![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 17 months ago
Closed 17 months ago
#15364 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000098fe000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007ff84dea5b80 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py", line 717 in __call__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py", line 1512 in __and__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 798 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 798 in decode_modifier_bits
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 790 in key_modifiers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 555 in _event_type
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 534 in _dispatch_mouse_event
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 651 in
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 55)
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{
"uptime" : 2200000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 270987,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2024-06-03 17:25:04.4540 -0700",
"codeSigningMonitor" : 0,
"incident" : "3B37F680-9D31-4F28-8D66-EBCE5DBE1B53",
"pid" : 78490,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-03 01:52:22.3081 -0700",
"procStartAbsTime" : 2154196179639878,
"procExitAbsTime" : 2210156649469968,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"82368D1D-151E-5B90-BB7C-1A0331B6D1D2","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BD5FC20C-ECB6-43AC-EB46-C14BBF6600ED",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 346010,
"bridgeVersion" : {"build":"21P2057","train":"8.2"},
"sleepWakeUUID" : "48E948FA-3DA3-40C9-A3F5-008BE2320DB2",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737488076631\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffbc000-7ffffffbd000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":78490},
"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" : "0xa9 is not in any region. Bytes before following region: 140737488076631\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffbc000-7ffffffbd000 [ 4K] r-x\/r-x SM=SHM ",
"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
---
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
[Repeated 1 time(s)]
> open
> /Users/APCamargo-M55/Downloads/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Summary of feedback from opening
/Users/APCamargo-M55/Downloads/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK The PDB FILE IS CREATED BY CY's PROGRAM CurvatureSurface AT Mon Jun 3
23:17:28 2024
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
[Repeated 1 time(s)]
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> color bfactor protein palette viridis
308 atoms, 40 residues, atom bfactor range 0.81 to 4.32
> select #1.1/A
308 atoms, 312 bonds, 40 residues, 1 model selected
> hbonds sel #1.2/A
Expected a keyword
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> hbonds #1.1/A #1.2/A
40 hydrogen bonds found
> ~hbonds
> hbonds #1.1/A restrict #1.2/A
0 hydrogen bonds found
> ~hbonds
> hbonds sel reveal true
38 hydrogen bonds found
> close
> open
> /Users/APCamargo-M55/Downloads/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
> format pdb
Summary of feedback from opening
/Users/APCamargo-M55/Downloads/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
warning | Ignored bad PDB record found on line 1
REMARK The PDB FILE IS CREATED BY CY's PROGRAM CurvatureSurface AT Mon Jun 3
23:17:28 2024
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> hbonds reveal true
40 hydrogen bonds found
> ~hbonds
> hbonds #1.1/A #1.2/A
40 hydrogen bonds found
> hbonds #1.1/A restrict #1.2/A
0 hydrogen bonds found
> hbonds reveal true
40 hydrogen bonds found
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> color bfactor protein palette viridis
308 atoms, 40 residues, atom bfactor range 0.81 to 4.32
> lighting soft
> color bfactor protein palette viridis
308 atoms, 40 residues, atom bfactor range 0.81 to 4.32
> color bfactor protein palette rocket
Fetching compressed palette rocket from
https://www.colourlovers.com/api/palettes?keywords=rocket&format=json&numResults=100
Found 2 ColourLover palettes with name "rocket", using palette id 110215 by
author vipanchi with most views (458). To choose a different one use "name by
author" or id number.
308 atoms, 40 residues, atom bfactor range 0.81 to 4.32
> color bfactor protein palette araucaria
308 atoms, 40 residues, atom bfactor range 0.81 to 4.32
> color bfactor protein palette tokyo
308 atoms, 40 residues, atom bfactor range 0.81 to 4.32
> color bfactor protein palette sunset
308 atoms, 40 residues, atom bfactor range 0.81 to 4.32
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 12 color #363644 depthJump 0.05
> color bfactor protein palette viridis
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 12 color #363644 depthJump 0.05
> color bfactor protein palette viridis
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 82 target s
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 4 color #363644 depthJump 0.05
> color bfactor protein palette viridis
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 82 target s
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 2 color #363644 depthJump 0.05
> color bfactor protein palette sunset
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 85 target s
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 2 color #363644 depthJump 0.05
> color bfactor protein palette tokyo
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 80 target s
> hbonds reveal true
40 hydrogen bonds found
> ~hbonds
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 2 color #363644 depthJump 0.05
> color bfactor protein palette araucaria
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 80 target s
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 2 color #363644 depthJump 0.05
> color bfactor protein palette burg
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 80 target s
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 2 color #363644 depthJump 0.05
> color bfactor protein palette tokyo
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 80 target s
> select ::name="ALA"
20 atoms, 16 bonds, 4 residues, 1 model selected
> select 271
Expected an objects specifier or a keyword
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> select #1.1 271
Expected a keyword
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> select #1.1 residues 271
Invalid "residues" argument: Expected true or false (or 1 or 0)
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> select residues #1.1 271
Invalid "residues" argument: Expected true or false (or 1 or 0)
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> select clear
> hide #1.2 models
> show #1.2 models
> hide #2 models
> show #2 models
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 2 color #363644 depthJump 0.05
> color bfactor protein palette tokyo
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 80 target s
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 2 color #363644 depthJump 0.05
> color bfactor protein palette tokyo
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 80 target s
> ui tool show "Show Sequence Viewer"
> sequence chain #1.1/A
Alignment identifier is 1.1/A
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> select #1.1/A:265
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.1/A:265
14 atoms, 15 bonds, 1 residue, 1 model selected
> select #1.1/A:265,271
25 atoms, 25 bonds, 2 residues, 1 model selected
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293
91 atoms, 86 bonds, 11 residues, 1 model selected
> select clear
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293
91 atoms, 86 bonds, 11 residues, 1 model selected
> hbonds sel & /1.2 distance 3.5 angle 30
Expected a keyword
> hbonds sel & #1.2/A distance 3.5 angle 30
Expected a keyword
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293
91 atoms, 86 bonds, 11 residues, 1 model selected
> select #1.2/A
58 atoms, 59 bonds, 1 residue, 1 model selected
> hbonds selRestrict any reveal true
Expected a keyword
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> hbonds selRestrict any reveal true
Expected a keyword
> findhbond selRestrict any reveal true
Unknown command: findhbond selRestrict any reveal true
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293
91 atoms, 86 bonds, 11 residues, 1 model selected
> select #1.2/A
58 atoms, 59 bonds, 1 residue, 1 model selected
> select clear
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293
91 atoms, 86 bonds, 11 residues, 1 model selected
> select #1.2/A
58 atoms, 59 bonds, 1 residue, 1 model selected
> select ~sel & ##selected
Nothing selected
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
149 atoms, 145 bonds, 12 residues, 2 models selected
> hbonds selRestrict any reveal true
Expected a keyword
> makePseudobonds selRestrict any reveal true
Unknown command: makePseudobonds selRestrict any reveal true
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
149 atoms, 145 bonds, 12 residues, 2 models selected
> hbonds sel ::#1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
Expected a keyword
> hbonds sel::#1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
Expected a keyword
> hbonds sel:: select #1.1/A:260,261,267,268,269,271,272,286,289,290,293
> #1.2/A
Expected a keyword
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
149 atoms, 145 bonds, 12 residues, 2 models selected
> hbonds sel #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
Expected a keyword
> hbonds cutoffDistance 3.5 cutoffAngle 30
Expected a keyword
> hbonds cutoffDistance 3.5 cutoffAngle 30
Expected a keyword
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
20 hydrogen bonds found
> hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A restrict
> cross
12 hydrogen bonds found
> hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
20 hydrogen bonds found
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A)
Atom specifier selects no atoms
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) reveal
> true showDist true
Atom specifier selects no atoms
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) reveal
> true showDist true
Atom specifier selects no atoms
> ~hbonds
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) reveal
> true showDist true
Atom specifier selects no atoms
> addh #1.1/A
Summary of feedback from adding hydrogens to
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.1
---
notes | No usable SEQRES records for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb (#1.1) chain A;
guessing termini instead
Chain-initial residues that are actual N termini:
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.1/A THR 254
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.1/A LEU 293
36 hydrogen bonds
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.1/A LEU 293
is not terminus, removing H atom from 'C'
291 hydrogens added
> addh #1.B/A
Expected a keyword
> addh #1.2/A
Summary of feedback from adding hydrogens to
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.2
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
2 hydrogen bonds
31 hydrogens added
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) reveal
> true showDist true
Atom specifier selects no atoms
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A)
Atom specifier selects no atoms
> hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
20 hydrogen bonds found
Could not find virtual screen for QCocoaScreen(0x600000d3ca50, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, )
with displayId 4128833
> hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A
20 hydrogen bonds found
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A)
Atom specifier selects no atoms
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius
> 2
Atom specifier selects no atoms
> ~hbonds
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius
> 2
Atom specifier selects no atoms
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius
> 10
Atom specifier selects no atoms
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius
> 10 reveal true
Atom specifier selects no atoms
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & 1.2/A) radius
> 10 reveal t
Expected a keyword
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius
> 10 reveal true
Atom specifier selects no atoms
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293@H & #1.2/A)
> radius 10 reveal true
Atom specifier selects no atoms
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@H
11 atoms, 11 residues, 1 model selected
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@CA
11 atoms, 11 residues, 1 model selected
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@N
11 atoms, 11 residues, 1 model selected
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@H,CA
22 atoms, 11 residues, 1 model selected
> select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@H
11 atoms, 11 residues, 1 model selected
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293@H & #1.2/A@H)
> radius 10 reveal true
Atom specifier selects no atoms
> select #1.2/A@H
Nothing selected
> select #1.2@H
Nothing selected
> select #1.2/A
89 atoms, 90 bonds, 1 residue, 1 model selected
> select #1.2/A@HC
1 atom, 1 residue, 1 model selected
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 2 color #363644 depthJump 0.05
> color bfactor protein palette tokyo
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 80 target s
> select #1.2/A@H
Nothing selected
> select H
13 atoms, 1 residue, 1 model selected
> select @H
Nothing selected
> select H
13 atoms, 1 residue, 1 model selected
> select clear
> select H
13 atoms, 1 residue, 1 model selected
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293@H & H) radius 10
> reveal true
Atom specifier selects no atoms
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 10
18 hydrogen bonds found
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 3
18 hydrogen bonds found
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius1
Expected a keyword
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 1
18 hydrogen bonds found
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 0.5
18 hydrogen bonds found
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 0.1
18 hydrogen bonds found
> hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) relax true
18 hydrogen bonds found
> hbonds protein relax true
38 hydrogen bonds found
> hbonds (protein & #1.2/A) relax true
Atom specifier selects no atoms
> hbonds #1.2/A relax true
2 hydrogen bonds found
> hbonds (protein & #1.2/A) relax true
Atom specifier selects no atoms
> hbonds (protein & #1.2/A) relax true interSubmodel true
Atom specifier selects no atoms
> hbonds (protein & #1.2/A) relax true interSubmodel true
Atom specifier selects no atoms
> hbonds (protein #1.2/A) relax true interSubmodel true
Expected a keyword
> hbonds (protein,#1.2/A) relax true interSubmodel true
Expected a keyword
> hbonds relax true interSubmodel true
48 hydrogen bonds found
> hbonds relax true interSubmodel true intraModel false
8 hydrogen bonds found
> hbonds relax false interSubmodel true intraModel false
5 hydrogen bonds found
> hbonds relax true interSubmodel true intraModel false
8 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 1
10 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 1 angleSlop 30
12 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30
33 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 20
22 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30
33 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 30
28 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 20
20 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 25
24 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 20
22 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30
33 hydrogen bonds found
> close
> runscript
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py
New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`,
`sunset`, `burg`, `tealrose`, `tokyo`, `araucaria`
Default colormap for `rainbow` set to 'turbo'
To unpatch, run `runscript viridis_colormaps.py --reset_defaults`
> open
> /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_2.-5.0.complex.pdb
Chain information for
cw_7_Structure2D_COMPOUND_CID_118984439_out_2.-5.0.complex.pdb
---
Chain | Description
1.1/A | No description available
> set bgColor white
> show surfaces
> lighting soft intensity 0.1
> graphics silhouettes true width 2 color #363644 depthJump 0.05
> color bfactor protein palette tokyo
308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32
> surface smooth #1 factor 0.6
> transparency 80 target s
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30
33 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 3 angleSlop 30
25 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 3 angleSlop 25
22 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 3 angleSlop 30
25 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 30
30 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 3 angleSlop 30
25 hydrogen bonds found
> hide surfaces
> show surfaces
> hide surfaces
> show surfaces
> hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 30
30 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 3 angleSlop 30
25 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 2 angleSlop 30
10 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 2.5 angleSlop 30
15 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 2.75 angleSlop 30
19 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30
33 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 20
24 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 15
18 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 10
17 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 5
12 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4.5 angleSlop 5
13 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 5 angleSlop 5
13 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 7 angleSlop 5
23 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 6 angleSlop 5
19 hydrogen bonds found
> hbonds interSubmodel true intraModel false distSlop 4 angleSlop 5
12 hydrogen bonds found
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
Could not find virtual screen for QCocoaScreen(0x600002e000b0, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, <NSScreen: 0x600003d14b40>)
with displayId 4128833
Could not find virtual screen for QCocoaScreen(0x600002e000b0, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, <NSScreen: 0x600003d14b40>)
with displayId 4128833
Could not find virtual screen for QCocoaScreen(0x600002e000b0, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, <NSScreen: 0x600003d14b40>)
with displayId 4128833
Could not find virtual screen for QCocoaScreen(0x600002e000b0, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, <NSScreen: 0x600003d14b40>)
with displayId 4128833
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
Could not find virtual screen for QCocoaScreen(0x600002e000b0, "ASUS VG289",
QRect(0,0 1920x1080), dpr=2, displayId=4128833, <NSScreen: 0x600003d14b40>)
with displayId 4128833
[Repeated 3 time(s)]
OpenGL version: 4.1 ATI-5.2.4
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.61.1.0.0 (iBridge: 21.16.2057.0.0,0)
OS Loader Version: 580~1053
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 49 days, 4 hours, 17 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: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
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)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
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: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
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-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
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
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
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-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 17 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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