![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17443 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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)
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{
"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. Bytes before following region: 4505870336\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10c922000-10c926000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":66238},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4505870336\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10c922000-10c926000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
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/2B6/4rql.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
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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