id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20778 ChimeraX bug report submission aleksandr.kharchenko@… "{{{ 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 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 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 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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 }}} " defect new normal Unassigned