![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17583 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Web Services | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.9.dev202406122300 (2024-06-12 23:00:04 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 490000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 2653,
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"build" : "22A380",
"releaseType" : "User"
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"captureTime" : "2025-05-08 19:21:22.1745 +0900",
"incident" : "3044B9D6-6CC7-465F-879B-D0155CBF834F",
"pid" : 93136,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-05-08 14:39:41.3933 +0900",
"procStartAbsTime" : 11488669015955,
"procExitAbsTime" : 11894239224855,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
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"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BAD2AE41-161A-1B52-2311-32EA41EAEBF4",
"wakeTime" : 33591,
"sleepWakeUUID" : "8D553A02-A6B4-4945-AB86-315977B41102",
"sip" : "enabled",
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"arch" : "arm64e",
"base" : 6780030976,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3358720,
"uuid" : "02b9797f-c47d-30b7-b7b0-802d0d26f31c",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4410556416,
"size" : 4849664,
"uuid" : "113c92ac-6022-34c0-8532-0a96c67af294",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4422893568,
"size" : 3112960,
"uuid" : "ee8cff87-6a5d-38d1-8403-031c9916b0fb",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4317839360,
"CFBundleShortVersionString" : "3.11.4, (c) 2001-2023 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 3948544,
"uuid" : "88bffd37-99d8-36ab-9b95-9f54b30bd667",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
"name" : "Python",
"CFBundleVersion" : "3.11.4"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4302995456,
"CFBundleShortVersionString" : "1.9.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.9.0.0"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6618226688,
"size" : 566448,
"uuid" : "1f56ab4e-f398-3a9c-bfba-fbbd17808963",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6621306880,
"size" : 233468,
"uuid" : "6d6644d3-3db3-34c4-b1e3-c675ec5360f0",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6621540352,
"size" : 53244,
"uuid" : "886caca0-5762-3640-8db2-3fa3b911c062",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4429971456,
"size" : 21299200,
"uuid" : "9854a721-2573-3169-81ec-19ea40ce8077",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6620786688,
"size" : 421876,
"uuid" : "ae8ea4b2-b8fd-33e3-a0af-0b7485ab97c0",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 13824425984,
"size" : 18235392,
"uuid" : "f1e25325-d9be-3248-a55c-48b550d2fc20",
"path" : "\/Applications\/ChimeraX_Daily.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/scipy\/.dylibs\/libopenblas.0.dylib",
"name" : "libopenblas.0.dylib"
}
],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=17.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=17.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1792K 14 \nActivity Tracing 256K 1 \nCG backing stores 3136K 8 \nCG image 848K 40 \nColorSync 640K 29 \nCoreAnimation 1280K 76 \nCoreGraphics 144K 9 \nCoreUI image data 3504K 48 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 16.1G 1578 \nMALLOC guard page 192K 10 \nMALLOC_MEDIUM (reserved) 464.0M 6 reserved VM address space (unallocated)\nMach message 96K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.7M 47 \nStack 159.7M 47 \nVM_ALLOCATE 385.3M 479 \nVM_ALLOCATE (reserved) 384.0M 6 reserved VM address space (unallocated)\n__AUTH 1944K 373 \n__AUTH_CONST 25.1M 606 \n__CTF 756 1 \n__DATA 22.9M 832 \n__DATA_CONST 39.8M 829 \n__DATA_DIRTY 2040K 242 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 798.0M 223 \n__OBJC_CONST 4875K 341 \n__OBJC_RO 65.1M 1 \n__OBJC_RW 1981K 1 \n__TEXT 881.2M 851 \ndyld private memory 560K 5 \nmapped file 592.3M 116 \nshared memory 3344K 29 \n=========== ======= ======= \nTOTAL 19.9G 6861 \nTOTAL, minus reserved VM space 19.1G 6861 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63582c5f8a53461413999550",
"factorPackIds" : {
"PROACTIVE_MAIL_INTELLIGENCE_SALIENCY" : "636525247ea6e25a76dc2008"
},
"deploymentId" : 240000002
},
{
"rolloutId" : "5f72dc58705eff005a46b3a9",
"factorPackIds" : {
},
"deploymentId" : 240000015
}
],
"experiments" : [
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.9.dev202406122300 (2024-06-12)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/uijin/Desktop/Phenix/SLC46A2/cryosparc_P370_J385_005_volume_map_sharp.mrc
> format mrc
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc as #1, grid size
280,280,280, pixel 0.938, shown at level 0.0717, step 2, values float32
> open
> /Users/uijin/Desktop/Phenix/SLC46A2/RealSpaceRefine_95/385-coot-6_real_space_refined_095.pdb
> format pdb
Chain information for 385-coot-6_real_space_refined_095.pdb #2
---
Chain | Description
B | No description available
> volume #1 level 0.2428
> select clear
> set bgColor white
> hide #!1 models
> select ~sel & ##selected
Nothing selected
> color #2:1-232 cyan
> select #2:1-232 cyan
Expected a keyword
> select #2:1-232
1582 atoms, 1618 bonds, 1 pseudobond, 204 residues, 2 models selected
> ui tool show "Color Actions"
> color sel turquoise
> show #!1 models
> ui tool show "Color Zone"
> color zone #1 near #2 distance 5.63
> lighting soft
> color sel tan
> color zone #1 near #2 distance 5.63
> color sel wheat
> color zone #1 near #2 distance 5.63
> color sel sky blue
> color zone #1 near #2 distance 5.63
> select #2:240-1000
1454 atoms, 1486 bonds, 189 residues, 1 model selected
> color sel blue
> color zone #1 near #2 distance 5.63
> color sel royal blue
> color zone #1 near #2 distance 5.63
> color sel dodger blue
> color zone #1 near #2 distance 5.63
> select clear
> volume #1 step 1
> color zone #1 near #2 distance 3
> color /A red
> color zone #1 near #2 distance 3
> color zone #1 near #2 distance 4
> color zone #1 near #2 distance 3
> color zone #1 near #2 distance 3.5
> color zone #1 near #2 distance 3
> color zone #1 near #2 distance 3.7
> color zone #1 near #2 distance 3.75
> color zone #1 near #2 distance 3.7
> color zone #1 near #2 distance 3
> color zone #1 near #2 distance 3.6
> volume #1 level 0.229
> volume splitbyzone #1
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 0 as #3.1, grid size
280,280,280, pixel 0.938, shown at level 0.229, step 1, values float32
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 1 as #3.2, grid size
280,280,280, pixel 0.938, shown at level 0.229, step 1, values float32
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 2 as #3.3, grid size
280,280,280, pixel 0.938, shown at level 0.229, step 1, values float32
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 3 as #3.4, grid size
280,280,280, pixel 0.938, shown at level 0.229, step 1, values float32
> hide #!3.1 models
> show #!3.1 models
> volume #3.1 step 2
> volume #3.1 level 0.1005
> volume #3.1 step 4
> vop gaussian #3.1 level 3
> volume gaussian #3.1 level 3
Expected a keyword
> vop gaussian #3.1 sd level 3
Must specify float or 3 comma-separated floats, got level
> vop gaussian #3.1 sd 3
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 0 gaussian as #4, grid
size 280,280,280, pixel 0.938, shown at step 1, values float32
> vop gaussian #3.1 sd 1.5
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 0 gaussian as #5, grid
size 280,280,280, pixel 0.938, shown at step 1, values float32
> close #4
> volume #5 level 0.09056
> vop gaussian #3.1 sd 2
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 0 gaussian as #4, grid
size 280,280,280, pixel 0.938, shown at step 1, values float32
> close #4
> close #5
> vop gaussian #3.1 sd 2
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 0 gaussian as #4, grid
size 280,280,280, pixel 0.938, shown at step 1, values float32
> volume #4 level 0.08825
> vop gaussian #3.1 sd 3
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 0 gaussian as #5, grid
size 280,280,280, pixel 0.938, shown at step 1, values float32
> close #4
> volume #5 level 0.07025
> volume #5 level 0.0687
> color #5 silver models
> color #5 #c0c0c04d models
> show #!3.1 models
> hide #!5 models
> volume #3.1 step 1
> volume #3.1 step 2
> color #3.1 #b2b2b24d models
> volume #3.1 level 0.06176
> select add #3.1
2 models selected
> surface dust #3.1 size 9.38
> volume #3.1 level 0.08599
> select subtract #3.1
Nothing selected
> volume #3.1 step 1
> select add #3.1
2 models selected
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> select subtract #3.1
Nothing selected
> select add #3.1
2 models selected
> lighting shadows true intensity 0.5
> lighting soft
> select clear
> lighting shadows true intensity 0 #3.1
Expected a keyword
> lighting #3.1 shadows true intensity 0
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> select clear
> graphics silhouettes false
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> hide #!3.1 models
> show #!3.1 models
> graphics silhouettes true
> lighting soft
> select #2:1-232
1582 atoms, 1618 bonds, 1 pseudobond, 204 residues, 2 models selected
> color sel wheat
> color zone #1 near #2 distance 3.6
> close #3
> show #!1 models
> color /A red
> color zone #1 near #2 distance 3.6
> volume splitbyzone #1
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 0 as #3.1, grid size
280,280,280, pixel 0.938, shown at level 0.229, step 1, values float32
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 1 as #3.2, grid size
280,280,280, pixel 0.938, shown at level 0.229, step 1, values float32
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 2 as #3.3, grid size
280,280,280, pixel 0.938, shown at level 0.229, step 1, values float32
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 3 as #3.4, grid size
280,280,280, pixel 0.938, shown at level 0.229, step 1, values float32
> hide #!3.3 models
> show #!3.3 models
> hide #!3.2 models
> show #!3.2 models
> hide #!3.1 models
> show #!3.1 models
> volume #3.1 level 0.126
> color #3.1 #b2b2b233 models
> select clear
> select add #3.1
2 models selected
> surface dust #3.1 size 9.38
> select clear
> graphics silhouettes false
> graphics silhouettes #3.1 false
Expected true or false or a keyword
> graphics silhouettes false #3.1
Expected a keyword
> graphics silhouettes false #3
Expected a keyword
> select clear
> graphics silhouettes true
> select clear
> volume #3.1 level 0.07894
> vop gaussian #3.1 sd 1
Opened cryosparc_P370_J385_005_volume_map_sharp.mrc 0 gaussian as #4, grid
size 280,280,280, pixel 0.938, shown at step 1, values float32
> close #5
> color #4 #ffb2ff33 models
> volume #4 level 0.06504
> select add #4
2 models selected
> surface dust #4 size 9.38
> select clear
> color #4 silver models
> select clear
> volume #3.4 level 0.3841
> select add #3.4
2 models selected
> surface dust #3.4 size 9.38
> volume #3.4 level 0.3167
> select add #3.3
4 models selected
> select subtract #3.4
2 models selected
> volume #3.3 level 0.3587
> select subtract #3.3
Nothing selected
> show #!3.1 models
> hide #!4 models
> volume #3.1 level 0.159
> hide #!3.1 models
> show #!4 models
> volume #4 level 0.07149
> volume #3.2 level 0.1544
> volume #3.2 level 0.1783
> color /A byhetero
> select clear
> color /A orange
> select clear
> color #3.2 orange
> select clear
> color #3.2 #ff000080 models
> color /A byhetero
> select clear
> color #3.2 red models
> color #3.2 darkgrey models
> color #3.2 orange
> select clear
> hide #!3.2 models
> show #!3.2 models
> volume #3.2 level 0.06647
> volume #3.2 level 0.03814
> hide #!4 models
> volume #3.2 level 0.1902
> volume #3.2 level 0.1276
> volume #3.2 level 0.2305
> select add #3.2
2 models selected
> surface dust #3.2 size 9.38
> surface dust #3.2 size 3
> surface dust #3.2 size 4
> surface dust #3.2 size 5
> volume #3.2 level 0.1619
> select clear
> volume #3.2 level 0.1917
> volume #3.2 level 0.1798
> hide H
> select clear
> show #!4 models
> hide #!4 models
> color #3.2 #4f8f00ff models
> color #3.2 #ff9300ff models
> show #!4 models
> hide #!4 models
> volume #3.3 level 0.3287
> select add #3.3
2 models selected
> surface dust #3.3 size 9.38
> volume #3.3 level 0.3121
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!2 models
> rainbow #2
> select clear
> color /A orange
> color byhetero
> select clear
> open
> /Users/uijin/Desktop/Phenix/SLC46A2/RealSpaceRefine_95/385-coot-6_real_space_refined_095.pdb
Chain information for 385-coot-6_real_space_refined_095.pdb #5
---
Chain | Description
B | No description available
> hide #!2 models
> select add #5
3036 atoms, 3104 bonds, 2 pseudobonds, 393 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 385-coot-6_real_space_refined_095.pdb_B SES surface #5.2:
minimum, -10.78, mean 1.28, maximum 14.79
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> color #5/A orange
> color /A byhetero
> hide H
> select clear
> ui tool show "Side View"
> color #5 #d6d6d6ff
> color #5 silver
> select add #5
3036 atoms, 3104 bonds, 2 pseudobonds, 393 residues, 3 models selected
> coulombic sel
Coulombic values for 385-coot-6_real_space_refined_095.pdb_B SES surface #5.2:
minimum, -10.78, mean 1.28, maximum 14.79
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> close #5
> open
> /Users/uijin/Desktop/Phenix/SLC46A2/RealSpaceRefine_95/385-coot-6_real_space_refined_095.pdb
> format pdb
Chain information for 385-coot-6_real_space_refined_095.pdb #5
---
Chain | Description
B | No description available
> color #5 silver
> select add #5
3036 atoms, 3104 bonds, 2 pseudobonds, 393 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 385-coot-6_real_space_refined_095.pdb_B SES surface #5.2:
minimum, -10.78, mean 1.28, maximum 14.79
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> color byhetero
> undo
> color /A byhetero
> select clear
> hide H
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> select clear
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> ui mousemode right "mark surface"
> marker #6 position 157.6,140.3,133.7 color yellow radius 1
> marker #6 position 153,139.4,125 color yellow radius 1
> ui mousemode right "link markers"
> marker link #6:2,1 color #659cef radius 0.5
> undo
> hide H
> select clear
> close #6
> open
> /Users/uijin/Desktop/Phenix/SLC46A2/RealSpaceRefine_95/385-coot-6_real_space_refined_095.pdb
> format pdb
Chain information for 385-coot-6_real_space_refined_095.pdb #6
---
Chain | Description
B | No description available
> color #6 black
> hide #!5 models
> select add #6
3036 atoms, 3104 bonds, 2 pseudobonds, 393 residues, 2 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 385-coot-6_real_space_refined_095.pdb_B SES surface #6.2:
minimum, -10.78, mean 1.28, maximum 14.79
To also show corresponding color key, enter the above coulombic command and
add key true
> select clear
> show #!5 models
> hide #!5 models
> open
> /Users/uijin/Desktop/Phenix/SLC46A2/RealSpaceRefine_95/385-coot-6_real_space_refined_095.pdb
> format pdb
Chain information for 385-coot-6_real_space_refined_095.pdb #7
---
Chain | Description
B | No description available
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> color /A orange
> color byhetero
> undo
> color /A byhetero
> hide H
> select clear
> hide #6.1 models
Cell requested for row 9 is out of bounds for table with 13 rows! Resizing
table model.
> hide #!3.2 models
> hide #!3.3 models
> hide #!3.4 models
> hide #!6.2 models
> show #6.2 models
> show #6.1 models
> hide #6.1 models
> show #6.1 models
> hide #6.1 models
> hide #!6 models
> show #!6 models
> hide #2.1 models
Cell requested for row 4 is out of bounds for table with 14 rows! Resizing
table model.
> lighting soft
> lighting full
> lighting shadows false
> lighting soft
> select clear
> hide #!6 models
Cell requested for row 9 is out of bounds for table with 13 rows! Resizing
table model.
> show #!7 models
> hide #!2 models
> rainbow #7
> select clear
> show #!6 models
Cell requested for row 9 is out of bounds for table with 13 rows! Resizing
table model.
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
Mismatch between Cocoa '\x0' and Carbon '\u314a' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\u314a' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> color #7/B byhetero
> select clear
> delete #7:65-120
> delete #7:65-130
> delete #7:65-132
> delete #7:164-200
> delete #7:164-220
> delete #7:164-240
> delete #7:345-150
> delete #7:345-350
> delete #7:345-360
> delete #7:345-367
> delete #7:345-369
> delete #7:345-370
> delete #7:399-1000
> select clear
> show #!6 models
> hide #!6 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!6 models
> hide #!6 models
> hide #!2 models
> hide #7/A
> hide #7.1 models
> save /Users/uijin/Desktop/TMs.tif width 1736 height 1149 supersample 3
> transparentBackground true
> delete #7:278-315
> save /Users/uijin/Desktop/TMs.tif width 1736 height 1149 supersample 3
> transparentBackground true
> hide #7 atoms
> save /Users/uijin/Desktop/TMs.tif width 1736 height 1149 supersample 3
> transparentBackground true
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> hide #!7 models
> show #!2 models
> open 7bc7
7bc7 title:
Cryo-EM structure of the proton coupled folate transporter at pH 6.0 bound to
pemetrexed [more info...]
Chain information for 7bc7 #8
---
Chain | Description | UniProt
A | Proton-coupled folate transporter | E6Y8U5_CHICK 1-473
B | nanobody |
Non-standard residues in 7bc7 #8
---
LYA —
2-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-D]pyrimidin-5-yl)-ethyl]-benzoylamino}-pentanedioic
acid (LY231514)
> matchmaker #8 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 385-coot-6_real_space_refined_095.pdb, chain B (#2) with 7bc7,
chain A (#8), sequence alignment score = 719
RMSD between 250 pruned atom pairs is 1.134 angstroms; (across all 389 pairs:
5.343)
> ui tool show "Side View"
> color #8 magnesium
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #8 silver
> select clear
> open 7bc6
7bc6 title:
Cryo-EM structure of the outward open proton coupled folate transporter at pH
7.5 [more info...]
Chain information for 7bc6 #9
---
Chain | Description | UniProt
A | Proton-coupled folate transporter | E6Y8U5_CHICK 1-473
B | nanobody |
> matchmaker #9 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 385-coot-6_real_space_refined_095.pdb, chain B (#2) with 7bc6,
chain A (#9), sequence alignment score = 708.7
RMSD between 248 pruned atom pairs is 1.146 angstroms; (across all 389 pairs:
5.397)
> color #9 silver
> hide #8
> select clear
> hide #8 models
> select clear
> delete #9/B
> select clear
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> hide #9 models
> show #!7 models
> hide #!2 models
> ui tool show "Side View"
> show #!6 models
> hide #!6 models
> hide #7:1-100
> hide #7:1-100 atoms
> hide #7:1-100 cartoons
> save /Users/uijin/Desktop/TMs.tif width 1736 height 1149 supersample 3
> transparentBackground true
> hide #!7 models
> show #!2 models
> interfaces #!2 & ~solvent
1 buried areas: B A 471
> show sel atoms
> hide H
> select clear
> color #2/B silver
> select clear
> color #2/B byhetero
> select clear
> lighting flat
> lighting soft
> select clear
> lighting shadows true intensity 0.5
> lighting soft
> select #2:30,33,37,149,180,181,184,301,328,330,331,378,384,385
111 atoms, 103 bonds, 14 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> save /Users/uijin/Desktop/binding.tif width 1736 height 1149 supersample 3
> transparentBackground true
> undo
> select clear
> lighting flat
> color #2 darkgrey
> color #2 silver
> color #2 #929292ff
> color #2 silver
> color #2/A orange
> color #2/A byhetero
> select #2:30,33,37,149,180,181,184,301,328,330,331,378,384,385
111 atoms, 103 bonds, 14 residues, 1 model selected
> color sel byhetero
> select clear
> color #2 byhetero
> select clear
> save /Users/uijin/Desktop/binding.tif width 1736 height 1149 supersample 3
> transparentBackground true
> show #!3.2 models
> color #3.2 #ff930080 models
> color #3.2 #ff93004d models
> select add #3.2
2 models selected
> volume sel style mesh
> select clear
> select add #3.2
2 models selected
> color #3.2 #0433ffff models
> color #3.2 #9437ffff models
> color #3.2 #0096ffff models
> select clear
> save /Users/uijin/Desktop/overall.tif width 1736 height 1149 supersample 3
> transparentBackground true
> lighting soft
> save /Users/uijin/Desktop/overall.tif width 1736 height 1149 supersample 3
> transparentBackground true
> show #9 models
> hide #!3 models
> show #!7 models
> hide #!7 models
> show #!5 models
> rainbow #5
> hide #5 surfaces
> select clear
> hide #5/B
> select clear
> hide #!2 models
> hide #9 models
> show #9 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #5/B cartoons
> select clear
> select add #9
3269 atoms, 3346 bonds, 432 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> select clear
> show #8 models
> hide #9 models
> show #8/B cartoons
> show #8/B atoms
> show #8/A atoms
> hide #8/A atoms
> select clear
> hide #8 models
> show #8 models
> select clear
> hide #8/C atoms
> hide #8:LYA atoms
> show #8:LYA atoms
> color #8/C blue
> color #8:LYA blue
> color #8:LYA byhetero
> select clear
> ribstyle #8 tube
Unknown command: ribstyle #8 tube
> ribbon ribrepr #8 tube
> cartoon ribrepr #8 tube
Expected an atoms specifier or a keyword
> select add #8
4209 atoms, 4313 bonds, 550 residues, 1 model selected
> ribbon ribrepr tube
> cartoon ribrepr tube
Expected an atoms specifier or a keyword
> ribrepr tube
Unknown command: ribrepr tube
> ribrepr tube #8
Unknown command: ribrepr tube #8
> ribbon
> hide #!3.2 models
> hide #!5 models
> ribrepr rounded
Unknown command: ribrepr rounded
> ribbon #8
> select clear
> select add #8
4209 atoms, 4313 bonds, 550 residues, 1 model selected
> cartoon style helices cylindrical
Expected an atoms specifier or a keyword
> cartoon style cylindrical
Expected an atoms specifier or a keyword
> cartoon style #8 cylinder
Expected a keyword
> cartoon style #8 cylinderical
Expected a keyword
> cartoon style #8 modeHelix tube radius 2 sides 24
> select clear
> delete #8/B
> select clear
> show #!3 models
> hide #!3 models
Cell requested for row 2 is out of bounds for table with 14 rows! Resizing
table model.
> show #!2 models
> hide #!2 models
> show #!7 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #5/B cartoons
> select clear
> cartoon style #8 modeHelix tube radius 3 sides 24
> cartoon style #8 modeHelix tube radius 2.5 sides 24
> select clear
> save /Users/uijin/Desktop/a1.tif width 1736 height 1149 supersample 3
> transparentBackground true
> cartoon style #8 modeHelix tube radius 2 sides 24
> cartoon style #2 modeHelix tube radius 2 sides 24
> show #5 cartoons
> cartoon style #5 modeHelix tube radius 2 sides 24
> select clear
> ui tool show "Side View"
> hide #!5 models
> show #!5 models
> hide #5 cartoons
> select clear
> delete #8:60-82
> delete #8:60-100
> delete #8:60-110
> delete #8:60-115
> select clear
> hide #8.1 models
> select #5/A
67 atoms, 73 bonds, 1 residue, 1 model selected
> style sel ball
Changed 67 atom styles
> style sel sphere
Changed 67 atom styles
> select clear
> select #8/C
Nothing selected
> select #8:LYA
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 31 atom styles
> select clear
> vdwdefine +0.5
Unknown command: vdwdefine +0.5
> style :100.A sphere
Expected a keyword
> radius 2.0 :100.A
Unknown command: radius 2.0 :100.A
> size ligand atomRadius +.5
Changed 299 atom radii
> size ligand atomRadius -1
Changed 299 atom radii
> select clear
> size ligand atomRadius -0.5
Cannot reduce atom radius to size ligand atomRadius -.5
Cannot reduce atom radius to size ligand atomRadius -.5
Cannot reduce atom radius to select clear
> open 7bc7
7bc7 title:
Cryo-EM structure of the proton coupled folate transporter at pH 6.0 bound to
pemetrexed [more info...]
Chain information for 7bc7 #10
---
Chain | Description | UniProt
A | Proton-coupled folate transporter | E6Y8U5_CHICK 1-473
B | nanobody |
Non-standard residues in 7bc7 #10
---
LYA —
2-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-D]pyrimidin-5-yl)-ethyl]-benzoylamino}-pentanedioic
acid (LY231514)
> hide #!5 models
> show #!5 models
> hide #!8 models
Mismatch between Cocoa '\x0' and Carbon '\u3161' for virtual key 46 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\u3161' for virtual key 46 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'M' for virtual key 46 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'm' for virtual key 46 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 46 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> matchmaker #10 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 385-coot-6_real_space_refined_095.pdb, chain B (#5) with 7bc7,
chain A (#10), sequence alignment score = 719
RMSD between 250 pruned atom pairs is 1.134 angstroms; (across all 389 pairs:
5.343)
> delete #10/B
> color #10 silver
> color #10 darkgrey
> color #10 silver
> show #5 cartoons
> select clear
> show #10#!5 cartoons
> style #10#!5 stick
Changed 6336 atom styles
> style #10#!5 stick
Changed 6336 atom styles
> select add #5
3036 atoms, 3104 bonds, 2 pseudobonds, 393 residues, 2 models selected
> style sel stick
Changed 3036 atom styles
> style sel sphere
Changed 3036 atom styles
> style sel stick
Changed 3036 atom styles
> hide sel cartoons
> show sel cartoons
> close #5
> open
> /Users/uijin/Desktop/Phenix/SLC46A2/RealSpaceRefine_95/385-coot-6_real_space_refined_095.pdb
> format pdb
Chain information for 385-coot-6_real_space_refined_095.pdb #5
---
Chain | Description
B | No description available
> rainbow #5
> color #5/A orange
> color byhetero
> hide H
> select clear
> show #10:370 atoms
> select clear
> select #5/A
67 atoms, 73 bonds, 1 residue, 1 model selected
> select #5/A #10/C
67 atoms, 73 bonds, 1 residue, 1 model selected
> select #5/A #10/A
3367 atoms, 3452 bonds, 434 residues, 2 models selected
> select clear
> select #5/A
67 atoms, 73 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 67 atom styles
> select #10/A
3300 atoms, 3379 bonds, 433 residues, 1 model selected
> select clear
> select #10:LYA
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 31 atom styles
> select up
3300 atoms, 3379 bonds, 433 residues, 1 model selected
> select up
19543 atoms, 19989 bonds, 2545 residues, 12 models selected
> select up
19543 atoms, 19989 bonds, 2 pseudobonds, 2545 residues, 14 models selected
> select up
19543 atoms, 19989 bonds, 2 pseudobonds, 2545 residues, 14 models selected
> select up
19543 atoms, 19989 bonds, 2 pseudobonds, 2545 residues, 14 models selected
> size ligand atomRadius -0.5
Cannot reduce atom radius to select clear
> size ligand atomRadius -0.5
Cannot reduce atom radius to select #10:LYA
31 atoms, 33 bonds, 1 residue, 1 model selected
> size ligand atomRadius -0.5
Cannot reduce atom radius to select clear
> style #10#!5 ball
Changed 6336 atom styles
> undo
> select #10:LYA
31 atoms, 33 bonds, 1 residue, 1 model selected
> style sel ball
Changed 31 atom styles
> select up
3300 atoms, 3379 bonds, 433 residues, 1 model selected
> select up
19543 atoms, 19989 bonds, 2545 residues, 12 models selected
> select down
3300 atoms, 3379 bonds, 433 residues, 2 models selected
> select down
31 atoms, 33 bonds, 1 residue, 1 model selected
> select up
3300 atoms, 3379 bonds, 433 residues, 1 model selected
> select #10/A
3300 atoms, 3379 bonds, 433 residues, 1 model selected
> select #5/A
67 atoms, 73 bonds, 1 residue, 1 model selected
> style sel ball
Changed 67 atom styles
> select clear
> coulombic #10#!5
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 7bc7_A SES surface #10.1: minimum, -13.27, mean -0.65,
maximum 9.68
Coulombic values for 385-coot-6_real_space_refined_095.pdb_B SES surface #5.2:
minimum, -10.78, mean 1.28, maximum 14.79
To also show corresponding color key, enter the above coulombic command and
add key true
> hide #!10 models
> show #!10 models
> hide #!5 models
> close #10
Cell requested for row 6 is out of bounds for table with 11 rows! Resizing
table model.
> open
> /Users/uijin/Desktop/Phenix/SLC46A2/RealSpaceRefine_95/385-coot-6_real_space_refined_095.pdb
> format pdb
Chain information for 385-coot-6_real_space_refined_095.pdb #10
---
Chain | Description
B | No description available
Cell requested for row 0 is out of bounds for table with 10 rows! Resizing
table model.
> open 7bc6v
'7bc6v' has no suffix
> open 7bc6
7bc6 title:
Cryo-EM structure of the outward open proton coupled folate transporter at pH
7.5 [more info...]
Chain information for 7bc6 #11
---
Chain | Description | UniProt
A | Proton-coupled folate transporter | E6Y8U5_CHICK 1-473
B | nanobody |
> color #10 silver
> color #11 silver
> select add #10
3036 atoms, 3104 bonds, 2 pseudobonds, 393 residues, 2 models selected
> select add #11
7214 atoms, 7384 bonds, 2 pseudobonds, 942 residues, 3 models selected
> coulombic sel
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for 385-coot-6_real_space_refined_095.pdb_B SES surface
#10.2: minimum, -10.78, mean 1.28, maximum 14.79
Coulombic values for 7bc6_A SES surface #11.1: minimum, -15.91, mean -0.53,
maximum 12.60
Coulombic values for 7bc6_B SES surface #11.2: minimum, -13.27, mean 0.38,
maximum 11.39
To also show corresponding color key, enter the above coulombic command and
add key true
> select #10/A
67 atoms, 73 bonds, 1 residue, 1 model selected
> style sel ball
Changed 67 atom styles
> select clear
> select #10/A
67 atoms, 73 bonds, 1 residue, 1 model selected
> color sel orange
> color sel byhetero
> select clear
> hide H
> hide #!11 models
> lighting shadows true intensity 0.5
> lighting shadows false
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> hide #10/B
> hide #10/B surfaces
> select ~sel & ##selected
Nothing selected
> select ~sel & ##selected
Nothing selected
> hide #10/B cartoons
> select clear
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> delete #11/B
> show #10 surfaces
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> select ~sel & ##selected
Nothing selected
> show #10 surfaces
> hide #10 surfaces
> show #9 models
> hide #9 models
> show #10 surfaces
> hide #!11 models
> show #!11 models
> hide #!10 models
> show #!10 models
> hide #!11 models
> show #!11 models
> show #10 surfaces
> hide #10 surfaces
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9.dev202406122300 (2024-06-12)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/uijin/Downloads/fold_2025_05_08_23_17/fold_2025_05_08_23_17_model_0.cif
Chain information for fold_2025_05_08_23_17_model_0.cif #1
---
Chain | Description
A | .
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> coulombic
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for fold_2025_05_08_23_17_model_0.cif_A SES surface #1.1:
minimum, -11.42, mean 0.85, maximum 15.01
To also show corresponding color key, enter the above coulombic command and
add key true
> ui tool show "Side View"
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11C001DKKH/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.41.10
OS Loader Version: 8419.41.10
Software:
System Software Overview:
System Version: macOS 13.0 (22A380)
Kernel Version: Darwin 22.1.0
Time since boot: 29 days, 5 hours, 37 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
LG FULL HD:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.13
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.2
ChimeraX-AtomicLibrary: 14.1.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
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: 2.2.4
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.dev202406122300
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-DeepMutationalScan: 1.0
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
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: 1.1.1
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.4
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
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-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.1.5
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.12.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.6
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: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
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: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.32.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Web Services |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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