![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17354 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.2.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x00000001e6448140 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, chimerax.atomic._ribbons, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, PIL._webp (total: 56)
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"incident" : "18BFA975-C9CD-413A-9198-FE563D527DD2",
"pid" : 66832,
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"procLaunch" : "2025-04-09 13:27:38.4330 -0700",
"procStartAbsTime" : 10420726292156,
"procExitAbsTime" : 10770656162958,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"crashReporterKey" : "49A7EAB0-B44A-F787-66C8-922581B31ABB",
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"sleepWakeUUID" : "5A0BAB21-11DB-432D-BB11-8A6A175664AC",
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"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.300"
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"size" : 10723328,
"uuid" : "c62e0110-c636-396a-9cb6-c3c08392b3fa",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "1953.300"
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"size" : 4292608,
"uuid" : "4f4ac9ca-134a-3290-bd36-22bd7bd03f7f",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
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"arch" : "arm64e",
"base" : 6624059392,
"size" : 294912,
"uuid" : "4d52c3a5-32e6-37a2-9d6c-23c612038354",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
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"arch" : "arm64e",
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"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
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"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
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"arch" : "arm64",
"base" : 5200166912,
"size" : 3080192,
"uuid" : "ac9bb37f-d5ad-31aa-8307-d081879d1aef",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
"name" : "QtWidgets.abi3.so"
},
{
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"arch" : "arm64",
"base" : 4372185088,
"CFBundleShortVersionString" : "1.9.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "17982d98-65bc-3327-8526-577ec996453c",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
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{
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"uuid" : "191e84f1-4b95-39c8-b253-1c1ef56c0fa8",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
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"base" : 11125424128,
"size" : 173883392,
"uuid" : "309d9313-74e8-3f16-8acc-0f13b36d8e00",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
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{
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"base" : 5133828096,
"size" : 21299200,
"uuid" : "9854a721-2573-3169-81ec-19ea40ce8077",
"path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=5.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=5.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1920K 15 \nActivity Tracing 256K 1 \nCG backing stores 2304K 12 \nCG image 1728K 69 \nCG raster data 480K 10 \nColorSync 592K 29 \nCoreAnimation 1184K 56 \nCoreGraphics 128K 7 \nCoreServices 368K 2 \nCoreUI image data 5328K 50 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 4.3G 902 \nMALLOC guard page 192K 9 \nMALLOC_MEDIUM (reserved) 512.0M 8 reserved VM address space (unallocated)\nMach message 128K 8 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.7M 44 \nStack 210.5M 44 \nVM_ALLOCATE 392.2M 375 \nVM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated)\n__AUTH 2019K 390 \n__AUTH_CONST 25.5M 623 \n__CTF 756 1 \n__DATA 20.8M 777 \n__DATA_CONST 39.4M 783 \n__DATA_DIRTY 2050K 247 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 797.1M 159 \n__OBJC_CONST 5004K 357 \n__OBJC_RO 65.5M 1 \n__OBJC_RW 1988K 1 \n__TEXT 861.3M 804 \ndyld private memory 304K 3 \nmapped file 530.0M 93 \nshared memory 3376K 34 \n=========== ======= ======= \nTOTAL 7.9G 5925 \nTOTAL, minus reserved VM space 7.2G 5925 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "6112e3d2fc54bc3389840661",
"factorPackIds" : {
"SIRI_TEXT_TO_SPEECH" : "648b9b0febdf9e3e398fa6b5"
},
"deploymentId" : 240000478
},
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
}
],
"experiments" : [
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages
---
warning | No presets found in custom preset folder /Users/tgewering/Desktop/ChimeraX_preferences
note | available bundle cache has not been initialized yet
> set bgColor white
> lighting soft
> show cartoons
> hide atoms
> cartoon style thickness 1.2
> graphics silhouettes true
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/tgewering/Desktop/science/projects/EBOVGPcl_MR72scFv/MARV_model_Jan2025/marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb
Chain information for marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb #1
---
Chain | Description
A H | No description available
B F | No description available
C G K | No description available
D I | No description available
E | No description available
J | No description available
L | No description available
> open
> /Users/tgewering/Desktop/science/projects/EBOVGPcl_MR72scFv/MARV_model_Jan2025/MARV_MR72_DeepEM_J987flipped.mrc
Opened MARV_MR72_DeepEM_J987flipped.mrc as #2, grid size 370,370,370, pixel
0.66, shown at level 0.00201, step 2, values float32
> volume #2 step 1
> volume #2 level 0.06089
> show cartoons
> style stick
Changed 11598 atom styles
> open
> /Users/tgewering/Desktop/science/projects/EBOVGPcl_MR72scFv/2024October_model/EBOV_MR72_refinement21-coot-0_glyco.pdb
Chain information for EBOV_MR72_refinement21-coot-0_glyco.pdb #3
---
Chain | Description
A B C | No description available
D E F | No description available
G I K | No description available
H L | No description available
J | No description available
> open
> /Users/tgewering/Desktop/science/projects/EBOVGPcl_MR72scFv/2024October_model/J638_EBOV_Mr72_DeepEM.mrc
Opened J638_EBOV_Mr72_DeepEM.mrc as #4, grid size 370,370,370, pixel 0.66,
shown at level 0.00161, step 2, values float32
> volume #4 step 1
> volume #4 level 0.05678
> mmaker #3 to #1 bring #4
Computing secondary structure
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 marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb, chain B (#1)
with EBOV_MR72_refinement21-coot-0_glyco.pdb, chain H (#3), sequence alignment
score = 602.8
RMSD between 119 pruned atom pairs is 0.470 angstroms; (across all 120 pairs:
1.128)
> style stick
Changed 23091 atom styles
> show cartoons
> preset cartoons/nucleotides licorice/ovals
Using preset: Cartoons/Nucleotides / Licorice/Ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> hide #!3 models
> hide #!4 models
> hide #!2 models
> select add #1
11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 1/E
Alignment identifier is 1/J
Alignment identifier is 1/L
Alignment identifier is 4
> select subtract #1
Nothing selected
> select #1/K,C,G:40
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #1/K,C,G:40-41
45 atoms, 42 bonds, 6 residues, 1 model selected
> select #1/K,C,G:35
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/K,C,G:35-180
3411 atoms, 3498 bonds, 438 residues, 1 model selected
> select #1/D,I:471
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/D,I:471-600
1576 atoms, 1608 bonds, 6 pseudobonds, 196 residues, 2 models selected
> select #1/L:471-472
13 atoms, 13 bonds, 2 residues, 1 model selected
> select #1/L:471-614
872 atoms, 889 bonds, 3 pseudobonds, 112 residues, 2 models selected
> select #1/B,F:1
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/B,F:1-64
902 atoms, 928 bonds, 2 pseudobonds, 116 residues, 2 models selected
> select #1/J:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/J:2-58
390 atoms, 400 bonds, 1 pseudobond, 51 residues, 2 models selected
> select #1/D,I:471-472
26 atoms, 26 bonds, 4 residues, 1 model selected
> select #1/D,I:471-554
820 atoms, 840 bonds, 6 pseudobonds, 104 residues, 2 models selected
> select #1/L:474
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1/L:474-608
812 atoms, 827 bonds, 3 pseudobonds, 103 residues, 2 models selected
> select #1/J:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/J:2-58
390 atoms, 400 bonds, 1 pseudobond, 51 residues, 2 models selected
> select #1/E:3
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/E:3-108
784 atoms, 804 bonds, 106 residues, 1 model selected
> select #1/B,F:1
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/B,F:1-24
258 atoms, 256 bonds, 2 pseudobonds, 36 residues, 2 models selected
> select #1/A,H:2
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/A,H:2-19
246 atoms, 250 bonds, 36 residues, 1 model selected
> color #1/C/G/K #30924D
> select add #1
11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected
> select subtract #1
Nothing selected
> color #1/D/I/L #667255
> color #1/B/F/J #FFB300
> color #1/E/A/H #CC9D1C
> color :NAG,BMA,MAN peach puff
> lighting soft
> show #!2 models
> cartoon style thickness 1.2
> hide #!2 models
> show #!2 models
> volume #2 level 0.08514
Unsupported scale factor (0.000000) detected on Display2
> view orient
> color zone #2 near #1 distance 3.96
> volume splitbyzone #2
Opened MARV_MR72_DeepEM_J987flipped.mrc 0 as #5.1, grid size 370,370,370,
pixel 0.66, shown at level 0.0851, step 1, values float32
Opened MARV_MR72_DeepEM_J987flipped.mrc 1 as #5.2, grid size 370,370,370,
pixel 0.66, shown at level 0.0851, step 1, values float32
Opened MARV_MR72_DeepEM_J987flipped.mrc 2 as #5.3, grid size 370,370,370,
pixel 0.66, shown at level 0.0851, step 1, values float32
Opened MARV_MR72_DeepEM_J987flipped.mrc 3 as #5.4, grid size 370,370,370,
pixel 0.66, shown at level 0.0851, step 1, values float32
Opened MARV_MR72_DeepEM_J987flipped.mrc 4 as #5.5, grid size 370,370,370,
pixel 0.66, shown at level 0.0851, step 1, values float32
Opened MARV_MR72_DeepEM_J987flipped.mrc 5 as #5.6, grid size 370,370,370,
pixel 0.66, shown at level 0.0851, step 1, values float32
> hide #!5.1 models
> surface dust
Missing or invalid "surfaces" argument: empty atom specifier
> surface dust #5
> volume #5.2 level 0.1421
> volume #5.3 level 0.142
> volume #5.4 level 0.142
> volume #5.5 level 0.142
> volume #5.6 level 0.142
> hide #!1 models
> ui tool show "Side View"
> show #!4 models
> show #!3 models
> hide #!5 models
> hide #!4 models
> select add #3
11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3/J
Alignment identifier is 3
Alignment identifier is 4
> select subtract #3
Nothing selected
> select #3/C,B,A:32
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #3/C,B,A:32-79
1053 atoms, 1056 bonds, 144 residues, 1 model selected
> select #3/C,B,A:32
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #3/C,B,A
3583 atoms, 3676 bonds, 471 residues, 1 model selected
> select #3/H,L:1-5
86 atoms, 84 bonds, 10 residues, 1 model selected
> select #3/H,L:1-52
794 atoms, 814 bonds, 104 residues, 1 model selected
> select #3/F,E,D:505
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #3/F,E,D:505-607
2303 atoms, 2363 bonds, 3 pseudobonds, 291 residues, 2 models selected
> select #3/J:2-5
34 atoms, 33 bonds, 4 residues, 1 model selected
> select #3/J:4-17
100 atoms, 101 bonds, 14 residues, 1 model selected
> select #3/J:2
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/J:2-126
964 atoms, 993 bonds, 125 residues, 1 model selected
> select #3/H,L:1-49
758 atoms, 778 bonds, 98 residues, 1 model selected
> select #3/H,L:1-53
810 atoms, 830 bonds, 106 residues, 1 model selected
> select #3/G,K,I:2-3
39 atoms, 36 bonds, 6 residues, 1 model selected
> select #3/G,K,I:2-49
1047 atoms, 1074 bonds, 144 residues, 1 model selected
> select add #3
11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected
> select subtract #3
Nothing selected
> color #3/A/B/C #00468D
> color #3/D/E/F #335C71
> color #3/J/H/L #FFB300
> color #3/G/I/K #CC9D1C
> color :NAG,BMA,MAN peach puff
> toolshed show
> show #!4 models
> color zone #4 near #3 distance 3.96
> volume #4 level 0.09687
> ui tool show "Side View"
> volume splitbyzone #4
Opened J638_EBOV_Mr72_DeepEM.mrc 0 as #6.1, grid size 370,370,370, pixel 0.66,
shown at level 0.0969, step 1, values float32
Opened J638_EBOV_Mr72_DeepEM.mrc 1 as #6.2, grid size 370,370,370, pixel 0.66,
shown at level 0.0969, step 1, values float32
Opened J638_EBOV_Mr72_DeepEM.mrc 2 as #6.3, grid size 370,370,370, pixel 0.66,
shown at level 0.0969, step 1, values float32
Opened J638_EBOV_Mr72_DeepEM.mrc 3 as #6.4, grid size 370,370,370, pixel 0.66,
shown at level 0.0969, step 1, values float32
Opened J638_EBOV_Mr72_DeepEM.mrc 4 as #6.5, grid size 370,370,370, pixel 0.66,
shown at level 0.0969, step 1, values float32
Opened J638_EBOV_Mr72_DeepEM.mrc 5 as #6.6, grid size 370,370,370, pixel 0.66,
shown at level 0.0969, step 1, values float32
> hide #!6.1 models
> surface dust #6
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> mmaker #1/B to #3/B bring #5
Computing secondary structure
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 EBOV_MR72_refinement21-coot-0_glyco.pdb, chain B (#3) with
marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb, chain B (#1), sequence
alignment score = 22.1
RMSD between 5 pruned atom pairs is 1.503 angstroms; (across all 37 pairs:
20.017)
> show #!3 models
> show #!1 models
> hide #!5 models
> hide #!6 models
> mmaker #1/C to #3/B bring #5
Computing secondary structure
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 EBOV_MR72_refinement21-coot-0_glyco.pdb, chain B (#3) with
marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb, chain C (#1), sequence
alignment score = 382.6
RMSD between 124 pruned atom pairs is 0.670 angstroms; (across all 138 pairs:
1.330)
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!1 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!6 models
> show #!5 models
> hide #!6 models
> save /Users/tgewering/Desktop/MARV_GP_MR72_density.tif width 1344 height 903
> supersample 4 transparentBackground true
> show #!6 models
> hide #!5 models
> save /Users/tgewering/Desktop/EBOV_GP_MR72_density.tif width 1344 height 903
> supersample 4 transparentBackground true
> show #!3 models
> hide #!6 models
> lighting soft
> hide atoms
> set bgColor white
> graphics silhouettes true width 5
> camera ortho
> cartoon suppressBackboneDisplay false
> lighting model #1,2 depthCue false
> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2
> show cartoons
> style stick
Changed 23091 atom styles
> graphics silhouettes true width 3
> show :NAG,BMA,MAN
> size stickRadius 0.4
Changed 23716 bond radii
> color byhetero
> show #3/D/E/F:563
> show #3/D:563
> show #3/E:563
> show #3/F:563
> hide #!3 models
> show #!3 models
> show #3/J:30
> show #3/H:30
> show #3/L:30
> show atoms
> hide atoms
> show :NAG
> show :563
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> lighting model #1,2 depthCue true
> show #!3 models
> hide #!3 models
> save /Users/tgewering/Desktop/MARV_GP_MR72_modeltif.tif width 1344 height
> 903 supersample 4 transparentBackground true
> show #!3 models
> hide #!1 models
> save /Users/tgewering/Desktop/EBOV_GP_MR72_model.tif width 1344 height 903
> supersample 4 transparentBackground true
> show #!1 models
> show #!2 models
> hide #!3 models
> hide #!2 models
> show #!5 models
> hide #!1 models
> save /Users/tgewering/Desktop/MARV_GP_MR72_density.tif width 1344 height 903
> supersample 4 transparentBackground true
> show #!6 models
> hide #!5 models
> save /Users/tgewering/Desktop/EBOV_GP_MR72_density.tif width 1344 height 903
> supersample 4 transparentBackground true
> hide #!6 models
> show #!1 models
> turn x 90
> save /Users/tgewering/Desktop/MARV_GP_MR72_model_top.tif width 1344 height
> 903 supersample 4 transparentBackground true
> show #!3 models
> hide #!1 models
> save /Users/tgewering/Desktop/EBOV_GP_MR72_model_top.tif width 1344 height
> 903 supersample 4 transparentBackground true
> show #!1 models
> hide #!3 models
> turn x -90
> show #!6 models
> show #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> view orient
> hide #!5 models
> hide #!6 models
> hide #!3 models
> show #!3 models
> hide /J/H/L
> hide /J/H/L ribbons
> hide /G/I/K ribbons
> undo
> hide #3:/G/I/K ribbons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #3/G/I/K ribbons
> hide #1/B/F/J ribbons
> hide #1/E/A/H ribbons
> ui mousemode right zoom
> ui tool show "Similar Structures"
> select add #1
11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 1/E
Alignment identifier is 1/J
Alignment identifier is 1/L
Alignment identifier is 4
> select #1/D,I:471
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/D,I:471-604
1634 atoms, 1666 bonds, 6 pseudobonds, 204 residues, 2 models selected
> select #1/D,I:471
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/D,I:471-614
1770 atoms, 1806 bonds, 6 pseudobonds, 224 residues, 2 models selected
> select #1/K,C,G:35-36
39 atoms, 36 bonds, 6 residues, 1 model selected
> select #1/K,C,G:35-38
75 atoms, 72 bonds, 12 residues, 1 model selected
> select #1/B,F:2
16 atoms, 14 bonds, 2 residues, 1 model selected
> select #1/B,F:2-23
226 atoms, 224 bonds, 2 pseudobonds, 32 residues, 2 models selected
> select #1/A,H:2
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/A,H:2-21
274 atoms, 278 bonds, 40 residues, 1 model selected
> select #1/K,C,G:35
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/K,C,G:35-42
159 atoms, 156 bonds, 24 residues, 1 model selected
> select #1/B,F:1
18 atoms, 16 bonds, 2 residues, 1 model selected
> select #1/B,F:1-80
1152 atoms, 1180 bonds, 2 pseudobonds, 148 residues, 2 models selected
> select #1/L:471
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/L:471-614
872 atoms, 889 bonds, 3 pseudobonds, 112 residues, 2 models selected
> select #1/D,I:473
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/D,I:473-556
824 atoms, 842 bonds, 6 pseudobonds, 104 residues, 2 models selected
> select #1/D,I:471
12 atoms, 10 bonds, 2 residues, 1 model selected
> select #1/D,I:471-614
1770 atoms, 1806 bonds, 6 pseudobonds, 224 residues, 2 models selected
> select #1/C
1190 atoms, 1223 bonds, 150 residues, 1 model selected
Alignment identifier is 1/C
> select #1/C:35
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/C:35-180
1137 atoms, 1166 bonds, 146 residues, 1 model selected
> select #2/C
Nothing selected
> select add #3
11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected
> hide #!1 models
> select #23/C
Nothing selected
> select #3/C
1195 atoms, 1226 bonds, 157 residues, 1 model selected
Alignment identifier is 3/C
> select #3/C:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/C
1195 atoms, 1226 bonds, 157 residues, 1 model selected
> select #3/D
852 atoms, 876 bonds, 1 pseudobond, 106 residues, 2 models selected
Alignment identifier is 3/D
> select #3/D:504
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/D:504-612
813 atoms, 834 bonds, 1 pseudobond, 103 residues, 2 models selected
> select add #3
11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected
> select subtract #3
Nothing selected
> open /Users/tgewering/Downloads/MARV_EBOV_aligned.praln
Unrecognized file suffix '.praln'
> open /Users/tgewering/Downloads/MARV_EBOV_aligned.praln
Unrecognized file suffix '.praln'
> open /Users/tgewering/Downloads/MARV_EBOV_aligned.aln
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/__init__.py", line 74, in open
return open_file(session, data, file_name,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/parse.py", line 44, in open_file
seqs, file_attrs, file_markups = ns['read'](session, stream)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/seqalign/io/readALN.py", line 36, in read
for line in f.readlines():
^^^^^^^^^^^^^
File "", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xfc in position 23:
invalid start byte
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xfc in position 23:
invalid start byte
File "", line 322, in decode
See log for complete Python traceback.
> open /Users/tgewering/Downloads/MARV_EBOV_aligned.aln
Failed opening file /Users/tgewering/Downloads/MARV_EBOV_aligned.aln:
'utf-8' codec can't decode byte 0xfc in position 23: invalid start byte
> open /Users/tgewering/Downloads/MARV_EBOV_aligned.fa
Summary of feedback from opening
/Users/tgewering/Downloads/MARV_EBOV_aligned.fa
---
notes | Alignment identifier is MARV_EBOV_aligned.fa
Showing conservation header ("seq_conservation" residue attribute) for
alignment MARV_EBOV_aligned.fa
Opened 2 sequences from MARV_EBOV_aligned.fa
> select clear
> hide #!3 models
> show #!3 models
> select clear
> show #!1 models
> hide #!3 models
> select clear
> color byattribute seq_conservation palette blue:red:yellow
23091 atoms, 2984 residues, atom seq_conservation range 100 to 100
> color byattribute seq_conversation
No known/registered numeric attribute seq_conversation
> color byattribute seq_conservation
23091 atoms, 2984 residues, atom seq_conservation range 100 to 100
> open /Users/tgewering/Downloads/MARV_EBOV_aligned.fa
Summary of feedback from opening
/Users/tgewering/Downloads/MARV_EBOV_aligned.fa
---
notes | Alignment identifier is MARV_EBOV_aligned.fa
Showing conservation header ("seq_conservation" residue attribute) for
alignment MARV_EBOV_aligned.fa
Opened 2 sequences from MARV_EBOV_aligned.fa
> color byattribute seq_conservation
23091 atoms, 2984 residues, atom seq_conservation range 100 to 100
> color byattribute seq_conservation
23091 atoms, 2984 residues, atom seq_conservation range 100 to 100
> color byattribute seq_conservation
23091 atoms, 2984 residues, atom seq_conservation range 100 to 100
> color byattribute seq_conservation
23091 atoms, 2984 residues, atom seq_conservation range 100 to 100
> select add #1
11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 1/E
Alignment identifier is 1/J
Alignment identifier is 1/L
Alignment identifier is 4
> select #1/J:5
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/J:5-60
384 atoms, 395 bonds, 1 pseudobond, 50 residues, 2 models selected
> select #1/K,C,G:35-36
39 atoms, 36 bonds, 6 residues, 1 model selected
> select #1/K,C,G:35-41
132 atoms, 129 bonds, 21 residues, 1 model selected
> select #1/K,C,G:41
24 atoms, 21 bonds, 3 residues, 1 model selected
> select #1/K,C,G:41-180
3303 atoms, 3390 bonds, 420 residues, 1 model selected
> select #1/K,C,G:35
18 atoms, 15 bonds, 3 residues, 1 model selected
> select #1/K,C,G:35-180
3411 atoms, 3498 bonds, 438 residues, 1 model selected
> select add #3
14904 atoms, 15304 bonds, 3 pseudobonds, 1934 residues, 3 models selected
> select add #1
23091 atoms, 23716 bonds, 16 pseudobonds, 2984 residues, 4 models selected
> select subtract #1
11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected
> show #!3 models
> hide #!1 models
> select #3/A
1199 atoms, 1230 bonds, 157 residues, 1 model selected
Alignment identifier is 3/A
> select #3/A:32
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A
1199 atoms, 1230 bonds, 157 residues, 1 model selected
> open /Users/tgewering/Downloads/EBOV_MARV_GP1_aligned.fa
Summary of feedback from opening
/Users/tgewering/Downloads/EBOV_MARV_GP1_aligned.fa
---
notes | Alignment identifier is EBOV_MARV_GP1_aligned.fa
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain C to
MARV_GP1 (0 aa) with 0 mismatches
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain G to
MARV_GP1 (0 aa) with 0 mismatches
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain K to
MARV_GP1 (0 aa) with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain A to EBOV_GP1 (0 aa)
with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain B to EBOV_GP1 (0 aa)
with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain C to EBOV_GP1 (0 aa)
with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment EBOV_MARV_GP1_aligned.fa
Opened 2 sequences from EBOV_MARV_GP1_aligned.fa
> select #1/C,G,K:36-38
57 atoms, 54 bonds, 9 residues, 1 model selected
> select #1/C,G,K:36-49
315 atoms, 315 bonds, 42 residues, 1 model selected
> select add #1
11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected
> select subtract #1
Nothing selected
> show #!1 models
> select #1/C,G,K:36
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #1/C,G,K:36-111
1725 atoms, 1761 bonds, 228 residues, 1 model selected
> undo
> select subtract #3
Nothing selected
> select add #3
11493 atoms, 11806 bonds, 3 pseudobonds, 1496 residues, 2 models selected
> select subtract #3
Nothing selected
> show #!1 models
> open /Users/tgewering/Downloads/EBOV_MARV_GP1_aligned.fa
Summary of feedback from opening
/Users/tgewering/Downloads/EBOV_MARV_GP1_aligned.fa
---
notes | Alignment identifier is EBOV_MARV_GP1_aligned.fa
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain C to
MARV_GP1 (0 aa) with 0 mismatches
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain G to
MARV_GP1 (0 aa) with 0 mismatches
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain K to
MARV_GP1 (0 aa) with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain A to EBOV_GP1 (0 aa)
with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain B to EBOV_GP1 (0 aa)
with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain C to EBOV_GP1 (0 aa)
with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment EBOV_MARV_GP1_aligned.fa
Opened 2 sequences from EBOV_MARV_GP1_aligned.fa
> color #3/D/E/F #335C71
> color #1/D/I/L #667255
> select #1/C,G,K:36
21 atoms, 18 bonds, 3 residues, 1 model selected
> select #1/C,G,K:36-78
975 atoms, 996 bonds, 129 residues, 1 model selected
> select add #1
11598 atoms, 11910 bonds, 13 pseudobonds, 1488 residues, 2 models selected
> select subtract #1
Nothing selected
> color byattribute seq_conservation
23091 atoms, 2984 residues, atom seq_conservation range -0.918 to 100
> color #1/C/G/K byattr seq_conservation
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color byattribute #1/C/G/K seq_conservation
Expected a collection of one of 'atoms', 'cartoons', 'ribbons', or 'surfaces'
or a keyword
> color byattribute seq_conservation #1/C/G/K
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation palette cyanmaroon range -0.918 0.918
> #1/C/G/K
Invalid "range" argument: Expected 2-tuple of numbers or 'full'
> color byattribute seq_conservation palette cyanmaroon range -0.918,0.918
> #1/C/G/K
Expected a keyword
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,0.918
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> hide #!3 models
> show #3/D/I/L ribbons
> show #1/D/I/L ribbons
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,20
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,5
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,10
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,12
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,1
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,3
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,3 noValueColor grey
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,10 noValueColor grey
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,8 noValueColor grey
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,7 noValueColor grey
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,6 noValueColor grey
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #1/C/G/K palette cyanmaroon range
> -0.918,5 noValueColor grey
3570 atoms, 450 residues, atom seq_conservation range -0.918 to 100
> hide #!1 models
> show #!3 models
> hide #3/G/I/K ribbons
> hide #3/J/H/L ribbons
> color byattribute seq_conservation #3/A/B/C palette cyanmaroon range
> -0.918,5 noValueColor grey
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette pastel2-8 range -0.918,5
> noValueColor grey
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
Fetching palette PuBu-5range from
https://www.colourlovers.com/api/palettes?keywords=PuBu-5range&format=json&numResults=100
Could not find palette PuBu-5range at COLOURlovers.com using keyword search
> color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,5
> noValueColor grey
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,5
> noValueColor white
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,10
> noValueColor white
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,3
> noValueColor white
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette pubu-5 range -0.918,3
> noValueColor white key true
> key pubu :-0.92 :0.06 :1.04 :2.02 :3.00 showTool true
> ui mousemode right "color key"
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> key ^pubu :3.00 :2.02 :1.04 :0.06 :-0.92
> key pubu :-0.92 :0.06 :1.04 :2.02 :3.00
> key ^pubu :3.00 :2.02 :1.04 :0.06 :-0.92
> color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,3
> noValueColor white key true
> key ylgnbu :-0.92 :0.06 :1.04 :2.02 :3.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,2
> noValueColor white key true
> key ylgnbu :-0.92 :-0.19 :0.54 :1.27 :2.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,1
> noValueColor white key true
> key ylgnbu :-0.92 :-0.44 :0.04 :0.52 :1.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range
> -0.918,100 noValueColor white key true
> key ylgnbu :0 :24 :50 :75 :100 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,10
> noValueColor white key true
> key ylgnbu :-0.9 :1.8 :4.5 :7.3 :10.0 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,3
> noValueColor white key true
> key ylgnbu :-0.92 :0.06 :1.04 :2.02 :3.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,3
> noValueColor grey key true
> key ylgnbu :-0.92 :0.06 :1.04 :2.02 :3.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color #3/A/B/C:1-52 grey
> color #3/A:1-52 grey
> color #3/B:1-52 grey
> color #3/C:1-52 grey
> color byattribute seq_conservation #3/A/B/C palette ylgnbu-5 range -0.918,1
> noValueColor grey key true
> key ylgnbu :-0.92 :-0.44 :0.04 :0.52 :1.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C range -0.918,1 noValueColor grey
> key true
> key blue-white-red :-0.92 :0.04 :1.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A range -0.918,1 noValueColor grey key
> true
> key blue-white-red :-0.92 :0.04 :1.00 showTool true
1199 atoms, 157 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A range -0.500,0.500 noValueColor grey
> key true
> key blue-white-red :-0.5 :0.0 :0.5 showTool true
1199 atoms, 157 residues, atom seq_conservation range -0.918 to 100
Fetching palette YlOrBr-5novalue from
https://www.colourlovers.com/api/palettes?keywords=YlOrBr-5novalue&format=json&numResults=100
Could not find palette YlOrBr-5novalue at COLOURlovers.com using keyword
search
> color byattribute seq_conservation #3/A range -0.500,0.500 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.50 :-0.25 :0.00 :0.25 :0.50 showTool true
1199 atoms, 157 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C range -0.500,0.500 palette
> ylorbr-5 noValueColor grey key true
> key ylorbr :-0.50 :-0.25 :0.00 :0.25 :0.50 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C range -0.500,7 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.50 :1.38 :3.25 :5.12 :7.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C range -0.500,10 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.5 :2.1 :4.8 :7.4 :10.0 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C range -0.500,18 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.5 :4.1 :8.8 :13.4 :18.0 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> color byattribute seq_conservation #3/A/B/C range -0.500,6 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.50 :1.12 :2.75 :4.38 :6.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.918 to 100
> open /Users/tgewering/Downloads/EBOV_MARV_GP1_global_align.fa
Summary of feedback from opening
/Users/tgewering/Downloads/EBOV_MARV_GP1_global_align.fa
---
notes | Alignment identifier is EBOV_MARV_GP1_global_align.fa
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain C to
MARV_GP1 (0 aa) with 0 mismatches
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain G to
MARV_GP1 (0 aa) with 0 mismatches
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain K to
MARV_GP1 (0 aa) with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain A to EBOV_GP1 (0 aa)
with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain B to EBOV_GP1 (0 aa)
with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain C to EBOV_GP1 (0 aa)
with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment EBOV_MARV_GP1_global_align.fa
Opened 2 sequences from EBOV_MARV_GP1_global_align.fa
> select #1/C,G,K:36-37
39 atoms, 36 bonds, 6 residues, 1 model selected
> select #1/C,G,K:36-37 #3/A-C:52-53
78 atoms, 72 bonds, 12 residues, 2 models selected
EBOV_MARV_GP1_global_align.fa [ID: EBOV_MARV_GP1_global_align.fa] region
MARV_GP1 (0 aa)..EBOV_GP1 (0 aa) [21-22] RMSD: 1.961
> color byattribute seq_conservation #3/A/B/C range -0.500,6 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.50 :1.12 :2.75 :4.38 :6.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #3/A/B/C range -0.918,20 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.9 :4.3 :9.5 :14.8 :20.0 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #3/A/B/C range -0.918,5 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.92 :0.56 :2.04 :3.52 :5.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #3/A/B/C range -0.918,5 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.92 :0.56 :2.04 :3.52 :5.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #3/A/B/C range -0.918,1 palette ylorbr-5
> noValueColor grey key true
> key ylorbr :-0.92 :-0.44 :0.04 :0.52 :1.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> key colorTreatment distinct
Fetching compressed palette GIant from
https://www.colourlovers.com/api/palettes?keywords=GIant&format=json&numResults=100
Could not find palette GIant at COLOURlovers.com using keyword search
> color name taupe #483C32
Color 'taupe' is opaque: rgb(28.2%, 23.5%, 19.6%) hex: #483c32
> color name copper #B87333
Color 'copper' is opaque: rgb(72.2%, 45.1%, 20%) hex: #b87333
> color name tan #D2B48C
Can not override builtin color
> color byattribute seq_conservation #3/A/B/C range -0.918,1 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:0.04 tan:1.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> select #1/C,G,K:141
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #1/C,G,K:141-148
210 atoms, 216 bonds, 24 residues, 1 model selected
> select #3/A-C:157
12 atoms, 9 bonds, 3 residues, 1 model selected
> select #3/A-C:157-164
210 atoms, 216 bonds, 24 residues, 1 model selected
> select #3/A-C:156
27 atoms, 24 bonds, 3 residues, 1 model selected
> select #1/C,G,K:139-140 #3/A-C:155-156
120 atoms, 120 bonds, 12 residues, 2 models selected
EBOV_MARV_GP1_global_align.fa [ID: EBOV_MARV_GP1_global_align.fa] region
MARV_GP1 (0 aa)..EBOV_GP1 (0 aa) [124-125] RMSD: 0.364
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3171, in run
self._process_keyword_arguments(final, prev_annos)
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3088, in
_process_keyword_arguments
value, text = self._parse_arg(anno, text, session, final)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2780, in _parse_arg
value, replacement, rest = annotation.parse(text, session)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 958, in parse
return anno.parse(text, session)
^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 855, in parse
token, text, rest = next_token(text, convert=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2056, in next_token
token = unescape(token)
^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1933, in unescape
return unescape_with_index_map(text)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1962, in unescape_with_index_map
if text[index + count] not in "01234567":
~~~~^^^^^^^^^^^^^^^
IndexError: string index out of range
IndexError: string index out of range
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 1962, in unescape_with_index_map
if text[index + count] not in "01234567":
~~~~^^^^^^^^^^^^^^^
See log for complete Python traceback.
> color byattribute seq_conservation #3/A/B/C range -0.918,15 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.9 #b87333:7.0 tan:15.0 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #3/A/B/C range -0.918,2 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:0.54 tan:2.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #3/A/B/C range -0.918,1 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:0.04 tan:1.00 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #3/A/B/C range -0.918,0.7 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true
3583 atoms, 471 residues, atom seq_conservation range -0.913 to 1.09
> select add #3
11559 atoms, 11875 bonds, 3 pseudobonds, 1502 residues, 3 models selected
> select subtract #3
66 atoms, 69 bonds, 6 residues, 1 model selected
> hide #!3 models
> show #!1 models
> color byattribute seq_conservation #1/D/I/L range -0.918,0.7 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true
2814 atoms, 350 residues, atom seq_conservation range 100 to 100
> undo
> color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> open /Users/tgewering/Downloads/EBOV_MARV_GP1_clustal.aln
Summary of feedback from opening
/Users/tgewering/Downloads/EBOV_MARV_GP1_clustal.aln
---
notes | Alignment identifier is EBOV_MARV_GP1_clustal.aln
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain C to
MARV_GP1 with 0 mismatches
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain G to
MARV_GP1 with 0 mismatches
Associated marvGPdMuc_MR72_formodelinJ987-coot-20_March28.pdb chain K to
MARV_GP1 with 0 mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain A to EBOV_GP1 with 0
mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain B to EBOV_GP1 with 0
mismatches
Associated EBOV_MR72_refinement21-coot-0_glyco.pdb chain C to EBOV_GP1 with 0
mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment EBOV_MARV_GP1_clustal.aln
Opened 2 sequences from EBOV_MARV_GP1_clustal.aln
> color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #1/C/G/K range -0.918,0.7 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:-0.11 tan:0.70 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #1/C/G/K range -0.918,7 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:3.04 tan:7.00 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #1/C/G/K range -0.918,2 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:0.54 tan:2.00 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #1/C/G/K range -0.918,1 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.92 #b87333:0.04 tan:1.00 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #1/C/G/K range -0.918,0.2 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.918 #b87333:-0.359 tan:0.200 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> color byattribute seq_conservation #1/C/G/K range -0.918,0.1 palette
> taupe:copper:tan noValueColor grey key true
> key #483c32:-0.918 #b87333:-0.409 tan:0.100 showTool true
3570 atoms, 450 residues, atom seq_conservation range -0.913 to 1.09
> color similarity matrix blosum62 threshold 0.5
Unknown command: sequence color similarity matrix blosum62 threshold 0.5
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #1/H #3/G #3/I #3/K
Alignment identifier is 1
===== Log before crash end =====
Log:
Startup Messages
---
warning | No presets found in custom preset folder /Users/tgewering/Desktop/ChimeraX_preferences
note | available bundle cache has not been initialized yet
> set bgColor white
> lighting soft
> show cartoons
> hide atoms
> cartoon style thickness 1.2
> graphics silhouettes true
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: MPHE3LL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 23 days, 22 hours, 18 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
EA244WMi:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
ASUS VE278:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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