id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17443 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-x86_64-i386-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Current thread 0x00007ff859599b00 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 56) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-20 23:51:51.00 -0400"",""app_version"":""1.9.0"",""slice_uuid"":""079d39d3-a489-3e56-92d8-c781f5a4bb98"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""3C44DB7B-B218-4001-BEEB-6C6FF4DB1984""} { ""uptime"" : 670000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 504, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 99949, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-04-20 23:51:40.1508 -0400"", ""codeSigningMonitor"" : 0, ""incident"" : ""3C44DB7B-B218-4001-BEEB-6C6FF4DB1984"", ""pid"" : 66238, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-04-18 00:15:56.0784 -0400"", ""procStartAbsTime"" : 584723084990023, ""procExitAbsTime"" : 672441281018028, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.9.0"",""CFBundleVersion"":""1.9.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""ABE1D350-2A1A-5F02-B3DF-6EFD7FF01F30"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""10E5AAB0-2D77-F053-6FC6-967B8EE6BFCB"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""bootSessionUUID"" : ""265710F5-76F1-4A70-8487-31B64DD94190"", ""wakeTime"" : 5758, ""bridgeVersion"" : {""build"":""22P3060"",""train"":""9.3""}, ""sleepWakeUUID"" : ""BC8E368D-64EB-4893-9281-7C94EAAEAF3D"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/4rql.cif"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2B6/4rql.cif --- notes | Fetching CCD CM5 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/5/CM5/CM5.cif Fetching CCD EDO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif Fetching CCD SNE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/SNE/SNE.cif 4rql.cif title: Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with a monoterpene - sabinene [more info...] Chain information for 4rql.cif #1 --- Chain | Description | UniProt A B | Cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql.cif #1 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) SNE — Sabinene ((1S,5S)-4-methylidene-1-(propan-2-yl)bicyclo[3.1.0]hexane) 4rql.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/4RQL_WT/4rql.pdb"" 4rql.pdb title: Crystal structure of A human cytochrome P450 2B6 (Y226H/K262R) In complex with A monoterpene - sabinene [more info...] Chain information for 4rql.pdb #2 --- Chain | Description | UniProt A B | cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql.pdb #2 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) SNE — sabinene ((1S,5S)-4-methylidene-1-(propan-2-yl)bicyclo[3.1.0]hexane) > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4RQL_WT/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2B6/4RQL_WT/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: 6.175 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: 6.352 Ignored bad PDB record found on line 4 REMARK INTER: 6.536 Ignored bad PDB record found on line 5 REMARK INTRA: -0.184 Ignored bad PDB record found on line 6 REMARK UNBOUND: -0.184 37 messages similar to the above omitted Opened vina_dock.pdbqt containing 3 structures (30 atoms, 33 bonds) > viewdockx #3.1-3 > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/4RQL_WT/4rql.pdb"" > format pdb 4rql.pdb title: Crystal structure of A human cytochrome P450 2B6 (Y226H/K262R) In complex with A monoterpene - sabinene [more info...] Chain information for 4rql.pdb #1 --- Chain | Description | UniProt A B | cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql.pdb #1 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) SNE — sabinene ((1S,5S)-4-methylidene-1-(propan-2-yl)bicyclo[3.1.0]hexane) > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4RQL_WT/vina_dock.pdbqt"" format pdbqt Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2B6/4RQL_WT/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: 6.175 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: 6.352 Ignored bad PDB record found on line 4 REMARK INTER: 6.536 Ignored bad PDB record found on line 5 REMARK INTRA: -0.184 Ignored bad PDB record found on line 6 REMARK UNBOUND: -0.184 37 messages similar to the above omitted Opened vina_dock.pdbqt containing 3 structures (30 atoms, 33 bonds) > viewdockx #2.1-3 > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/4rql.cif"" format > mmcif 4rql.cif title: Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with a monoterpene - sabinene [more info...] Chain information for 4rql.cif #3 --- Chain | Description | UniProt A B | Cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql.cif #3 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) SNE — Sabinene ((1S,5S)-4-methylidene-1-(propan-2-yl)bicyclo[3.1.0]hexane) 4rql.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select ::name=""SNE"" 40 atoms, 44 bonds, 4 residues, 2 models selected > style sel ball Changed 40 atom styles > hide #2.3 models > show #2.3 models > hide #2.2 models > show #2.2 models > hide #2.1 models > show #2.1 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #3.1 models > show #3.1 models > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4rql_WT_Apo/4rql_apo.pdb"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2B6/4rql_WT_Apo/4rql_apo.pdb --- warnings | Ignored bad PDB record found on line 8337 Ignored bad PDB record found on line 8385 CONECT record for nonexistent atom: 7626 4rql_apo.pdb title: Crystal structure of A human cytochrome P450 2B6 (Y226H/K262R) In complex with A monoterpene - sabinene [more info...] Chain information for 4rql_apo.pdb #1 --- Chain | Description | UniProt A B | cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql_apo.pdb #1 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4rql_WT_Apo/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2B6/4rql_WT_Apo/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.294 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -7.504 Ignored bad PDB record found on line 4 REMARK INTER: -7.721 Ignored bad PDB record found on line 5 REMARK INTRA: 0.217 Ignored bad PDB record found on line 6 REMARK UNBOUND: 0.217 261 messages similar to the above omitted Opened vina_dock.pdbqt containing 19 structures (190 atoms, 209 bonds) > viewdockx #2.1-19 > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/4rql.cif"" 4rql.cif title: Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with a monoterpene - sabinene [more info...] Chain information for 4rql.cif #3 --- Chain | Description | UniProt A B | Cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql.cif #3 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) SNE — Sabinene ((1S,5S)-4-methylidene-1-(propan-2-yl)bicyclo[3.1.0]hexane) 4rql.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select ::name=""SNE"" 20 atoms, 22 bonds, 2 residues, 1 model selected > cofr sel > style sel ball Changed 20 atom styles > hide #2.1-19 models > show #2.1 models > show #2.2 models > show #2.3 models > show #2.4 models > show #2.5 models > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif"" > format mmcif Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif --- warning | Atom C1 has no neighbors to form bonds with according to residue template for KLN /C:1499 2v0m.cif title: Crystal structure of human P450 3A4 in complex with ketoconazole [more info...] Chain information for 2v0m.cif #1 --- Chain | Description | UniProt A B C D | CYTOCHROME P450 3A4 | CP3A4_HUMAN 25-503 Non-standard residues in 2v0m.cif #1 --- HEM — protoporphyrin IX containing Fe (HEME) KLN — 1-acetyl-4-(4-{[(2S,4R)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine 2v0m.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select ::name=""KLN"" 246 atoms, 270 bonds, 8 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_apo.pdb"" > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj.cif"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj.cif --- notes | Fetching CCD 225 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/5/225/225.cif Fetching CCD PLM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/PLM/PLM.cif 2nnj.cif title: CYP2C8dH complexed with felodipine [more info...] Chain information for 2nnj.cif #1 --- Chain | Description | UniProt A | Cytochrome P450 2C8 | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj.cif #1 --- 225 — felodipine (ethyl methyl (4R)-4-(2,3-dichlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > select ::name=""225"" 25 atoms, 26 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj_apo.pdb"" > relModel #1 > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/4RQL_K139E.pdb"" Chain information for 4RQL_K139E.pdb #1 --- Chain | Description A B | No description available > select ::name=""SNE"" 20 atoms, 22 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4RQL_K139E_apo.pdb"" relModel #1 > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4RQL_K262R_Q172H.pdb"" Chain information for 4RQL_K262R_Q172H.pdb #1 --- Chain | Description A B | No description available > select ::name=""SNE"" 20 atoms, 22 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4RQL_K262R_Q172H_apo.pdb"" relModel #1 > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4RQL_K262R_Q172H_apo.pdb"" format pdb Chain information for 4RQL_K262R_Q172H_apo.pdb #1 --- Chain | Description A B | No description available > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/4RQL_K262R.pdb"" Chain information for 4RQL_K262R.pdb #1 --- Chain | Description A B | No description available > select ::name=""SNE"" 20 atoms, 22 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4RQL_K262R_apo.pdb"" relModel #1 > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4RQL_K262R_apo.pdb"" format pdb Chain information for 4RQL_K262R_apo.pdb #1 --- Chain | Description A B | No description available > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/4RQL_Q172H.pdb"" Chain information for 4RQL_Q172H.pdb #1 --- Chain | Description A B | No description available > select ::name=""SNE"" 20 atoms, 22 bonds, 2 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4RQL_Q172H_apo.pdb"" relModel #1 > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_L293P.pdb"" Chain information for 2v0m_L293P.pdb #1 --- Chain | Description A B C D | No description available > select ::name=""KLN"" 246 atoms, 270 bonds, 8 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_L293P_apo.pdb"" > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_R130Q.pdb"" Chain information for 2v0m_R130Q.pdb #1 --- Chain | Description A B C D | No description available > select ::name=""KLN"" 246 atoms, 270 bonds, 8 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_R130Q_apo.pdb"" > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_T185S.pdb"" Chain information for 2v0m_T185S.pdb #1 --- Chain | Description A B C D | No description available > select ::name=""KLN"" 246 atoms, 270 bonds, 8 residues, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_T185S_apo.pdb"" > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj_I264M.pdb"" 2nnj_I264M.pdb title: CYP2C8DH complexed with felodipine [more info...] Chain information for 2nnj_I264M.pdb #1 --- Chain | Description | UniProt A | CYPIIC8; P450 FORM 1; P450 MP-12/MP-20; P450 IIC2; S- mephenytoin 4-hydroxylase | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj_I264M.pdb #1 --- 225 — felodipine (ethyl methyl (4R)-4-(2,3-dichlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > select ::name=""225"" 25 atoms, 26 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/2C8/2nnj_I264M_apo.pdb"" relModel #1 > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj_I269F.pdb"" 2nnj_I269F.pdb title: CYP2C8DH complexed with felodipine [more info...] Chain information for 2nnj_I269F.pdb #1 --- Chain | Description | UniProt A | CYPIIC8; P450 FORM 1; P450 MP-12/MP-20; P450 IIC2; S- mephenytoin 4-hydroxylase | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj_I269F.pdb #1 --- 225 — felodipine (ethyl methyl (4R)-4-(2,3-dichlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > select ::name=""225"" 25 atoms, 26 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/2C8/2nnj_I269F_apo.pdb"" relModel #1 > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/2C8/2nnj_K399R_R139K.pdb"" 2nnj_K399R_R139K.pdb title: CYP2C8DH complexed with felodipine [more info...] Chain information for 2nnj_K399R_R139K.pdb #1 --- Chain | Description | UniProt A | CYPIIC8; P450 FORM 1; P450 MP-12/MP-20; P450 IIC2; S- mephenytoin 4-hydroxylase | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj_K399R_R139K.pdb #1 --- 225 — felodipine (ethyl methyl (4R)-4-(2,3-dichlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > select ::name=""225"" 25 atoms, 26 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/2C8/2nnj_K399R_R139K_apo.pdb"" relModel #1 > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_WT_holo/2v0m.pdb"" 2v0m.pdb title: Crystal structure of human P450 3A4 In complex with ketoconazole [more info...] Chain information for 2v0m.pdb #1 --- Chain | Description | UniProt A B C D | cytochrome P450 3A4 | CP3A4_HUMAN 25-503 Non-standard residues in 2v0m.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) KLN — 1-acetyl-4-(4-{[(2S,4R)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_WT_holo/2v0m.pdb"" 2v0m.pdb title: Crystal structure of human P450 3A4 In complex with ketoconazole [more info...] Chain information for 2v0m.pdb #1 --- Chain | Description | UniProt A B C D | cytochrome P450 3A4 | CP3A4_HUMAN 25-503 Non-standard residues in 2v0m.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) KLN — 1-acetyl-4-(4-{[(2S,4R)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) > set bgColor #ffffff00 Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > undo > set bgColor black > set bgColor transparent > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_WT_apo/2v0m_apo.pdb"" Chain information for 2v0m_apo.pdb #1 --- Chain | Description A B C D | No description available > ui tool show ViewDockX No suitable models found for ViewDockX > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_WT_apo/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m_WT_apo/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -10.331 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -15.570 Ignored bad PDB record found on line 4 REMARK INTER: -14.558 Ignored bad PDB record found on line 5 REMARK INTRA: -1.012 Ignored bad PDB record found on line 6 REMARK UNBOUND: -1.012 546 messages similar to the above omitted Opened vina_dock.pdbqt containing 19 structures (684 atoms, 760 bonds) > viewdockx #2.1-19 > open ""/Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif --- warning | Atom C1 has no neighbors to form bonds with according to residue template for KLN /C:1499 2v0m.cif title: Crystal structure of human P450 3A4 in complex with ketoconazole [more info...] Chain information for 2v0m.cif #3 --- Chain | Description | UniProt A B C D | CYTOCHROME P450 3A4 | CP3A4_HUMAN 25-503 Non-standard residues in 2v0m.cif #3 --- HEM — protoporphyrin IX containing Fe (HEME) KLN — 1-acetyl-4-(4-{[(2S,4R)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine 2v0m.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > hide #!2 models > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > select ::name=""KLN"" 246 atoms, 270 bonds, 8 residues, 1 model selected > style sel ball Changed 246 atom styles > color sel byhetero > color sel byelement > show #!2 models > hide #2.1-19 models > show #2.1 models > show #2.2 models > show #2.3 models > show #2.4 models > show #2.5 models > select clear > select #1/B 3666 atoms, 3755 bonds, 8 pseudobonds, 452 residues, 3 models selected > cartoon hide (#!1 & sel) > hide (#!1 & sel) target a > hide #!3 models > show #!3 models > select #3/B 3724 atoms, 3819 bonds, 9 pseudobonds, 454 residues, 3 models selected > select add #1/C 7501 atoms, 7688 bonds, 15 pseudobonds, 920 residues, 6 models selected > select add #1/D 11186 atoms, 11464 bonds, 22 pseudobonds, 1374 residues, 6 models selected > select add #3/C 15021 atoms, 15395 bonds, 29 pseudobonds, 1842 residues, 6 models selected > select add #3/D 18764 atoms, 19235 bonds, 37 pseudobonds, 2298 residues, 6 models selected > hide sel cartoons > hide sel atoms > select ::name=""KLN"" 246 atoms, 270 bonds, 8 residues, 1 model selected > cofr sel > color sel magenta > color sel cyan > color sel orange red > color sel byelement > hide #2.1-5 models > show #2.5 models > show #2.1 models > hide #2.5 models > show #2.2 models > show #2.3 models > color sel lime > ui tool show ""Color Actions"" > color sel byhetero > color sel hot pink > color sel byhetero > color sel magenta > select clear > select ::name=""KLN"" 246 atoms, 270 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel byhetero > select ::name=""HEM"" 344 atoms, 368 bonds, 32 pseudobonds, 8 residues, 4 models selected > color (#!1,3 & sel) red > color (#!1,3 & sel) byhetero > select ~sel & ##selected 29546 atoms, 30272 bonds, 28 pseudobonds, 3656 residues, 6 models selected > select clear > hide #2.1-3 models > show #2.2 models > hide #2.2 models > show #2.1 models > show #2.2 models > show #2.3 models > hide #2.2 models > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_apo.png"" width 1211 height 797 supersample 3 > select add #1 14822 atoms, 15185 bonds, 28 pseudobonds, 1828 residues, 4 models selected > select subtract #1 Nothing selected > hide #2.3 models > hide #!3 models > show #!3 models > select add #3 15068 atoms, 15455 bonds, 32 pseudobonds, 1836 residues, 4 models selected > hide sel atoms > show sel atoms > undo > select ::name=""KLN"" 246 atoms, 270 bonds, 8 residues, 1 model selected > show sel atoms > select #2:293,130,185 Nothing selected > show #2.1#!1,3 atoms > undo > select #3:293,130,185 104 atoms, 92 bonds, 12 residues, 1 model selected > show sel atoms > style sel ball Changed 104 atom styles > color sel white > hide sel atoms > select #3/a:293,130,185 26 atoms, 23 bonds, 3 residues, 1 model selected > show sel atoms > ui tool show ""Side View"" > select #3/b:kln 58 atoms, 64 bonds, 2 residues, 1 model selected > hide sel atoms > select #3/c:kln 58 atoms, 62 bonds, 2 residues, 1 model selected > hide sel atoms > select #3/d:kln 58 atoms, 64 bonds, 2 residues, 1 model selected > hide sel atoms > select up 3743 atoms, 3840 bonds, 456 residues, 1 model selected > select #3/a:293,130,185 26 atoms, 23 bonds, 3 residues, 1 model selected > label sel attribute name > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select clear > hide #2.1#!1,3 cartoons > undo No visible atoms selected > hide #!3.2 models > show #!3.2 models > hide #!1.2 models > hide #1.2.1 models > hide #3.2.1 models > hide #3.3 models > show #3.3 models > show #1.2.1 models > hide #1.2.1 models > show #3.2.1 models > hide #3.2.1 models > set bgColor white > set bgColor #ffffff00 > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_docked_labels.png"" width 1211 height 797 supersample 3 > select #3/a:293,130,185 26 atoms, 23 bonds, 3 residues, 1 model selected > color sel dark gray > color sel gray > color sel #797979ff > color sel #5e5e5eff > color sel #424242ff > color sel #797979ff > color sel byhetero > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_Docked_labeled.png"" width 1211 height 797 supersample 3 > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_WT_docked.cxs"" > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_L293Pmutant/2v0m_L293P_apo.pdb"" Chain information for 2v0m_L293P_apo.pdb #1 --- Chain | Description A B C D | No description available > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_L293Pmutant/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m_L293Pmutant/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -10.271 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -15.551 Ignored bad PDB record found on line 4 REMARK INTER: -14.475 Ignored bad PDB record found on line 5 REMARK INTRA: -1.076 Ignored bad PDB record found on line 6 REMARK UNBOUND: -1.076 488 messages similar to the above omitted Opened vina_dock.pdbqt containing 17 structures (612 atoms, 680 bonds) > viewdockx #2.1-17 > open ""/Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif"" > format mmcif Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif --- warning | Atom C1 has no neighbors to form bonds with according to residue template for KLN /C:1499 2v0m.cif title: Crystal structure of human P450 3A4 in complex with ketoconazole [more info...] Chain information for 2v0m.cif #3 --- Chain | Description | UniProt A B C D | CYTOCHROME P450 3A4 | CP3A4_HUMAN 25-503 Non-standard residues in 2v0m.cif #3 --- HEM — protoporphyrin IX containing Fe (HEME) KLN — 1-acetyl-4-(4-{[(2S,4R)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine 2v0m.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > select ::name=""KLN"" 246 atoms, 270 bonds, 8 residues, 1 model selected > style sel ball Changed 246 atom styles > hide #2.1-17 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 #2.1 models > show #2.2 models > select #3/b,c,d 11302 atoms, 11590 bonds, 24 pseudobonds, 1378 residues, 3 models selected > hide sel cartoons > hide sel atoms > select #1/b,c,d 11125 atoms, 11400 bonds, 21 pseudobonds, 1372 residues, 3 models selected > hide sel cartoons > hide sel atoms > select clear > select #3/a:293,130,185 26 atoms, 23 bonds, 3 residues, 1 model selected > show sel atoms > style sel ball Changed 26 atom styles > color sel #797979ff > label sel text ""{0.name} {0.number}{0.insertion_code}"" > hide sel atoms > select #1/a:293,130,185 25 atoms, 23 bonds, 3 residues, 1 model selected > show sel atoms > style sel ball Changed 25 atom styles > color sel #797979ff > color sel byelement > color sel #797979ff > color sel byhetero > select ::name=""HEM"" 344 atoms, 368 bonds, 32 pseudobonds, 8 residues, 4 models selected > color (#!1,3 & sel) red > color (#!1,3 & sel) byhetero > hide #2.2 models > show #2.2 models > select #3/a:kln 72 atoms, 80 bonds, 2 residues, 1 model selected > color sel #008f00ff > color sel #4f8f00ff > color sel #009051ff > color sel #4f8f00ff > color sel #929000ff > color sel #4f8f00ff > color sel #d783ffff > color sel #ff85ffff > color sel #942193ff > color sel #941751ff > color sel #531b93ff > color sel #942193ff > color sel #c0c0c0ff > color sel #941100ff > color sel #ff2600ff > color sel #4f8f00ff > color sel #008f00ff > color sel #009051ff > color sel #009193ff > color sel #009051ff > color sel #00fa92ff > color sel #00f900ff > color sel #ff85ffff > color sel #ff40ffff > color sel #ff2f92ff > color sel byhetero > select clear > hide #3.2.1 models > hide #1.2.1 models > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_L293P_docked.cxs"" > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_L293P_docked.png"" width 1211 height 797 supersample 3 > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_R130Qmutant/2v0m_R130Q_apo.pdb"" Chain information for 2v0m_R130Q_apo.pdb #1 --- Chain | Description A B C D | No description available > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_R130Qmutant/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m_R130Qmutant/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -10.234 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -15.499 Ignored bad PDB record found on line 4 REMARK INTER: -14.421 Ignored bad PDB record found on line 5 REMARK INTRA: -1.077 Ignored bad PDB record found on line 6 REMARK UNBOUND: -1.077 575 messages similar to the above omitted Opened vina_dock.pdbqt containing 20 structures (720 atoms, 800 bonds) > viewdockx #2.1-20 > open ""/Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif"" > format mmcif Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif --- warning | Atom C1 has no neighbors to form bonds with according to residue template for KLN /C:1499 2v0m.cif title: Crystal structure of human P450 3A4 in complex with ketoconazole [more info...] Chain information for 2v0m.cif #3 --- Chain | Description | UniProt A B C D | CYTOCHROME P450 3A4 | CP3A4_HUMAN 25-503 Non-standard residues in 2v0m.cif #3 --- HEM — protoporphyrin IX containing Fe (HEME) KLN — 1-acetyl-4-(4-{[(2S,4R)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine 2v0m.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > hide #2.1-20 models > show #2.1 models > show #2.2 models > show #2.3 models > show #2.4 models > close session > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_T185S/2v0m_T185S_apo.pdb"" Chain information for 2v0m_T185S_apo.pdb #1 --- Chain | Description A B C D | No description available > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/3A4/2V0M/2v0m_T185S/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m_T185S/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -10.034 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -15.306 Ignored bad PDB record found on line 4 REMARK INTER: -14.140 Ignored bad PDB record found on line 5 REMARK INTRA: -1.166 Ignored bad PDB record found on line 6 REMARK UNBOUND: -1.166 575 messages similar to the above omitted Opened vina_dock.pdbqt containing 20 structures (720 atoms, 800 bonds) > viewdockx #2.1-20 > open ""/Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif"" > format mmcif Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/3A4/2V0M/2v0m.cif --- warning | Atom C1 has no neighbors to form bonds with according to residue template for KLN /C:1499 2v0m.cif title: Crystal structure of human P450 3A4 in complex with ketoconazole [more info...] Chain information for 2v0m.cif #3 --- Chain | Description | UniProt A B C D | CYTOCHROME P450 3A4 | CP3A4_HUMAN 25-503 Non-standard residues in 2v0m.cif #3 --- HEM — protoporphyrin IX containing Fe (HEME) KLN — 1-acetyl-4-(4-{[(2S,4R)-2-(2,4-dichlorophenyl)-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy}phenyl)piperazine 2v0m.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > hide #2.1-20 models > show #2.1 models > show #2.2 models > show #2.3 models > show #2.4 models > show #2.5 models > hide #2.3 models > hide #2.4 models > show #2.6 models > hide #2.6 models > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2NNJ I264M > ZIP/2nnj_I264M_apo.pdb"" 2nnj_I264M_apo.pdb title: CYP2C8DH complexed with felodipine [more info...] Chain information for 2nnj_I264M_apo.pdb #4 --- Chain | Description | UniProt A | CYPIIC8; P450 FORM 1; P450 MP-12/MP-20; P450 IIC2; S- mephenytoin 4-hydroxylase | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj_I264M_apo.pdb #4 --- HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2NNJ I264M > ZIP/2nnj_I264M_apo.pdb"" format pdb 2nnj_I264M_apo.pdb title: CYP2C8DH complexed with felodipine [more info...] Chain information for 2nnj_I264M_apo.pdb #1 --- Chain | Description | UniProt A | CYPIIC8; P450 FORM 1; P450 MP-12/MP-20; P450 IIC2; S- mephenytoin 4-hydroxylase | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj_I264M_apo.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2NNJ I264M > ZIP/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2C8/2NNJ I264M ZIP/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.246 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -10.568 Ignored bad PDB record found on line 4 REMARK INTER: -9.788 Ignored bad PDB record found on line 5 REMARK INTRA: -0.780 Ignored bad PDB record found on line 6 REMARK UNBOUND: -0.780 333 messages similar to the above omitted Opened vina_dock.pdbqt containing 13 structures (338 atoms, 351 bonds) > viewdockx #2.1-13 > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj.cif"" 2nnj.cif title: CYP2C8dH complexed with felodipine [more info...] Chain information for 2nnj.cif #3 --- Chain | Description | UniProt A | Cytochrome P450 2C8 | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj.cif #3 --- 225 — felodipine (ethyl methyl (4R)-4-(2,3-dichlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > select ::name=""225"" 25 atoms, 26 bonds, 1 residue, 1 model selected > style sel ball Changed 25 atom styles > color sel #ff2f92ff > color sel byhetero > hide #2.1-13 models > show #2.1 models > show #2.2 models > show #2.3 models > show #2.4 models > show #2.5 models > hide #2.5 models > hide #2.1-4 models > show #2.4 models > hide #2.4 models > show #2.1 models > show #2.2 models > show #2.3 models > hide #2.3 models > show #2.3 models > hide #2.2 models > hide #2.1 models > show #2.4 models > show #2.5 models > hide #2.5 models > show #2.5 models > hide #2.3 models > hide #2.4 models > select #3/a:264,269,399 25 atoms, 22 bonds, 3 residues, 1 model selected > show sel atoms > style sel ball Changed 25 atom styles > color sel #797979ff > color sel byhetero > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select ::name=""HEM"" 86 atoms, 92 bonds, 8 pseudobonds, 2 residues, 4 models selected > color (#!1,3 & sel) red > color (#!1,3 & sel) byhetero > ui tool show ""Side View"" > select ::name=""PLM"" 36 atoms, 34 bonds, 2 residues, 2 models selected > select ::name=""SO4"" 30 atoms, 24 bonds, 6 residues, 2 models selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select clear > show #2.1 models > hide #2.5 models > show #2.5 models > hide #2.5 models > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/2C8/2nnj_I264M_Docked.png"" width 1211 height 797 supersample 3 > save ""/Users/stephenmills/Documents/Research/CYP > Stuff/2C8/2nnj_I264M_Docked.cxs"" > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2NNJ I269F > ZIP/2nnj_I269F_apo.pdb"" 2nnj_I269F_apo.pdb title: CYP2C8DH complexed with felodipine [more info...] Chain information for 2nnj_I269F_apo.pdb #1 --- Chain | Description | UniProt A | CYPIIC8; P450 FORM 1; P450 MP-12/MP-20; P450 IIC2; S- mephenytoin 4-hydroxylase | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj_I269F_apo.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2NNJ I269F > ZIP/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2C8/2NNJ I269F ZIP/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.454 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -11.680 Ignored bad PDB record found on line 4 REMARK INTER: -10.069 Ignored bad PDB record found on line 5 REMARK INTRA: -1.611 Ignored bad PDB record found on line 6 REMARK UNBOUND: -1.611 333 messages similar to the above omitted Opened vina_dock.pdbqt containing 13 structures (338 atoms, 351 bonds) > viewdockx #2.1-13 > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj.cif"" format > mmcif 2nnj.cif title: CYP2C8dH complexed with felodipine [more info...] Chain information for 2nnj.cif #3 --- Chain | Description | UniProt A | Cytochrome P450 2C8 | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj.cif #3 --- 225 — felodipine (ethyl methyl (4R)-4-(2,3-dichlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > hide #2.1-13 models > show #2.1 models > show #2.2 models > show #2.3 models > show #2.4 models > show #2.5 models > show #2.6 models > show #2.7 models > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj K399R > ZIP/2nnj_K399R_R139K_apo.pdb"" 2nnj_K399R_R139K_apo.pdb title: CYP2C8DH complexed with felodipine [more info...] Chain information for 2nnj_K399R_R139K_apo.pdb #1 --- Chain | Description | UniProt A | CYPIIC8; P450 FORM 1; P450 MP-12/MP-20; P450 IIC2; S- mephenytoin 4-hydroxylase | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj_K399R_R139K_apo.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj K399R > ZIP/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj K399R ZIP/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.132 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -10.563 Ignored bad PDB record found on line 4 REMARK INTER: -9.634 Ignored bad PDB record found on line 5 REMARK INTRA: -0.929 Ignored bad PDB record found on line 6 REMARK UNBOUND: -0.929 333 messages similar to the above omitted Opened vina_dock.pdbqt containing 13 structures (338 atoms, 351 bonds) > viewdockx #2.1-13 > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2C8/2nnj.cif"" format > mmcif 2nnj.cif title: CYP2C8dH complexed with felodipine [more info...] Chain information for 2nnj.cif #3 --- Chain | Description | UniProt A | Cytochrome P450 2C8 | CP2C8_HUMAN 28-490 Non-standard residues in 2nnj.cif #3 --- 225 — felodipine (ethyl methyl (4R)-4-(2,3-dichlorophenyl)-2,6-dimethyl-1,4-dihydropyridine-3,5-dicarboxylate) HEM — protoporphyrin IX containing Fe (HEME) PLM — palmitic acid SO4 — sulfate ion > hide #2.1-13 models > show #2.1 models > show #2.2 models > show #2.3 models > ui tool show ""Find Cavities"" > help help:user/tools/findcavities.html > ui tool show ViewDockX > show #2.4-13 models > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/results- > 4rql_WTapo.pdb/4rql_WTapo.pdb"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2B6/results- 4rql_WTapo.pdb/4rql_WTapo.pdb --- warnings | Ignored bad PDB record found on line 8337 Ignored bad PDB record found on line 8385 CONECT record for nonexistent atom: 7626 4rql_WTapo.pdb title: Crystal structure of A human cytochrome P450 2B6 (Y226H/K262R) In complex with A monoterpene - sabinene [more info...] Chain information for 4rql_WTapo.pdb #4 --- Chain | Description | UniProt A B | cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql_WTapo.pdb #4 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) > close session > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/results- > 4rql_WTapo.pdb/4rql_WTapo.pdb"" format pdb Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2B6/results- 4rql_WTapo.pdb/4rql_WTapo.pdb --- warnings | Ignored bad PDB record found on line 8337 Ignored bad PDB record found on line 8385 CONECT record for nonexistent atom: 7626 4rql_WTapo.pdb title: Crystal structure of A human cytochrome P450 2B6 (Y226H/K262R) In complex with A monoterpene - sabinene [more info...] Chain information for 4rql_WTapo.pdb #1 --- Chain | Description | UniProt A B | cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql_WTapo.pdb #1 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) > open ""/Users/stephenmills/Documents/Research/CYP Stuff/2B6/4rql.cif"" 4rql.cif title: Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with a monoterpene - sabinene [more info...] Chain information for 4rql.cif #2 --- Chain | Description | UniProt A B | Cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql.cif #2 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) SNE — Sabinene ((1S,5S)-4-methylidene-1-(propan-2-yl)bicyclo[3.1.0]hexane) 4rql.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > open ""/Users/stephenmills/Documents/Research/CYP > Stuff/2B6/4rql_WT_Apo/vina_dock.pdbqt"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2B6/4rql_WT_Apo/vina_dock.pdbqt --- warnings | Ignored bad PDB record found on line 2 REMARK VINA RESULT: -7.294 0.000 0.000 Ignored bad PDB record found on line 3 REMARK INTER + INTRA: -7.504 Ignored bad PDB record found on line 4 REMARK INTER: -7.721 Ignored bad PDB record found on line 5 REMARK INTRA: 0.217 Ignored bad PDB record found on line 6 REMARK UNBOUND: 0.217 261 messages similar to the above omitted Opened vina_dock.pdbqt containing 19 structures (190 atoms, 209 bonds) > viewdockx #3.1-19 > hide #3.1-19 models > show #3.1 models > show #3.2 models > show #3.3 models > show #3.4 models > show #3.5 models > show #3.6-19 models > hide #3.1-19 models > show #3.1 models > hide #3.1 models > show #3.2 models > hide #3.2 models > show #3.2 models > lighting simple > lighting soft > lighting full > lighting simple > lighting full > ui tool show ""Basic Actions"" > ui tool show ""Color Actions"" > toolshed show > close session ===== Log before crash end ===== Log: 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/stephenmills/Documents/Research/CYP Stuff/2B6/results- > 4rql_WTapo.pdb/4rql_WTapo.pdb"" Summary of feedback from opening /Users/stephenmills/Documents/Research/CYP Stuff/2B6/results- 4rql_WTapo.pdb/4rql_WTapo.pdb --- warnings | Ignored bad PDB record found on line 8337 Ignored bad PDB record found on line 8385 CONECT record for nonexistent atom: 7626 4rql_WTapo.pdb title: Crystal structure of A human cytochrome P450 2B6 (Y226H/K262R) In complex with A monoterpene - sabinene [more info...] Chain information for 4rql_WTapo.pdb #1 --- Chain | Description | UniProt A B | cytochrome P450 2B6 | CP2B6_HUMAN 20-491 Non-standard residues in 4rql_WTapo.pdb #1 --- CM5 — 5-cyclohexyl-1-pentyl-β-D-maltoside (5-cyclohexylpentyl 4-O-α-D- glucopyranosyl-β-D-glucopyranoside; cymal-5) EDO — 1,2-ethanediol (ethylene glycol) HEM — protoporphyrin IX containing Fe (HEME) OpenGL version: 4.1 ATI-6.1.13 OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.6 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13060.0.0,0) OS Loader Version: 582~3311 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 17 days, 23 hours, 26 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5300M: Chipset Model: AMD Radeon Pro 5300M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0043 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32207P1-020 Option ROM Version: 113-D32207P1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX