id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19834 Crash in QDockWidget::event() in Qt 6.9.2 showing Build Structure tool iamkaant@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.2-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. opened ""Build Structure"" tool Fatal Python error: Segmentation fault Current thread 0x00000001f530ec40 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, 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""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""932a93e8a50bcd05aac9f622376d9cf5b2df3941"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""645eb1d0417dab722a215927"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/P08684/MANUAL/P450-manual- > sel.cxs ### ViewDock hotkeys on If clicked into ViewDock dialog or main 3D graphics area, the following keys are active: g/m/b/u Assign good/maybe/bad/(unrated) rating to chosen compounds up/down arrow Move up/down compound list* Escape Turn hotkeys off (have to use context menu to re-enable) *Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens Log from Wed Feb 19 15:57:43 2025 Startup Messages --- 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 /Users/ak87/ownCloud/owncloud/Calculations/P450/RECEPTOR/Cyp3A4/rec- > minimized-final.pdb Summary of feedback from opening /Users/ak87/ownCloud/owncloud/Calculations/P450/RECEPTOR/Cyp3A4/rec-minimized- final.pdb --- warnings | CONECT record to nonexistent atom: (4664, 4678) CONECT record for nonexistent atom: 4678 rec-minimized-final.pdb title: 6MA7 - 5-removed waters [more info...] Chain information for rec-minimized-final.pdb #1 --- Chain | Description A | No description available Non-standard residues in rec-minimized-final.pdb #1 --- ACE — (ACE) HEM — protoporphyrin IX containing Fe NMA — (NMA) > open > /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/test.mol2.gz File reader requires uncompressed file; '/Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/test.mol2.gz' is compressed > open > /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/test.mol2 Opened test.mol2 containing 290 structures (11840 atoms, 12550 bonds) > viewdockx #2.1-290 > hide #2.1-290 models > show #2.1 models JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read properties of undefined (reading 'id') > hide #2.1 models JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read properties of undefined (reading 'id') > show #2.251 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 42 atoms, 45 bonds, 1 residue, 1 model selected > select sel : show sel & #!1 atoms > view sel > ui tool show ""Selection Inspector"" > size =sel stickRadius 0.05 Changed 12770 bond radii > label (#!1 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > select clear > save > /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/P450-manual- > sel.cxs > hide #2.251#!1 cartoons > open 8SPD Summary of feedback from opening 8SPD fetched from pdb --- notes | Fetching compressed mmCIF 8spd from http://files.rcsb.org/download/8spd.cif Fetching CCD CL6 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/CL6/CL6.cif 8spd title: Cytochrome P450 (CYP) 3A4 crystallized with clotrimazole [more info...] Chain information for 8spd #3 --- Chain | Description | UniProt A | Cytochrome P450 3A4 | CP3A4_HUMAN 24-503 Non-standard residues in 8spd #3 --- CL6 — 1-[(2-chlorophenyl)(diphenyl)methyl]-1H-imidazole (clotrimazole) HEM — protoporphyrin IX containing Fe (HEME) > mmaker #3 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 Desktop color scheme is dark Desktop color scheme is light Desktop color scheme is dark Desktop color scheme is light > ui windowfill toggle > open smiles:C12C3C4C5C1C1C6C2C2C3C3C4C4C5C1C1C6C2C3C41 Translated SMILES to 3D structure via NCI web service (SMILES: C12C3C4C5C1C1C6C2C2C3C3C4C4C5C1C1C6C2C3C41) Drag select of 40 atoms, 50 bonds > select clear > select HC 28772 atoms, 1656 residues, 1656 models selected > delete atoms (#5#3.4 & sel) > delete bonds (#5#3.4 & sel) Drag select of 20 atoms, 30 bonds > ui mousemode right ""translate selected models"" > view matrix models #5,1,0,0,-17.198,0,1,0,-16.063,0,0,1,-16.994 > view matrix models #5,1,0,0,-18.738,0,1,0,-18.248,0,0,1,-8.5941 > view matrix models #5,1,0,0,-19.436,0,1,0,-21.881,0,0,1,-9.7245 > ui windowfill toggle > hide #!3 models > ui windowfill toggle > view matrix models #5,1,0,0,-20.164,0,1,0,-21.647,0,0,1,-9.7962 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.99914,0.036516,0.019576,-20.164,-0.036651,0.99931,0.0066042,-21.647,-0.019322,-0.007316,0.99979,-9.7963 > view matrix models > #5,0.9998,0.011987,-0.016128,-20.164,-0.014308,0.9882,-0.15248,-21.648,0.01411,0.15268,0.98818,-9.7956 > view matrix models > #5,0.80576,-0.47257,0.35696,-20.165,0.58889,0.70334,-0.39815,-21.648,-0.062911,0.53103,0.84502,-9.7947 > view matrix models > #5,0.95901,-0.16352,0.23142,-20.164,0.25945,0.8351,-0.48508,-21.648,-0.11394,0.52524,0.84329,-9.7949 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.95901,-0.16352,0.23142,-20.296,0.25945,0.8351,-0.48508,-21.884,-0.11394,0.52524,0.84329,-9.1598 > view sel > ui tool show ""Selection Inspector"" > size =sel stickRadius 0.06 Changed 30 bond radii > view matrix models > #5,0.95901,-0.16352,0.23142,-20.243,0.25945,0.8351,-0.48508,-21.969,-0.11394,0.52524,0.84329,-9.1426 > select clear > ui tool show Distances > select #2/A:602@C7 1 atom, 1 residue, 1 model selected > select add #5/?:1@C9 2 atoms, 2 residues, 2 models selected > distance #2/A:602@C7 #5/?:1@C9 Distance between xtal-lig.pdb #2/A TPF 602 C7 and smiles:C12C3C4C5C1C1C6C2C2C3C3C4C4C5C1C1C6C2C3C41 #5/? UNL 1 C9: 0.519Å > select clear > select add #5/?:1@C1 1 atom, 1 bond, 1 residue, 2 models selected > select #2/A:602@C6 1 atom, 1 residue, 1 model selected > select add #5/?:1@C1 2 atoms, 2 residues, 2 models selected > distance #2/A:602@C6 #5/?:1@C1 Distance between xtal-lig.pdb #2/A TPF 602 C6 and smiles:C12C3C4C5C1C1C6C2C2C3C3C4C4C5C1C1C6C2C3C41 #5/? UNL 1 C1: 0.943Å > select clear > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 4615 atoms, 4708 bonds, 472 residues, 1 model selected > hide sel atoms > select clear > hide #5 models Drag select of 4 atoms, 5 bonds > ui tool show ""Build Structure"" 2 models"">hide #2.232 models > show #2.233 models > hide #2.233 models > show #2.234 models > hide #2.234 models > show #2.235 models > hide #2.235 models > show #2.236 models > hide #2.236 models > show #2.237 models > hide #2.237 models > show #2.238 models > hide #2.238 models > show #2.239 models > hide #2.239 models > show #2.240 models > hide #2.240 models > show #2.1 models > hide #!4 models > open 3NXU 3nxu title: Crystal structure of human cytochrome P4503A4 bound to an inhibitor ritonavir [more info...] Chain information for 3nxu #5 --- Chain | Description | UniProt A B | Cytochrome P450 3A4 | CP3A4_HUMAN 25-503 Non-standard residues in 3nxu #5 --- DMS — dimethyl sulfoxide HEM — protoporphyrin IX containing Fe (HEME) RIT — ritonavir (A-84538) 3nxu mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > mmaker #5 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 3nxu, chain A (#5), sequence alignment score = 2362.1 RMSD between 374 pruned atom pairs is 0.875 angstroms; (across all 457 pairs: 1.714) > hide #2.1#!1,5 cartoons > hide #2.1 models > show #2.2 models > hide #2.2 models > show #2.3 models > hide #2.3 models > show #2.4 models > hide #2.4 models > show #2.5 models > hide #2.5 models > show #2.6 models > hide #2.6 models > show #2.7 models > hide #2.7 models > show #2.8 models > hide #2.8 models > show #2.9 models > hide #2.9 models > show #2.10 models > hide #2.10 models > show #2.11 models > hide #2.11 models > show #2.10 models > hide #2.10 models > show #2.11 models > hide #2.11 models > show #2.11 models > hide #2.11 models > show #2.11 models > open 4D6Z Summary of feedback from opening 4D6Z fetched from pdb --- notes | Fetching compressed mmCIF 4d6z from http://files.rcsb.org/download/4d6z.cif Fetching CCD GOL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/GOL/GOL.cif Fetching CCD IMD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IMD/IMD.cif Fetching CCD PK9 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/PK9/PK9.cif 4d6z title: Cytochrome P450 3A4 bound to imidazole and an inhibitor [more info...] Chain information for 4d6z #6 --- Chain | Description | UniProt A | CYTOCHROME P450 3A4 | CP3A4_HUMAN 23-503 Non-standard residues in 4d6z #6 --- GOL — glycerol (glycerin; propane-1,2,3-triol) HEM — protoporphyrin IX containing Fe (HEME) IMD — imidazole PK9 — tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate 53 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > mmaker #6 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 4d6z, chain A (#6), sequence alignment score = 2377.1 RMSD between 449 pruned atom pairs is 0.366 angstroms; (across all 460 pairs: 0.618) > hide #!5 models > hide #2.11#!1,6 cartoons > show #!5 models > hide #!6 models > hide #2.11 models > show #2.1 models > hide #2.1 models > show #2.2 models > hide #2.2 models > show #2.3 models > hide #2.3 models > show #2.4 models > hide #2.4 models > show #2.5 models > hide #2.5 models > show #2.1 models > hide #2.1 models > show #2.21 models > hide #2.21 models > show #2.21 models > hide #2.21 models > show #2.21 models > show #!6 models > hide #!5 models > hide #2.21 models > show #2.20 models > hide #2.20 models > show #2.21 models > hide #2.21 models > show #2.20 models > hide #2.20 models > show #2.16 models > hide #2.16 models > show #2.17 models > hide #2.17 models > show #2.20 models > hide #2.20 models > show #2.21 models > hide #2.21 models > show #2.22 models > hide #2.22 models > show #2.24 models > hide #2.24 models > show #2.25 models > hide #2.25 models > show #2.19 models > hide #2.19 models > show #2.22 models > hide #2.22 models > show #2.31 models > hide #2.31 models > show #2.32 models > hide #2.32 models > show #2.41 models > hide #2.41 models > show #2.41 models > hide #2.41 models > show #2.41 models > hide #2.41 models > show #2.41 models > hide #2.41 models > show #2.41 models > hide #2.41 models > show #2.41 models > hide #2.41 models > show #2.41 models > open 4D75 Summary of feedback from opening 4D75 fetched from pdb --- note | Fetching compressed mmCIF 4d75 from http://files.rcsb.org/download/4d75.cif 4d75 title: Cytochrome P450 3A4 bound to an inhibitor [more info...] Chain information for 4d75 #7 --- Chain | Description | UniProt A | CYTOCHROME P450 3A4 | CP3A4_HUMAN 23-503 Non-standard residues in 4d75 #7 --- HEM — protoporphyrin IX containing Fe (HEME) PK9 — tert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate 3 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!6 models > mmaker #7 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 4d75, chain A (#7), sequence alignment score = 2329.7 RMSD between 451 pruned atom pairs is 0.438 angstroms; (across all 460 pairs: 0.607) > hide #2.41#!1,7 cartoons > hide #2.41 models > show #2.42 models > hide #2.42 models > show #2.43 models > hide #2.43 models > show #2.44 models > hide #2.44 models > show #2.44 models > hide #2.44 models > show #2.45 models > hide #2.45 models > show #2.47 models > hide #2.47 models > show #2.46 models > hide #2.46 models > show #2.47 models > hide #2.47 models > show #2.48 models > hide #2.48 models > show #2.49 models > hide #2.49 models > show #2.50 models > hide #2.50 models > show #2.41 models > hide #2.41 models > show #2.51 models > hide #2.51 models > show #2.51 models > open 4I4G Summary of feedback from opening 4I4G fetched from pdb --- notes | Fetching compressed mmCIF 4i4g from http://files.rcsb.org/download/4i4g.cif Fetching CCD Z8Z from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/Z8Z/Z8Z.cif 4i4g title: Crystal structure of CYP3A4 ligated to oxazole-substituted desoxyritonavir [more info...] Chain information for 4i4g #8 --- Chain | Description | UniProt A | Cytochrome P450 3A4 | CP3A4_HUMAN 21-503 Non-standard residues in 4i4g #8 --- HEM — protoporphyrin IX containing Fe (HEME) Z8Z — N~2~-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-N-[(2R,5R)-5-{[(1,3-oxazol-5-ylmethoxy)carbonyl]amino}-1,6-diphenylhexan-2-yl]-L-valinamide 4i4g mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly > mmaker #8 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 4i4g, chain A (#8), sequence alignment score = 2343.5 RMSD between 390 pruned atom pairs is 0.738 angstroms; (across all 459 pairs: 1.498) > hide #2.51#!1,7-8 cartoons > hide #!7 models > hide #2.51 models > show #2.52 models > hide #2.52 models > show #2.53 models > hide #2.53 models > show #2.54 models > hide #2.54 models > show #2.55 models > hide #2.55 models > show #2.56 models > hide #2.56 models > show #2.57 models > hide #2.57 models > show #2.58 models > hide #2.58 models > show #2.59 models > hide #2.59 models > show #2.60 models > hide #2.60 models > show #2.61 models > hide #2.61 models > show #2.51 models > hide #2.51 models > show #2.61 models > hide #2.61 models > show #2.61 models > open 4I4H Summary of feedback from opening 4I4H fetched from pdb --- notes | Fetching compressed mmCIF 4i4h from http://files.rcsb.org/download/4i4h.cif Fetching CCD Z9Z from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/Z9Z/Z9Z.cif 4i4h title: Crystal structure of CYP3A4 ligated to pyridine-substituted desoxyritonavir [more info...] Chain information for 4i4h #9 --- Chain | Description | UniProt A | Cytochrome P450 3A4 | CP3A4_HUMAN 21-503 Non-standard residues in 4i4h #9 --- HEM — protoporphyrin IX containing Fe (HEME) Z9Z — pyridin-3-ylmethyl [(2R,5S)-5-{[N-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-D-valyl]amino}-1,6-diphenylhexan-2-yl]carbamate 4i4h mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly > mmaker #9 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 4i4h, chain A (#9), sequence alignment score = 2326.7 RMSD between 386 pruned atom pairs is 0.772 angstroms; (across all 457 pairs: 1.531) > hide #!8 models > hide #2.61#!1,9 cartoons > save > /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/P450-manual- > sel.cxs > hide #2.61 models > show #2.62 models > hide #2.62 models > show #2.63 models > hide #2.63 models > show #2.64 models > hide #2.64 models > show #2.65 models > hide #2.65 models > show #2.66 models > hide #2.66 models > show #2.67 models > hide #2.67 models > show #2.68 models > hide #2.68 models > show #2.69 models > hide #2.69 models > show #2.70 models > hide #2.70 models > show #2.101 models > hide #2.101 models > show #2.101 models > hide #2.101 models > show #2.101 models > hide #2.101 models > show #2.101 models > open 4NY4 4ny4 title: Crystal structure of CYP3A4 in complex with an inhibitor [more info...] Chain information for 4ny4 #10 --- Chain | Description | UniProt A | Cytochrome P450 3A4 | CP3A4_HUMAN 25-503 Non-standard residues in 4ny4 #10 --- 2QH — (8R)-3,3-difluoro-8-[4-fluoro-3-(pyridin-3-yl)phenyl]-8-(4-methoxy-3-methylphenyl)-2,3,4,8-tetrahydroimidazo[1,5-a]pyrimidin-6-amine HEM — protoporphyrin IX containing Fe (HEME) 4ny4 mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly > hide #!9 models > mmaker #10 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 4ny4, chain A (#10), sequence alignment score = 2359.1 RMSD between 446 pruned atom pairs is 0.561 angstroms; (across all 460 pairs: 0.833) > hide #2.101#!1,10 cartoons > hide #2.101 models > show #2.71 models > hide #2.71 models > show #2.91 models > hide #2.91 models > show #2.81 models > hide #2.81 models > show #2.92 models > hide #2.92 models > show #2.82 models > hide #2.82 models > show #2.72 models > hide #2.72 models > show #2.93 models > hide #2.93 models > show #2.94 models > hide #2.94 models > show #2.95 models > hide #2.95 models > show #2.83 models > hide #2.83 models > show #2.73 models > hide #2.73 models > show #2.84 models > hide #2.84 models > show #2.96 models > hide #2.96 models > show #2.96 models > hide #2.96 models > show #2.85 models > hide #2.85 models > show #2.74 models > hide #2.74 models > show #2.97 models > hide #2.97 models > show #2.75 models > hide #2.75 models > show #2.102 models > hide #2.102 models > show #2.97 models > hide #2.97 models > show #2.74 models > hide #2.74 models > show #2.96 models > hide #2.96 models > show #2.161 models > hide #2.161 models > show #2.171 models > hide #2.171 models > show #2.140 models > hide #2.140 models > show #2.137 models > hide #2.137 models > show #2.171 models > hide #2.171 models > show #2.181 models > hide #2.181 models > show #2.140 models > hide #2.140 models > show #2.150 models > hide #2.150 models > show #2.149 models > hide #2.149 models > show #2.148 models > hide #2.148 models > show #2.147 models > hide #2.147 models > show #2.139 models > hide #2.139 models > show #2.138 models > hide #2.138 models > show #2.130 models > hide #2.130 models > show #2.129 models > hide #2.129 models > show #2.146 models > hide #2.146 models > show #2.137 models > hide #2.137 models > show #2.128 models > hide #2.128 models > show #2.136 models > hide #2.136 models > show #2.120 models > hide #2.120 models > show #2.101 models > hide #2.101 models > show #2.71 models > hide #2.71 models > show #2.91 models > hide #2.91 models > show #2.81 models > hide #2.81 models > show #2.92 models > hide #2.92 models > show #2.82 models > hide #2.82 models > show #2.72 models > hide #2.72 models > show #2.93 models > hide #2.93 models > show #2.94 models > hide #2.94 models > show #2.95 models > hide #2.95 models > show #2.83 models > hide #2.83 models > show #2.73 models > hide #2.73 models > show #2.83 models > hide #2.83 models > show #2.95 models > hide #2.95 models > show #2.191 models > hide #2.191 models > show #2.191 models > open 5TE8 Summary of feedback from opening 5TE8 fetched from pdb --- notes | Fetching compressed mmCIF 5te8 from http://files.rcsb.org/download/5te8.cif Fetching CCD 08J from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/J/08J/08J.cif 5te8 title: Crystal structure of the midazolam-bound human CYP3A4 [more info...] Chain information for 5te8 #11 --- Chain | Description | UniProt A B C | Cytochrome P450 3A4 | CP3A4_HUMAN 1-503 Non-standard residues in 5te8 #11 --- 08J — 8-chloro-6-(2-fluorophenyl)-1-methyl-4H-imidazo[1,5-a][1,4]benzodiazepine (Midazolam) HEM — protoporphyrin IX containing Fe (HEME) 5te8 mmCIF Assemblies --- 1| author_and_software_defined_assembly 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > mmaker #11 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 5te8, chain A (#11), sequence alignment score = 2328.5 RMSD between 403 pruned atom pairs is 0.880 angstroms; (across all 466 pairs: 1.969) > hide #2.191#!1,10-11 cartoons > hide #!10 models > hide #2.191 models > show #2.192 models > hide #2.192 models > show #2.193 models > hide #2.193 models > show #2.201 models > hide #2.201 models > show #2.194 models > hide #2.194 models > show #2.195 models > hide #2.195 models > show #2.196 models > hide #2.196 models > show #2.197 models > hide #2.197 models > show #2.202 models > hide #2.202 models > show #2.198 models > hide #2.198 models > show #2.199 models > hide #2.199 models > show #2.203 models > hide #2.203 models > show #2.204 models > hide #2.204 models > show #2.205 models > hide #2.205 models > show #2.205 models > hide #2.205 models > show #2.206 models > hide #2.206 models > show #2.207 models > hide #2.207 models > show #2.208 models > hide #2.208 models > show #2.209 models > hide #2.209 models > show #2.210 models > hide #2.210 models > show #2.200 models > hide #2.200 models > show #2.210 models > hide #2.210 models > show #2.200 models > hide #2.200 models > show #2.221 models > hide #2.221 models > show #2.221 models > open 6MA6 Summary of feedback from opening 6MA6 fetched from pdb --- warning | Cannot find consistent set of bond orders for ring system containing atom N1 in residue MYT /A:603 notes | Fetching compressed mmCIF 6ma6 from http://files.rcsb.org/download/6ma6.cif Fetching CCD MYT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/MYT/MYT.cif 6ma6 title: Human CYP3A4 bound to an inhibitor metyrapone [more info...] Chain information for 6ma6 #12 --- Chain | Description | UniProt A | Cytochrome P450 3A4 | CP3A4_HUMAN 23-503 Non-standard residues in 6ma6 #12 --- EDO — 1,2-ethanediol (ethylene glycol) GOL — glycerol (glycerin; propane-1,2,3-triol) HEM — protoporphyrin IX containing Fe (HEME) MYT — metyrapone 6ma6 mmCIF Assemblies --- 1| author_defined_assembly 2| software_defined_assembly 94 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > mmaker #12 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 6ma6, chain A (#12), sequence alignment score = 2410.7 RMSD between 460 pruned atom pairs is 0.367 angstroms; (across all 466 pairs: 0.538) > hide #2.221#!1,11-12 cartoons > hide #!11 models > hide #2.221 models > show #2.222 models > hide #2.222 models > show #2.223 models > hide #2.223 models > show #2.211 models > hide #2.211 models > show #2.212 models > hide #2.212 models > show #2.213 models > hide #2.213 models > show #2.224 models > hide #2.224 models > show #2.225 models > hide #2.225 models > show #2.225 models > hide #2.225 models > show #2.226 models > hide #2.226 models > show #2.214 models > hide #2.214 models > show #2.215 models > hide #2.215 models > show #2.227 models > hide #2.227 models > show #2.216 models > hide #2.216 models > show #2.228 models > hide #2.228 models > show #2.217 models > hide #2.217 models > show #2.229 models > hide #2.229 models > show #2.218 models > hide #2.218 models > show #2.230 models > hide #2.230 models > show #2.219 models > hide #2.219 models > show #2.220 models > hide #2.220 models > show #2.231 models > hide #2.231 models > show #2.241 models > hide #!12 models > hide #2.241 models > show #2.241 models > open 8SO1 Summary of feedback from opening 8SO1 fetched from pdb --- notes | Fetching compressed mmCIF 8so1 from http://files.rcsb.org/download/8so1.cif Fetching CCD CFF from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/CFF/CFF.cif 8so1 title: Human CYP3A4 bound to three caffeine molecules [more info...] Chain information for 8so1 #13 --- Chain | Description | UniProt A | Cytochrome P450 3A4 | CP3A4_HUMAN 1-503 Non-standard residues in 8so1 #13 --- CFF — caffeine (3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione) HEM — protoporphyrin IX containing Fe (HEME) 8so1 mmCIF Assemblies --- 1| author_defined_assembly 14 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > mmaker #13 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 8so1, chain A (#13), sequence alignment score = 2392.7 RMSD between 463 pruned atom pairs is 0.385 angstroms; (across all 467 pairs: 0.571) > hide #2.241#!1,13 cartoons > hide #2.241 models > show #2.242 models > hide #2.242 models > show #2.243 models > hide #2.243 models > show #2.244 models > hide #2.244 models > show #2.245 models > hide #2.245 models > show #2.246 models > hide #2.246 models > show #2.247 models > hide #2.247 models > show #2.248 models > hide #2.248 models > show #2.249 models > hide #2.249 models > show #2.250 models > hide #2.250 models > show #2.251 models > hide #2.251 models > show #2.261 models > hide #2.261 models > show #2.271 models > hide #2.271 models > show #2.250 models > hide #2.250 models > show #2.251 models > hide #2.251 models > show #2.251 models > hide #2.251 models > show #2.251 models > open 8SPD 8spd title: Cytochrome P450 (CYP) 3A4 crystallized with clotrimazole [more info...] Chain information for 8spd #14 --- Chain | Description | UniProt A | Cytochrome P450 3A4 | CP3A4_HUMAN 24-503 Non-standard residues in 8spd #14 --- CL6 — 1-[(2-chlorophenyl)(diphenyl)methyl]-1H-imidazole (clotrimazole) HEM — protoporphyrin IX containing Fe (HEME) > mmaker #14 to #1 Computing secondary structure [Repeated 1 time(s)] Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker rec-minimized-final.pdb, chain A (#1) with 8spd, chain A (#14), sequence alignment score = 2311.7 RMSD between 410 pruned atom pairs is 0.665 angstroms; (across all 454 pairs: 1.406) > hide #2.251#!1,13-14 cartoons > hide #!13 models > hide #2.251 models > show #2.261 models > hide #2.261 models > show #2.271 models > hide #2.271 models > show #2.281 models > hide #2.281 models > show #2.272 models > hide #2.272 models > show #2.262 models > hide #2.262 models > show #2.251 models JS console(viewdockx_table.js:133:error): Uncaught TypeError: Cannot read properties of undefined (reading 'id') > hide #2.251 models > show #2.273 models > hide #2.273 models > show #2.263 models > hide #2.263 models > show #2.273 models > hide #2.273 models > show #2.253 models > hide #2.253 models > show #2.254 models > hide #2.254 models > show #2.255 models > hide #2.255 models > show #2.284 models > hide #2.284 models > show #2.264 models > hide #2.264 models > show #2.275 models > hide #2.275 models > show #2.260 models > save > /Users/ak87/ownCloud/owncloud/Calculations/P450/DOCKING/Cyp3A4/P08684/MANUAL/P450-manual- > sel.cxs ——— End of log from Wed Feb 19 15:57:43 2025 ——— > view name session-start opened ChimeraX session > show #!7 models > hide #!14 models > hide #!7 models > show #!8 models > show #!9 models > hide #!8 models > hide #!9 models > show #!10 models > show #!9 models > hide #!9 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > show #!13 models > hide #!10 models Desktop color scheme is dark Desktop color scheme is light > show #!5 models > hide #!13 models > hide #!5 models Desktop color scheme is dark Desktop color scheme is light > hide #!2 models > show #!3 models > show #!4 models > show #!5 models > show #!6 models > show #!7 models > show #!9 models > show #!8 models > show #!10 models > show #!11 models > show #!12 models > show #!13 models > show #!14 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > hide #!14 models > hide #!12 models > hide #!11 models > hide #!10 models > hide #!9 models > hide #!8 models > hide #!7 models > hide #!6 models > hide #!5 models > hide #!4 models > hide #!3 models > show #!12 models > hide #!12 models > show #!11 models > hide #!11 models > show #!10 models > hide #!10 models > show #!10 models > select clear > select #10/A:602@N32 1 atom, 1 residue, 1 model selected > getcrd sel Atom #10/A:602@N32 -17.703 -22.119 -9.320 > open > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/RECEPTOR/Cyp3A4/dockfiles/matching_spheres.xyz opened matching_spheres.xyz as an XYZ coordinate file > select #15/a:1@O23 1 atom, 1 residue, 1 model selected > getcrd sel Atom #15/a:1@O23 -18.133 -22.477 -9.298 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs ### ViewDock hotkeys on If clicked into ViewDock dialog or main 3D graphics area, the following keys are active: g/m/b/u Assign good/maybe/bad/(unrated) rating to chosen compounds up/down arrow Move up/down compound list* Escape Turn hotkeys off (have to use context menu to re-enable) *Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens Log from Mon Feb 9 15:27:24 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs ### ViewDock hotkeys on If clicked into ViewDock dialog or main 3D graphics area, the following keys are active: g/m/b/u Assign good/maybe/bad/(unrated) rating to chosen compounds up/down arrow Move up/down compound list* Escape Turn hotkeys off (have to use context menu to re-enable) *Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens Log from Sat Feb 7 13:45:05 2026UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/RECEPTOR/Cyp3A4/rec- > minimized-final.pdb Summary of feedback from opening /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/RECEPTOR/Cyp3A4/rec- minimized-final.pdb --- warnings | CONECT record to nonexistent atom: (4664, 4678) CONECT record for nonexistent atom: 4678 rec-minimized-final.pdb title: 6MA7 - 5-removed waters [more info...] Chain information for rec-minimized-final.pdb #1 --- Chain | Description A | No description available Non-standard residues in rec-minimized-final.pdb #1 --- ACE — (ACE) HEM — protoporphyrin IX containing Fe NMA — (NMA) 3759 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > open > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/RECEPTOR/Cyp3A4/xtal- > lig.pdb > open > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.mol2 Opened p450_chembl_actives.mol2 containing 1655 structures (74072 atoms, 78160 bonds) ### ViewDock hotkeys on If clicked into ViewDock dialog or main 3D graphics area, the following keys are active: g/m/b/u Assign good/maybe/bad/(unrated) rating to chosen compounds up/down arrow Move up/down compound list* Escape Turn hotkeys off (have to use context menu to re-enable) *Unless in 3D graphics with a selection, in which case normal selection widening/narrowing happens > ui windowfill toggle > view > save > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs ——— End of log from Sat Feb 7 13:45:05 2026 ——— > view name session-start opened ChimeraX session > ui windowfill toggle > select ::name=""UNL"" 74072 atoms, 78160 bonds, 1655 residues, 1655 models selected > select sel :< 4 & ~sel 489 atoms, 485 bonds, 4 pseudobonds, 43 residues, 3 models selected > show sel atoms > ui tool show ""Selection Inspector"" > size =sel stickRadius 0.06 Changed 485 bond radii > label (#2#!1 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > view sel > save > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs > select clear > hide #3.1#!1-2 cartoons Drag select of 196 atoms, 5 pseudobonds, 196 bonds > ui tool show ""Selection Inspector"" > size =sel stickRadius 0.06 Changed 196 bond radii > select clear > select ::name=""HEM"" 43 atoms, 46 bonds, 4 pseudobonds, 1 residue, 2 models selected > ui tool show ""Selection Inspector"" > size =sel stickRadius 0.2 Changed 46 bond radii > select clear > save > /Users/ak87/ownCloud/owncloud/Calculations/Avoidome/P450/DOCKING/Cyp3A4/CHEMBL/p450_chembl_actives.cxs ——— End of log from Mon Feb 9 15:27:24 2026 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Model Number: MK193LL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 31 день, 19 годин і 48 хвилин Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 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: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 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 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-clix: 0.2.5 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11 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: 1.1.4 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: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 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: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 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: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 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-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 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: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 narwhals: 2.16.0 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: 2.4.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 plotly: 6.5.2 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pyKVFinder: 0.9.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.0.0 roman-numerals-py: 4.0.0 rpds-py: 0.30.0 scipy: 1.14.0 Send2Trash: 1.8.3 SEQCROW: 1.9.7 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tomlkit: 0.14.0 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit duplicate Eric Pettersen all ChimeraX