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Opened 6 hours ago
#20778 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.26200
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Find cavities.
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open C:/Users/Kharch0000/Desktop/sprtn/E@Sph.spartan
Unrecognized file suffix '.spartan'
> open C:/Users/Kharch0000/Desktop/sprtn/Sph.pdb
Summary of feedback from opening C:/Users/Kharch0000/Desktop/sprtn/Sph.pdb
---
warning | Ignored bad PDB record found on line 2
REMARK Spartan'24 exported M0001
> style ball
Changed 116 atom styles
> style sphere
Changed 116 atom styles
> style stick
Changed 116 atom styles
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue UNK (net charge +0) with am1-bcc method
Running ANTECHAMBER command: C:/Program Files/ChimeraX
1.12/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
C:\Users\KHARCH~1\AppData\Local\Temp\tmp431dtutj\ante.in.mol2 -fi mol2 -o
C:\Users\KHARCH~1\AppData\Local\Temp\tmp431dtutj\ante.out.mol2 -fo mol2 -c bcc
-nc 0 -j 5 -s 2 -dr n
(UNK) ``
(UNK) `Welcome to antechamber 20.0: molecular input file processor.`
(UNK) ``
(UNK) `Info: Finished reading file
(C:\Users\KHARCH~1\AppData\Local\Temp\tmp431dtutj\ante.in.mol2); atoms read
(116), bonds read (128).`
(UNK) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(UNK) `Running: "C:/Program Files/ChimeraX 1.12/bin/amber20/bin/bondtype" -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
(UNK) ``
(UNK) ``
(UNK) `Running: "C:/Program Files/ChimeraX 1.12/bin/amber20/bin/atomtype" -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(UNK) `bash.exe: warning: could not find /tmp, please create!`
(UNK) `Info: Total number of electrons: 472; net charge: 0`
(UNK) ``
(UNK) `Running: "C:/Program Files/ChimeraX 1.12/bin/amber20/bin/sqm" -O -i
sqm.in -o sqm.out`
(UNK) `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 =168
| QMMM: *** Selected Hamiltonian ***
| QMMM: AM1
| QMMM: *** Parameter sets in use ***
| QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
| QMMM: O : 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 = 320
| QMMM: diag iterations used for timing = 2
| QMMM:
| QMMM: Internal diag routine = 0.105782 seconds
| QMMM: Dspev diag routine = 0.091404 seconds
| QMMM: Dspevd diag routine = 0.071253 seconds
| QMMM: Dspevx diag routine = 0.271426 seconds
| QMMM: Dsyev diag routine = 0.096781 seconds
| QMMM: Dsyevd diag routine = 0.071224 seconds
| QMMM: Dsyevr diag routine = 0.071210 seconds
| QMMM:
| QMMM: Pseudo diag routine = 0.058209 seconds
| QMMM:
| QMMM: Using dsyevr routine (diag_routine=7).
QMMM: QM Region Cartesian Coordinates (*=link atom)
QMMM: QM_NO. MM_NO. ATOM X Y Z
QMMM: 1 1 C -2.0390 3.5250 -1.6350
QMMM: 2 2 C -3.2700 1.2360 -2.6200
QMMM: 3 3 C -3.1010 2.9550 -0.9050
QMMM: 4 4 C -1.5620 2.9580 -2.8330
QMMM: 5 5 C -2.1970 1.8100 -3.3160
QMMM: 6 6 C -3.7070 1.8020 -1.4140
QMMM: 7 7 H -4.5230 1.3370 -0.8620
QMMM: 8 8 C -3.9420 0.0000 -3.1580
QMMM: 9 9 H -5.0230 0.0000 -2.8990
QMMM: 10 10 H -3.9260 0.0000 -4.2690
QMMM: 11 11 C -3.2700 -1.2360 -2.6200
QMMM: 12 12 C -2.0390 -3.5250 -1.6350
QMMM: 13 13 C -3.7070 -1.8020 -1.4140
QMMM: 14 14 C -2.1970 -1.8100 -3.3160
QMMM: 15 15 C -1.5620 -2.9580 -2.8330
QMMM: 16 16 C -3.1010 -2.9550 -0.9050
QMMM: 17 17 H -4.5230 -1.3370 -0.8620
QMMM: 18 18 H -1.8440 -1.3500 -4.2380
QMMM: 19 19 O -1.4460 -4.7100 -1.2340
QMMM: 20 20 O -1.4460 4.7100 -1.2340
QMMM: 21 21 C 1.6350 3.5250 -2.0390
QMMM: 22 22 C 2.6200 1.2360 -3.2700
QMMM: 23 23 C 2.8330 2.9580 -1.5620
QMMM: 24 24 C 0.9050 2.9550 -3.1010
QMMM: 25 25 C 1.4140 1.8020 -3.7070
QMMM: 26 26 C 3.3160 1.8100 -2.1970
QMMM: 27 27 C 3.1580 0.0000 -3.9420
QMMM: 28 28 C 2.6200 -1.2360 -3.2700
QMMM: 29 29 C 1.6350 -3.5250 -2.0390
QMMM: 30 30 C 1.4140 -1.8020 -3.7070
QMMM: 31 31 C 3.3160 -1.8100 -2.1970
QMMM: 32 32 C 2.8330 -2.9580 -1.5620
QMMM: 33 33 C 0.9050 -2.9550 -3.1010
QMMM: 34 34 O 1.2340 -4.7100 -1.4460
QMMM: 35 35 O 1.2340 4.7100 -1.4460
QMMM: 36 36 C 2.0390 3.5250 1.6350
QMMM: 37 37 C 3.2700 1.2360 2.6200
QMMM: 38 38 C 3.1010 2.9550 0.9050
QMMM: 39 39 C 1.5620 2.9580 2.8330
QMMM: 40 40 C 2.1970 1.8100 3.3160
QMMM: 41 41 C 3.7070 1.8020 1.4140
QMMM: 42 42 C 3.9420 0.0000 3.1580
QMMM: 43 43 C 3.2700 -1.2360 2.6200
QMMM: 44 44 C 2.0390 -3.5250 1.6350
QMMM: 45 45 C 3.7070 -1.8020 1.4140
QMMM: 46 46 C 2.1970 -1.8100 3.3160
QMMM: 47 47 C 1.5620 -2.9580 2.8330
QMMM: 48 48 C 3.1010 -2.9550 0.9050
QMMM: 49 49 O 1.4460 -4.7100 1.2340
QMMM: 50 50 O 1.4460 4.7100 1.2340
QMMM: 51 51 C -1.6350 3.5250 2.0390
QMMM: 52 52 C -2.6200 1.2360 3.2700
QMMM: 53 53 C -2.8330 2.9580 1.5620
QMMM: 54 54 C -0.9050 2.9550 3.1010
QMMM: 55 55 C -1.4140 1.8020 3.7070
QMMM: 56 56 C -3.3160 1.8100 2.1970
QMMM: 57 57 C -3.1580 0.0000 3.9420
QMMM: 58 58 C -2.6200 -1.2360 3.2700
QMMM: 59 59 C -1.6350 -3.5250 2.0390
QMMM: 60 60 C -1.4140 -1.8020 3.7070
QMMM: 61 61 C -3.3160 -1.8100 2.1970
QMMM: 62 62 C -2.8330 -2.9580 1.5620
QMMM: 63 63 C -0.9050 -2.9550 3.1010
QMMM: 64 64 O -1.2340 -4.7100 1.4460
QMMM: 65 65 O -1.2340 4.7100 1.4460
QMMM: 66 66 H 0.8620 1.3370 -4.5230
QMMM: 67 67 H 4.2690 0.0000 -3.9260
QMMM: 68 68 H 2.8990 0.0000 -5.0230
QMMM: 69 69 H 0.8620 -1.3370 -4.5230
QMMM: 70 70 H 4.2380 -1.3500 -1.8440
QMMM: 71 71 H 4.5230 -1.3370 0.8620
QMMM: 72 72 H 4.5230 1.3370 0.8620
QMMM: 73 73 H 1.8440 1.3500 4.2380
QMMM: 74 74 H -0.8620 1.3370 4.5230
QMMM: 75 75 H -4.2380 -1.3500 1.8440
QMMM: 76 76 H -0.8620 -1.3370 4.5230
QMMM: 77 77 H -2.8990 0.0000 5.0230
QMMM: 78 78 H -4.2690 0.0000 3.9260
QMMM: 79 79 H 5.0230 0.0000 2.8990
QMMM: 80 80 H 3.9260 0.0000 4.2690
QMMM: 81 81 H -1.8440 1.3500 -4.2380
QMMM: 82 82 H 1.8440 -1.3500 4.2380
QMMM: 83 83 C -3.5640 -3.5620 0.3930
QMMM: 84 84 H -4.6610 -3.4320 0.5100
QMMM: 85 85 H -3.4140 -4.6680 0.3800
QMMM: 86 86 C -0.3930 -3.5620 -3.5640
QMMM: 87 87 H -0.3800 -4.6680 -3.4140
QMMM: 88 88 H -0.5100 -3.4320 -4.6610
QMMM: 89 89 C 0.3930 -3.5620 3.5640
QMMM: 90 90 H 0.5100 -3.4320 4.6610
QMMM: 91 91 H 0.3800 -4.6680 3.4140
QMMM: 92 92 C 3.5640 -3.5620 -0.3930
QMMM: 93 93 H 4.6610 -3.4320 -0.5100
QMMM: 94 94 H 3.4140 -4.6680 -0.3800
QMMM: 95 95 C 0.3930 3.5620 3.5640
QMMM: 96 96 H 0.3800 4.6680 3.4140
QMMM: 97 97 H 0.5100 3.4320 4.6610
QMMM: 98 98 C -0.3930 3.5620 -3.5640
QMMM: 99 99 H -0.5100 3.4320 -4.6610
QMMM: 100 100 H -0.3800 4.6680 -3.4140
QMMM: 101 101 C -3.5640 3.5620 0.3930
QMMM: 102 102 H -4.6610 3.4320 0.5100
QMMM: 103 103 H -3.4140 4.6680 0.3800
QMMM: 104 104 H -4.2380 1.3500 1.8440
QMMM: 105 105 H 4.2380 1.3500 -1.8440
QMMM: 106 106 C 3.5640 3.5620 -0.3930
QMMM: 107 107 H 4.6610 3.4320 -0.5100
QMMM: 108 108 H 3.4140 4.6680 -0.3800
QMMM: 109 109 H 0.2170 4.8500 -1.5640
QMMM: 110 110 H 1.5640 4.8500 0.2170
QMMM: 111 111 H -1.5640 4.8500 -0.2170
QMMM: 112 112 H -0.2170 4.8500 1.5640
QMMM: 113 113 H -1.5640 -4.8500 -0.2170
QMMM: 114 114 H -0.2170 -4.8500 1.5640
QMMM: 115 115 H 0.2170 -4.8500 -1.5640
QMMM: 116 116 H 1.5640 -4.8500 0.2170
--------------------------------------------------------------------------------
RESULTS
--------------------------------------------------------------------------------
Failure running ANTECHAMBER for residue UNK Check reply log for details
> color bychain
[Repeated 1 time(s)]
> color byhetero
> hide #1 models
> show #1 models
> color #1 #42d264ff
> color #1 #73d29eff
> color #1 #d2c059ff
> color #1 #d27d44ff
> color #1 #aaaa00ff
> color #1 lime
> color #1 #aa55ffff
> color #1 #00557fff
> color #1 #005500ff
> color #1 #aa55ffff
> color #1 #a0a0a0ff
> color #1 #a5d7d2ff
> color #1 #d35230ff
> color #1 #145492ff
> color #1 white
> color #1 #b30b00ff
> color #1 #d88166ff
> color #1 #dee2efff
> color #1 #44d3b2ff
> color #1 #839ad0ff
> color #1 #eff4f9ff
> color #1 #c8bca9ff
> color byhetero
> view
> cofr frontCenter
> cartoon style xsection oval modeHelix default
Computing secondary structure
> style ringFill thick
Changed 1 residue ring style
> style ringFill thin
Changed 1 residue ring style
> ui tool show "Color Zone"
No surface chosen for color zoning
> select add #1
116 atoms, 128 bonds, 1 residue, 1 model selected
> select subtract #1
Nothing selected
> select add #1
116 atoms, 128 bonds, 1 residue, 1 model selected
> select subtract #1
Nothing selected
> select add #1
116 atoms, 128 bonds, 1 residue, 1 model selected
No surface chosen for color zoning
[Repeated 1 time(s)]
> select subtract #1
Nothing selected
> ui tool show "Volume Viewer"
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you
have numpy 2.4.6 which is incompatible.
scipy 1.14.0 requires numpy<2.3,>=1.23.5, but you have numpy 2.4.6 which is
incompatible.
\---
pip standard output:
\---
\---
pyKVFinder module installed from PyPi repository.
QWindowsWindow::setGeometry: Unable to set geometry 493x546+954+516 (frame:
511x593+945+478) on QWidgetWindow/"QDockWidgetClassWindow" on "DELL UP2516D".
Resulting geometry: 491x538+955+523 (frame: 509x585+946+485) margins: 9, 38,
9, 9 minimum size: 394x411 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=511, y=561)))
> kvfinder
1 cavities found for Sph.pdb #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 131, in <lambda>
bbox.button(qbbox.Apply).clicked.connect(lambda *args, fc=self.find_cavities:
fc(apply=True))
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 172, in find_cavities
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 142, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'KAA'
KeyError: 'KAA'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 142, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
> kvfinder
1 cavities found for Sph.pdb #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 172, in find_cavities
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 142, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'KAA'
KeyError: 'KAA'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 142, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
> ui tool show "Find Cavities"
> style ringFill off
Changed 1 residue ring style
> kvfinder
1 cavities found for Sph.pdb #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 131, in <lambda>
bbox.button(qbbox.Apply).clicked.connect(lambda *args, fc=self.find_cavities:
fc(apply=True))
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 172, in find_cavities
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 142, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'KAA'
KeyError: 'KAA'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 142, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
> kvfinder
1 cavities found for Sph.pdb #1
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\tool.py", line 172, in find_cavities
run(self.session, cmd)
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 142, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
KeyError: 'KAA'
KeyError: 'KAA'
File "C:\Program Files\ChimeraX 1.12\bin\Lib\site-
packages\chimerax\kvfinder\cmd.py", line 142, in cmd_kvfinder
non_backbone_contacting[cav_s] = non_backbone_contacting[k_index]
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
See log for complete Python traceback.
QWindowsWindow::setGeometry: Unable to set geometry 750x609+825+485 (frame:
768x656+816+447) on QWidgetWindow/"QDockWidgetClassWindow" on "DELL UP2516D".
Resulting geometry: 748x601+826+492 (frame: 766x648+817+454) margins: 9, 38,
9, 9 minimum size: 600x333 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=768, y=463)))
> ui tool show ViewDock
> ui tool show "Find Cavities"
OpenGL version: 3.3.0 - Build 31.0.101.2135
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Python: 3.11.9
Locale: de_CH.cp1252
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: windows
Manufacturer: LENOVO
Model: 11D7S0A300
OS: Microsoft Windows 11 Enterprise (Build 26200.8655)
Memory: 34,053,562,368
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: en-US
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2026.5.20
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
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: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
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-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
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: 1.0.1
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: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
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-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
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: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
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: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
comtypes: 1.4.11
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.4.6
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.9.3
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine-commercial: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pywin32: 311
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
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
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tomlkit: 0.15.1
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
tzdata: 2026.2
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
WMI: 1.5.1
yarl: 1.24.2
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