechain.pdb #1  
---  
notes | No usable SEQRES records for TfR1_onechain.pdb (#1) chain B; guessing termini instead  
Chain-initial residues that are actual N termini: /B ARG 120  
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: /B ASN 758  
613 hydrogen bonds  
/B ASN 758 is not terminus, removing H atom from 'C'  
5122 hydrogens added  
  

QWindowsWindow::setGeometry: Unable to set geometry 536x189+1269+815 (frame:
558x245+1258+770) on QWidgetWindow/"QWidgetClassWindow" on "LQ145N1".
Resulting geometry: 532x180+1271+822 (frame: 554x236+1260+777) margins: 11,
45, 11, 11 minimum size: 252x100 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=400, y=206)))  

Summary of feedback from adding hydrogens to TfR1_onechain.pdb #1  
---  
notes | No usable SEQRES records for TfR1_onechain.pdb (#1) chain B; guessing termini instead  
Chain-initial residues that are actual N termini: /B ARG 120  
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: /B ASN 758  
587 hydrogen bonds  
/B ASN 758 is not terminus, removing H atom from 'C'  
0 hydrogens added  
  

QWindowsWindow::setGeometry: Unable to set geometry 536x189+1269+815 (frame:
558x245+1258+770) on QWidgetWindow/"QWidgetClassWindow" on "LQ145N1".
Resulting geometry: 532x180+1271+822 (frame: 554x236+1260+777) margins: 11,
45, 11, 11 minimum size: 252x100 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=400, y=206)))  

Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  

QWindowsWindow::setGeometry: Unable to set geometry 960x531+1056+644 (frame:
982x587+1045+599) on QWidgetWindow/"QWidgetClassWindow" on "LQ145N1".
Resulting geometry: 956x522+1058+651 (frame: 978x578+1047+606) margins: 11,
45, 11, 11 minimum size: 640x354 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=982, y=587)))  

Assigning partial charges to residue NAG+ASN (net charge +0) with am1-bcc
method  
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.9/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\andre\AppData\Local\Temp\tmpb9ryg02z\ante.in.mol2 -fi mol2 -o
C:\Users\andre\AppData\Local\Temp\tmpb9ryg02z\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n  
(NAG+ASN) ``  
(NAG+ASN) `Welcome to antechamber 20.0: molecular input file processor.`  
(NAG+ASN) ``  
(NAG+ASN) `Info: Finished reading file
(C:\Users\andre\AppData\Local\Temp\tmpb9ryg02z\ante.in.mol2); atoms read (53),
bonds read (53).`  
(NAG+ASN) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(NAG+ASN) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/bondtype"
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAG+ASN) `bash.exe: warning: could not find /tmp, please create!`  
(NAG+ASN) ``  
(NAG+ASN) ``  
(NAG+ASN) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/atomtype"
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAG+ASN) `bash.exe: warning: could not find /tmp, please create!`  
(NAG+ASN) `Info: Total number of electrons: 208; net charge: 0`  
(NAG+ASN) ``  
(NAG+ASN) `Running: "C:/Program Files/ChimeraX 1.9/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`  
(NAG+ASN) `bash.exe: warning: could not find /tmp, please create!`  
(NAG+ASN) `/usr/bin/antechamber: Fatal Error!`  
(NAG+ASN) `Unable to find sqm charges in file (sqm.out).`  
(NAG+ASN) `Verify the filename and the file contents.`  
  
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 = 77
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: C : 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 =      134
    | QMMM:    diag iterations used for timing =       10
    | QMMM:
    | QMMM:              Internal diag routine = 0.030012 seconds
    | QMMM:                 Dspev diag routine = 0.021320 seconds
    | QMMM:                Dspevd diag routine = 0.016271 seconds
    | QMMM:                Dspevx diag routine = 0.127116 seconds
    | QMMM:                 Dsyev diag routine = 0.047784 seconds
    | QMMM:                Dsyevd diag routine = 0.027159 seconds
    | QMMM:                Dsyevr diag routine = 0.042565 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.012124 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      N       90.4320   91.3700  129.3110
      QMMM:     2        2      C       91.7310   91.8570  129.7490
      QMMM:     3        3      C       92.3110   90.8790  130.7580
      QMMM:     4        4      O       91.6020   90.3850  131.6380
      QMMM:     5        5      C       91.6400   93.2570  130.3660
      QMMM:     6        6      C       90.7660   93.2960  131.6020
      QMMM:     7        7      N       91.1090   94.1730  132.5370
      QMMM:     8        8      O       89.8010   92.5430  131.7210
      QMMM:     9        9      C       90.3580   94.3100  133.7580
      QMMM:    10       10      C       90.9770   93.5220  134.9140
      QMMM:    11       11      N       91.0670   92.1060  134.5970
      QMMM:    12       12      C       90.1660   93.7330  136.1890
      QMMM:    13       13      O       90.8160   93.0910  137.2800
      QMMM:    14       14      C       90.0100   95.2190  136.4820
      QMMM:    15       15      O       89.1430   95.4080  137.5950
      QMMM:    16       16      C       89.4300   95.9370  135.2680
      QMMM:    17       17      O       90.2540   95.6940  134.1180
      QMMM:    18       18      C       89.3640   97.4360  135.4450
      QMMM:    19       19      O       90.6220   97.9670  135.8390
      QMMM:    20       20      C       91.9560   91.2870  135.1690
      QMMM:    21       21      O       92.7620   91.6850  136.0030
      QMMM:    22       22      C       91.9080   89.8550  134.7320
      QMMM:    23       23      H       89.8200   90.9400  129.9900
      QMMM:    24       24      H       92.3950   91.9000  128.8860
      QMMM:    25       25      H       92.6440   93.5840  130.6380
      QMMM:    26       26      H       91.2340   93.9450  129.6240
      QMMM:    27       27      H       91.9180   94.7600  132.3880
      QMMM:    28       28      H       89.3530   93.9270  133.5840
      QMMM:    29       29      H       91.9860   93.8990  135.0840
      QMMM:    30       30      H       90.4290   91.7240  133.9140
      QMMM:    31       31      H       89.1780   93.2930  136.0570
      QMMM:    32       32      H       90.9870   95.6420  136.7140
      QMMM:    33       33      H       88.4270   95.5560  135.0750
      QMMM:    34       34      H       89.0670   97.8920  134.5010
      QMMM:    35       35      H       88.6210   97.6740  136.2060
      QMMM:    36       36      H       91.7460   92.9730  137.0740
      QMMM:    37       37      H       89.5040   94.9580  138.3620
      QMMM:    38       38      H       90.5500   98.9190  135.9440
      QMMM:    39       39      H       91.9930   89.2060  135.6030
      QMMM:    40       40      H       90.9630   89.6620  134.2250
      QMMM:    41       41      H       92.7340   89.6560  134.0490
      QMMM:    42       42      C       90.0210   91.4700  128.0520
      QMMM:    43       43      C       88.6980   90.7900  127.7110
      QMMM:    44       44      H       87.9320   91.5550  127.5140
      QMMM:    45       45      H       88.8280   90.1630  126.8170
      QMMM:    46       46      H       88.3800   90.1620  128.5560
      QMMM:    47       47      N       93.6010   90.5920  130.6150
      QMMM:    48       48      C       94.2260   89.5900  131.4540
      QMMM:    49       49      H       94.8130   90.0850  132.2420
      QMMM:    50       50      H       94.8900   88.9620  130.8420
      QMMM:    51       51      H       93.4500   88.9620  131.9150
      QMMM:    52       52      H       94.1490   91.0750  129.9170
      QMMM:    53       53      O       90.6790   92.0620  127.1920
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
          iter         sqm energy              rms gradient
          ----    -------------------    -----------------------
    xmin    10     -346.2686 kcal/mol        1.7308 kcal/(mol*A)
    xmin    20     -347.5350 kcal/mol        0.8094 kcal/(mol*A)
    xmin    30     -348.0852 kcal/mol        0.0939 kcal/(mol*A)
    xmin    40     -348.4643 kcal/mol        0.1987 kcal/(mol*A)
    xmin    50     -349.2236 kcal/mol        0.6466 kcal/(mol*A)
    

  
Failure running ANTECHAMBER for residue NAG+ASN  
Check reply log for details  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 154, in _finish_add_charge  
self.dock_prep_info['structures'] = AtomicStructures(self.structures)  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\add_charge\tool.py", line 124, in structures  
return self.structure_list.value  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 130, in value  
return self.get_value()  
^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 133, in get_value  
self._sleep_check()  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 86, in _sleep_check  
if not self._handlers and not hasattr(self, '_recursion'):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
RuntimeError: wrapped C/C++ object of type ShortASList has been deleted  
  
RuntimeError: wrapped C/C++ object of type ShortASList has been deleted  
  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 86, in _sleep_check  
if not self._handlers and not hasattr(self, '_recursion'):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

QWindowsWindow::setGeometry: Unable to set geometry 960x531+1056+644 (frame:
982x587+1045+599) on QWidgetWindow/"QWidgetClassWindow" on "LQ145N1".
Resulting geometry: 956x522+1058+651 (frame: 978x578+1047+606) margins: 11,
45, 11, 11 minimum size: 640x354 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=982, y=587)))  

QWindowsWindow::setGeometry: Unable to set geometry 900x731+1086+545 (frame:
922x787+1075+500) on QWidgetWindow/"QWidgetClassWindow" on "LQ145N1".
Resulting geometry: 896x722+1088+552 (frame: 918x778+1077+507) margins: 11,
45, 11, 11 minimum size: 600x333 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=922, y=556)))  

[Repeated 1 time(s)]




OpenGL version: 3.3.0 - Build 32.0.101.6733
OpenGL renderer: Intel(R) Arc(TM) Graphics
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: Dell Inc.
Model: XPS 14 9440
OS: Microsoft Windows 11 Home (Build 22631)
Memory: 33,775,378,432
MaxProcessMemory: 137,438,953,344
CPU: 22 Intel(R) Core(TM) Ultra 7 155H
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    Send2Trash: 1.8.3
    SEQCROW: 1.8.18
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

[Eric Pettersen]

But suspicious that there are consecutive loggings of "Closest equivalent command..." messages