![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 weeks ago
Closed 4 weeks ago
#19123 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-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 0x00000001f9e6df00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 58)
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"procRole" : "Background",
"version" : 2,
"userID" : 196921631,
"deployVersion" : 210,
"modelCode" : "Mac14,8",
"coalitionID" : 224980,
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-10-12 16:17:56.9352 -0700",
"codeSigningMonitor" : 1,
"incident" : "C08CF3BC-D2C0-44FA-BFE4-EFF5CE129214",
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"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-09-29 15:52:53.0024 -0700",
"procStartAbsTime" : 22965966648095,
"procExitAbsTime" : 49884988621956,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"FF06749C-3FDE-5094-84E2-A485DDEF93D5","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "495849F9-0053-6F47-F901-532221B9AF5C",
"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "EDB2730F-1767-4901-A340-F3D63C4FCD96",
"wakeTime" : 11,
"sleepWakeUUID" : "5A674303-76D1-4C4D-8B22-FD2A61A9EC50",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4296966120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1001e8000-1001ec000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":53474},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4296966120\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1001e8000-1001ec000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
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"name" : "AppKit",
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"uuid" : "8bf83cda-8db1-3d46-94b0-d811bd77e078",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
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===== Log before crash start =====
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Volumes/KaiZhou2024/Download/Ribo_john/2point15_with_models.cxs
Opened cryosparc_P1_J167_006_volume_map_sharp_flip.mrc as #2, grid size
720,720,720, pixel 0.819, shown at level 0.08, step 1, values float32
Log from Tue Dec 31 16:55:29 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/KaiZhou2024/Download/Ribo_john/8ccs_SSUbody_relative_tomap.pdb
Chain information for 8ccs_SSUbody_relative_tomap.pdb #1
---
Chain | Description
0 | No description available
2 | No description available
3 | No description available
6 | No description available
D | No description available
Z | No description available
c | No description available
d | No description available
e | No description available
f | No description available
h | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
q | No description available
x | No description available
y | No description available
z | No description available
> hide atoms
> show cartoons
> open
> /Volumes/KaiZhou2024/Download/Ribo_john/cryosparc_P1_J167_006_volume_map_sharp_flip.mrc
Opened cryosparc_P1_J167_006_volume_map_sharp_flip.mrc as #2, grid size
720,720,720, pixel 0.819, shown at step 1, values float32
> volume #2 level -0.02512,0 level 0.08725,0.8 level 0.6095,1
> volume #2 region 0,0,0,719,719,719 step 4
[Repeated 1 time(s)]
> volume #2 step 1
> surface dust #2 size 8.19
> open /Volumes/KaiZhou2024/Download/Ribo_john/5JUO_LSU_relative_tomap.pdb
Summary of feedback from opening
/Volumes/KaiZhou2024/Download/Ribo_john/5JUO_LSU_relative_tomap.pdb
---
warnings | Bad residue range for secondary structure: HELIX 34 34 GLU F 84 LYS F 92 1 9
Bad residue range for secondary structure: HELIX 74 74 ALA I 29 LYS I 41 1 13
Bad residue range for secondary structure: HELIX 130 130 ALA O 51 ARG O 55 1 5
Bad residue range for secondary structure: HELIX 131 131 LEU O 67 LYS O 75 1 9
Bad residue range for secondary structure: SHEET 59 59 1 VAL K 81 PHE K 85 0
1 messages similar to the above omitted
Chain information for 5JUO_LSU_relative_tomap.pdb #3
---
Chain | Description
A | No description available
B | No description available
B | No description available
C | No description available
C | No description available
D | No description available
D | No description available
E | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> hide #!1 models
> select add #3
133691 atoms, 144143 bonds, 7 pseudobonds, 10494 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select clear
> color #2 #b2b2b291 models
> hide #!2 models
> select #3/X:9
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
49 atoms, 49 bonds, 6 residues, 1 model selected
> select up
1446 atoms, 1482 bonds, 172 residues, 1 model selected
> color sel red
> select clear
> show #!2 models
> hide #!2 models
> ui tool show "Side View"
> show #!2 models
> select #3/X:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
43 atoms, 44 bonds, 5 residues, 1 model selected
> select up
1446 atoms, 1482 bonds, 172 residues, 1 model selected
> show sel target ab
> style sel stick
Changed 1446 atom styles
> select clear
> move z -2
[Repeated 2 time(s)]
> move z 2
[Repeated 1 time(s)]
> volume #2 level 0.055
> volume #2 level 0.07
> volume #2 level 0.08
> move z 2
> select add #3
133691 atoms, 144143 bonds, 7 pseudobonds, 10494 residues, 2 models selected
> show (#!3 & sel) target ab
> nucleotides sel atoms
> style nucleic & sel stick
Changed 80327 atom styles
> style sel stick
Changed 133691 atom styles
> select subtract #3
Nothing selected
> select clear
> ui tool show "Fit in Map"
> fitmap #3 inMap #2
Fit molecule 5JUO_LSU_relative_tomap.pdb (#3) to map
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) using 133691 atoms
average map value = 0.1051, steps = 48
shifted from previous position = 0.138
rotated from previous position = 0.105 degrees
atoms outside contour = 65457, contour level = 0.08
Position of 5JUO_LSU_relative_tomap.pdb (#3) relative to
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) coordinates:
Matrix rotation and translation
0.99999879 -0.00107725 -0.00112218 0.55803934
0.00107615 0.99999894 -0.00098206 -0.14261210
0.00112324 0.00098085 0.99999889 -0.71399215
Axis 0.53360518 -0.61040006 0.58538643
Axis point 618.89327677 -0.00000000 512.37204707
Rotation angle (degrees) 0.10538407
Shift along axis -0.03313820
> fitmap #1 inMap #2
Fit molecule 8ccs_SSUbody_relative_tomap.pdb (#1) to map
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) using 45477 atoms
average map value = 0.07723, steps = 132
shifted from previous position = 3.4
rotated from previous position = 8.55 degrees
atoms outside contour = 26231, contour level = 0.08
Position of 8ccs_SSUbody_relative_tomap.pdb (#1) relative to
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) coordinates:
Matrix rotation and translation
0.99004319 0.13274730 -0.04682553 -20.99922583
-0.13484177 0.98985279 -0.04482365 57.92987177
0.04040016 0.05069139 0.99789689 -25.03260090
Axis 0.32136938 -0.29347906 -0.90032869
Axis point 412.96123833 186.22944125 0.00000000
Rotation angle (degrees) 8.54616927
Shift along axis -1.21214386
> show #!1 models
> hide #!3 models
> select add #1
45477 atoms, 48613 bonds, 105 pseudobonds, 3839 residues, 2 models selected
> show (#!1 & sel) target ab
> nucleotides sel atoms
> style nucleic & sel stick
Changed 24134 atom styles
> style sel stick
Changed 45477 atom styles
> select subtract #1
Nothing selected
> select clear
> open /Volumes/KaiZhou2024/Download/Ribo_john/8ccs_SSUhead.pdb
Chain information for 8ccs_SSUhead.pdb #4
---
Chain | Description
1 | No description available
4 | No description available
5 | No description available
7 | No description available
8 | No description available
c | No description available
g | No description available
i | No description available
n | No description available
r | No description available
s | No description available
t | No description available
u | No description available
v | No description available
w | No description available
> ui tool show Matchmaker
> open /Volumes/KaiZhou2024/Download/Ribo_john/5JUO_relative_tomap.pdb
Summary of feedback from opening
/Volumes/KaiZhou2024/Download/Ribo_john/5JUO_relative_tomap.pdb
---
warnings | Bad residue range for secondary structure: HELIX 174 174 GLU F 84 LYS F 92 1 9
Bad residue range for secondary structure: HELIX 182 182 ALA I 29 LYS I 41 1
13
Bad residue range for secondary structure: HELIX 200 200 ALA O 51 ARG O 55 1 5
Bad residue range for secondary structure: HELIX 201 201 LEU O 67 LYS O 75 1 9
Bad residue range for secondary structure: HELIX 221 221 ASP W 51 LYS W 53 1 3
20 messages similar to the above omitted
Chain information for 5JUO_relative_tomap.pdb #5
---
Chain | Description
A | No description available
A | No description available
B | No description available
B | No description available
C | No description available
C | No description available
D | No description available
D | No description available
E | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
> ui tool show Matchmaker
> matchmaker #!4 to #5
Computing secondary structure
[Repeated 2 time(s)] 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 5JUO_relative_tomap.pdb, chain A (#5) with 8ccs_SSUhead.pdb, chain
c (#4), sequence alignment score = 2849.2
RMSD between 338 pruned atom pairs is 1.261 angstroms; (across all 475 pairs:
1.944)
> select add #4
23534 atoms, 24882 bonds, 61 pseudobonds, 2169 residues, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 10131 atom styles
> style sel stick
Changed 23534 atom styles
> show sel cartoons
> select subtract #4
Nothing selected
> hide #!4 models
> hide #!5 models
> select add #5
215363 atoms, 231001 bonds, 10 pseudobonds, 17961 residues, 3 models selected
> nucleotides #!1 atoms
> style nucleic & #!1 stick
Changed 24134 atom styles
> style #!1 stick
Changed 45477 atom styles
> show #!5 models
> show sel atoms
> show sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 117985 atom styles
> style sel stick
Changed 215363 atom styles
> select subtract #5
Nothing selected
> hide #!1 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!4 models
> volume #2 level 0.05
> color #2 #b2b2b2ff models
> fitmap #4 inMap #2
Fit molecule 8ccs_SSUhead.pdb (#4) to map
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) using 23534 atoms
average map value = 0.03515, steps = 232
shifted from previous position = 13.5
rotated from previous position = 15.2 degrees
atoms outside contour = 17303, contour level = 0.05
Position of 8ccs_SSUhead.pdb (#4) relative to
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) coordinates:
Matrix rotation and translation
-0.87845613 -0.45107947 0.15761388 610.86698022
-0.47329718 0.86672710 -0.15739734 241.33046814
-0.06560951 -0.21286486 -0.97487637 637.09144622
Axis -0.24003380 0.96599154 -0.09614635
Axis point 354.60416425 0.00000000 312.04627599
Rotation angle (degrees) 173.36516594
Shift along axis 25.24045332
> hide #!4 models
> show #!4 models
> volume #2 level 0.04
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> open /Volumes/KaiZhou2024/Download/Ribo_john/8bn3_Rpl20.pdb
Chain information for 8bn3_Rpl20.pdb #6
---
Chain | Description
N | No description available
Computing secondary structure
> hide #!3 models
> show #!3 models
> ui tool show Matchmaker
> matchmaker #6 to #3
Computing secondary structure
[Repeated 1 time(s)] 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 5JUO_LSU_relative_tomap.pdb, chain X (#3) with 8bn3_Rpl20.pdb,
chain N (#6), sequence alignment score = 788.1
RMSD between 166 pruned atom pairs is 0.979 angstroms; (across all 172 pairs:
1.123)
> hide #!3 models
> select add #6
1448 atoms, 1481 bonds, 175 residues, 1 model selected
> color sel red
> show sel target ab
> select clear
> show #!2 models
> hide #!2 models
> move z 2
> show #!2 models
> hide #!2 models
> volume #2 level 0.08
> show #!2 models
> fitmap #6 inMap #2
Fit molecule 8bn3_Rpl20.pdb (#6) to map
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) using 1448 atoms
average map value = 0.1701, steps = 44
shifted from previous position = 0.496
rotated from previous position = 0.7 degrees
atoms outside contour = 192, contour level = 0.08
Position of 8bn3_Rpl20.pdb (#6) relative to
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) coordinates:
Matrix rotation and translation
-0.40008314 0.91021423 -0.10697443 217.03033211
-0.91068481 -0.40794062 -0.06509700 557.73458535
-0.10289143 0.07137578 0.99212844 117.15292635
Axis 0.07473822 -0.00223602 -0.99720068
Axis point 294.17473082 205.69502627 0.00000000
Rotation angle (degrees) 114.07597496
Shift along axis -101.85162453
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #6 models
> hide #!4 models
> volume #2 level 0.04
> show #!4 models
> volume #2 level 0.06
> hide #!4 models
> save /Volumes/KaiZhou2024/Download/Ribo_john/2point15_with_models.cxs
> includeMaps true
> show #!1 models
> hide #!2 models
> select #1/Z:12
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
149 atoms, 147 bonds, 15 residues, 1 model selected
> show #!2 models
> hide #!2 models
> move z 2
[Repeated 2 time(s)]
> move z -2
[Repeated 1 time(s)]
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> show #!3 models
> select #3/S:20
18 atoms, 16 bonds, 2 residues, 1 model selected
> select up
537 atoms, 545 bonds, 62 residues, 1 model selected
> select up
1955 atoms, 1993 bonds, 228 residues, 1 model selected
> color sel red
> select clear
> show #!2 models
> hide #!3 models
> show #!3 models
> select add #1
45477 atoms, 48613 bonds, 105 pseudobonds, 3839 residues, 2 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 24134 atom styles
> style sel stick
Changed 45477 atom styles
> show sel atoms
> select subtract #1
Nothing selected
> color #2 #b2b2b258 models
> fitmap #1 inMap #2
Fit molecule 8ccs_SSUbody_relative_tomap.pdb (#1) to map
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) using 45477 atoms
average map value = 0.07724, steps = 40
shifted from previous position = 0.0173
rotated from previous position = 0.00953 degrees
atoms outside contour = 19601, contour level = 0.06
Position of 8ccs_SSUbody_relative_tomap.pdb (#1) relative to
cryosparc_P1_J167_006_volume_map_sharp_flip.mrc (#2) coordinates:
Matrix rotation and translation
0.99003230 0.13286315 -0.04672726 -21.05107750
-0.13495509 0.98983455 -0.04488523 57.99085350
0.04028866 0.05074391 0.99789873 -25.01999134
Axis 0.32155687 -0.29259455 -0.90054962
Axis point 413.04289750 186.51245859 0.00000000
Rotation angle (degrees) 8.55142921
Shift along axis -1.20518265
> hide #!3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
31 atoms, 30 bonds, 4 residues, 1 model selected
> select up
49 atoms, 48 bonds, 6 residues, 1 model selected
> select up
180 atoms, 178 bonds, 19 residues, 1 model selected
> select up
204 atoms, 202 bonds, 22 residues, 1 model selected
> select up
45477 atoms, 48613 bonds, 3839 residues, 1 model selected
> select down
204 atoms, 202 bonds, 22 residues, 1 model selected
> color sel red
> select clear
> volume #2 level 0.08
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> save /Volumes/KaiZhou2024/Download/Ribo_john/2point15_with_models.cxs
> includeMaps true
——— End of log from Tue Dec 31 16:55:29 2024 ———
opened ChimeraX session
> show #6 models
> ui tool show "Side View"
> open
> /Volumes/KaiZhou2024/backup_Feb2025/Manuscript_project/Ribosome_protein_folding_plasticity/Dec18_35C_ribosome.cxs
Opened class1-emready-bin1.mrc as #1, grid size 512,512,512, pixel 0.819,
shown at level 3, step 1, values float32
Opened class2-emready-bin1.mrc as #3, grid size 512,512,512, pixel 0.819,
shown at level 3, step 1, values float32
Opened class3-emready-bin1.mrc as #4, grid size 512,512,512, pixel 0.819,
shown at level 3, step 1, values float32
opened ChimeraX session
> hide #!2 models
> show #!2 models
> move z -1
> open /Volumes/KaiZhou2024/Download/Ribo_john/Rpl14_Rpl20.cxs
Opened cryosparc_P1_J167_006_volume_map_sharp_flip.mrc 0 as #10.1, grid size
720,720,720, pixel 0.819, shown at level 0.08, step 1, values float32
Opened cryosparc_P1_J167_006_volume_map_sharp_flip.mrc 1 as #10.2, grid size
720,720,720, pixel 0.819, shown at level 0.08, step 1, values float32
opened ChimeraX session
> ui tool show "Model Panel"
> show #!10.1 models
> surface dust #10.1 size 8.19
> surface dust #10.2 size 8.19
> open
> /Volumes/KaiZhou2024/Download/Ribo_john/link_between_L20andH69andL41_withmap.cxs
Opened emd_6615.map as #6, grid size 320,320,320, pixel 1.32, shown at level
0.025, step 1, values float32
Opened emd_6615.map 0 as #7.1, grid size 320,320,320, pixel 1.32, shown at
level 0.025, step 1, values float32
Opened emd_6615.map 1 as #7.2, grid size 320,320,320, pixel 1.32, shown at
level 0.025, step 1, values float32
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #4 models
> hide #4 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #4 models
> hide #4 models
> show #!1 models
> hide #!1 models
> show #!1 models
> open /Volumes/KaiZhou2024/Download/Ribo_john/2point15_with_models.cxs
Opened cryosparc_P1_J167_006_volume_map_sharp_flip.mrc as #2, grid size
720,720,720, pixel 0.819, shown at level 0.08, step 1, values float32
opened ChimeraX session
> ui tool show "Model Panel"
> show #!5 models
> show #6 models
> hide #!2 models
> hide #!1 models
> hide #!5 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #6 models
> show #6 models
> hide #6 models
> move z 1
> move z -1
> show #6 models
> hide #!3 models
> show #!3 models
> hide #6 models
> open /Users/kzhou/Downloads/AF-P28795-F1-model_v6.pdb
AF-P28795-F1-model_v6.pdb title:
Alphafold monomer V2.0 prediction for peroxisomal biogenesis factor 3 (P28795)
[more info...]
Chain information for AF-P28795-F1-model_v6.pdb #7
---
Chain | Description | UniProt
A | peroxisomal biogenesis factor 3 | PEX3_YEAST 1-441
Computing secondary structure
> hide #!3 models
> hide #!2 models
> ui tool show "Side View"
> style #7 sphere
Changed 3566 atom styles
> show #7 atoms
> show #7 surfaces
> graphics silhouettes true
> lighting flat
> lighting soft
> lighting full
> lighting flat
> hide #!7 cartoons
> hide #!7 atoms
> color #7 #ed030bff
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting simple
> lighting flat
> set bgColor white
> save
> /Users/kzhou/Desktop/Manuscript/Proteome_aging/Figures/Figure_materials/pex3.png
> width 1405 height 763 supersample 3 transparentBackground true
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Volumes/KaiZhou2024/backup_Feb2025/Manuscript_project/Ribosome_protein_folding_plasticity/L41_neomycin_sensitivity.cxs
Log from Tue Dec 31 12:29:54 2024UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
> open
> /Users/kaizhou/Desktop/Manuscript_project/Ribosome_protein_folding_plasticity/Dec18_35C_ribosome.cxs
Opened class1-emready-bin1.mrc as #1, grid size 512,512,512, pixel 0.819,
shown at level 3, step 1, values float32
Opened class2-emready-bin1.mrc as #3, grid size 512,512,512, pixel 0.819,
shown at level 3, step 1, values float32
Opened class3-emready-bin1.mrc as #4, grid size 512,512,512, pixel 0.819,
shown at level 3, step 1, values float32
Log from Wed Dec 18 16:48:41 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/ZhouLab/Zhu/EM/20241211-yeast-
> lysate-35degree/maps/class1-emready-bin1.mrc
Opened class1-emready-bin1.mrc as #1, grid size 512,512,512, pixel 0.819,
shown at level 5.81, step 2, values float32
> volume #1 step 1
> open /Volumes/ZhouLab/Zhu/EM/20241211-yeast-
> lysate-35degree/pdb/class1-80S-fitting-using-8bn3.pdb
Summary of feedback from opening /Volumes/ZhouLab/Zhu/EM/20241211-yeast-
lysate-35degree/pdb/class1-80S-fitting-using-8bn3.pdb
---
warnings | Cannot find LINK/SSBOND residue MG (101 )
Cannot find LINK/SSBOND residue K (102 )
Cannot find LINK/SSBOND residue K (401 )
Cannot find LINK/SSBOND residue K (201 )
Cannot find LINK/SSBOND residue K (3401 )
71 messages similar to the above omitted
Chain information for class1-80S-fitting-using-8bn3.pdb #2
---
Chain | Description
1 | No description available
2 | No description available
3 | No description available
4 | No description available
B | No description available
C0 | No description available
C1 | No description available
C3 | No description available
C4 | No description available
C5 | No description available
C6 | No description available
C7 | No description available
C8 | No description available
C9 | No description available
D0 | No description available
D1 | No description available
D2 | No description available
D3 | No description available
D4 | No description available
D5 | No description available
D6 | No description available
D7 | No description available
D8 | No description available
D9 | No description available
E0 | No description available
E1 | No description available
L2 | No description available
L3 | No description available
L4 | No description available
L5 | No description available
L6 | No description available
L7 | No description available
L8 | No description available
L9 | No description available
M0 | No description available
M1 | No description available
M3 | No description available
M4 | No description available
M5 | No description available
M6 | No description available
M7 | No description available
M8 | No description available
M9 | No description available
N0 | No description available
N1 | No description available
N2 | No description available
N3 | No description available
N4 | No description available
N5 | No description available
N6 | No description available
N7 | No description available
N8 | No description available
N9 | No description available
O0 | No description available
O1 | No description available
O2 | No description available
O3 | No description available
O4 | No description available
O5 | No description available
O6 | No description available
O7 | No description available
O8 | No description available
O9 | No description available
P | No description available
Q0 | No description available
Q1 | No description available
Q2 | No description available
Q3 | No description available
S0 | No description available
S1 | No description available
S2 | No description available
S3 | No description available
S4 | No description available
S5 | No description available
S6 | No description available
S7 | No description available
S8 | No description available
S9 | No description available
SM | No description available
SR | No description available
eI | No description available
> hide atoms
> show cartoons
> show atoms
> nucleotides atoms
> style nucleic stick
Changed 110162 atom styles
> style stick
Changed 201660 atom styles
> select /L8
1706 atoms, 1737 bonds, 1 pseudobond, 216 residues, 2 models selected
> select /N0
1445 atoms, 1481 bonds, 172 residues, 1 model selected
> color sel red
> volume #1 level 3
> color #1 #b2b2b282 models
> color #1 #b2b2b2ba models
> lighting simple
> lighting soft
> volume #1 level 4.5
> ui tool show "Side View"
> move z 2
[Repeated 1 time(s)]
> color #2 #920e95ff
> color #2 #f60e95ff
> color #2 #f60effff
> move z 2
[Repeated 6 time(s)]
> color #1 #b2b2b28d models
> move z 2
[Repeated 12 time(s)]
> color sel yellow
> select add #2
201660 atoms, 214201 bonds, 1416 pseudobonds, 18543 residues, 3 models
selected
> select subtract #2
Nothing selected
> move z 2
[Repeated 22 time(s)]
> open /Volumes/ZhouLab/Zhu/EM/20241211-yeast-
> lysate-35degree/maps/class2-emready-bin1.mrc
Opened class2-emready-bin1.mrc as #3, grid size 512,512,512, pixel 0.819,
shown at level 5.29, step 2, values float32
> volume #3 step 1
> volume #3 level 4.5
> color #3 #00ffb2ff models
> color #3 lime models
> color #3 #00ff00a6 models
> move z -20
> move z -2
[Repeated 4 time(s)]
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> move z -2
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> move z -2
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> move z -2
> hide #!1 models
> show #!1 models
> move z -2
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> move z -2
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit map class2-emready-bin1.mrc in map class1-emready-bin1.mrc using 1748741
points
correlation = 0.9414, correlation about mean = 0.7187, overlap = 1.074e+08
steps = 68, shift = 0.177, angle = 0.539 degrees
Position of class2-emready-bin1.mrc (#3) relative to class1-emready-bin1.mrc
(#1) coordinates:
Matrix rotation and translation
0.99995990 0.00300716 0.00843555 -2.23724331
-0.00298304 0.99999143 -0.00287001 1.10729964
-0.00844411 0.00284473 0.99996030 1.25010659
Axis 0.30396544 0.89782420 -0.31861689
Axis point 143.63234633 0.00000000 262.86519931
Rotation angle (degrees) 0.53860624
Shift along axis -0.08418932
> show #!3 models
> move z -2
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> move z -2
[Repeated 1 time(s)]
> open /Volumes/ZhouLab/Zhu/EM/20241211-yeast-
> lysate-35degree/maps/class3-emready-bin1.mrc
Opened class3-emready-bin1.mrc as #4, grid size 512,512,512, pixel 0.819,
shown at level 5.8, step 2, values float32
> fitmap #4 inMap #1
Fit map class3-emready-bin1.mrc in map class1-emready-bin1.mrc using 167676
points
correlation = 0.9203, correlation about mean = 0.6313, overlap = 1.171e+07
steps = 80, shift = 0.388, angle = 1.3 degrees
Position of class3-emready-bin1.mrc (#4) relative to class1-emready-bin1.mrc
(#1) coordinates:
Matrix rotation and translation
0.99975074 -0.02231902 -0.00057237 5.09384975
0.02231669 0.99974378 -0.00378574 -3.97572908
0.00065671 0.00377203 0.99999267 -1.27459312
Axis 0.16688350 -0.02713936 0.98560304
Axis point 181.13583868 228.43635534 0.00000000
Rotation angle (degrees) 1.29750832
Shift along axis -0.29826462
> color #4 #b2c3ffff models
> color #4 #b2b2ffff models
> color #4 #b285ffff models
> move z 2
[Repeated 8 time(s)]
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> move z 2
[Repeated 11 time(s)]
> hide #!4 models
> show #!4 models
> show #!1 models
> move z 2
[Repeated 3 time(s)]
> hide #!3 models
> hide #!4 models
> show #!4 models
> show #!3 models
> move z 2
[Repeated 4 time(s)]
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> move z 2
[Repeated 8 time(s)]
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> move z 2
[Repeated 1 time(s)]
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> move z 2
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> move z 2
[Repeated 3 time(s)]
> hide #!1 models
> select /E1
271 atoms, 276 bonds, 35 residues, 1 model selected
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> move z 2
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> show #!1 models
> move z 2
[Repeated 4 time(s)]
> hide #!1 models
> show #!1 models
> move z 2
[Repeated 3 time(s)]
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> move z 2
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> move z 2
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> move z 2
[Repeated 1 time(s)]
> hide #!3 models
> show #!3 models
> move z 2
[Repeated 4 time(s)]
> hide #!1 models
> show #!1 models
> move z 2
[Repeated 2 time(s)]
> hide #!1 models
> show #!1 models
> hide #!3 models
> select clear
> volume #1 level 3
> ui tool show "Fit in Map"
> ui tool show "Color Zone"
> hide #!1 models
> select /N0:90
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
90 atoms, 91 bonds, 10 residues, 1 model selected
> select up
1445 atoms, 1481 bonds, 172 residues, 1 model selected
> color zone #1 near sel distance 3
> volume splitbyzone #1
Opened class1-emready-bin1.mrc 0 as #5.1, grid size 512,512,512, pixel 0.819,
shown at level 3, step 1, values float32
Opened class1-emready-bin1.mrc 1 as #5.2, grid size 512,512,512, pixel 0.819,
shown at level 3, step 1, values float32
> hide #!5.1 models
> color zone #3 near sel distance 3
> volume splitbyzone #3
Opened class2-emready-bin1.mrc 0 as #6.1, grid size 512,512,512, pixel 0.819,
shown at level 4.5, step 1, values float32
Opened class2-emready-bin1.mrc 1 as #6.2, grid size 512,512,512, pixel 0.819,
shown at level 4.5, step 1, values float32
> hide #!6.1 models
> color #6.2 #76ff00ff models
> color #5.2 #ff8e00ff models
> select clear
> hide #!2 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6.2 models
> show #!6.2 models
> color #6.2 #76ff00aa models
> color #5.2 #ff0f00ff models
> hide #!6.2 models
> show #!6.2 models
> hide #!5.2 models
> show #!5.2 models
> color #6.2 #76ff00ff models
> move z 2
> move z
[Repeated 1 time(s)]
> hide #!6.2 models
> show #!6.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> move z
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> move z
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> move z
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> move z
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> move z
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> move z
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> show #!2 models
> hide #!5 models
> hide #!6 models
> show #!6.1 models
> hide #!6 models
> hide #!6.1 models
> show #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> move z
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> move z
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> move z
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z
> hide #!5 models
> show #!5 models
> hide #!5 models
> move z
> show #!5 models
> hide #!5 models
> move z
> show #!5 models
> move z
> hide #!5 models
> move z
> show #!5 models
> move z
[Repeated 1 time(s)]
> hide #!5 models
> move z
> show #!5 models
> move z
[Repeated 1 time(s)]
No atoms selected for color zoning
Need to color zone map before it can be split
> show #!2 models
> hide #!5 models
> hide #!6 models
> select /N0:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
64 atoms, 64 bonds, 8 residues, 1 model selected
> select up
1445 atoms, 1481 bonds, 172 residues, 1 model selected
> color zone #4 near sel distance 3
> volume splitbyzone #4
Opened class3-emready-bin1.mrc 0 as #7.1, grid size 512,512,512, pixel 0.819,
shown at level 5.8, step 1, values float32
Opened class3-emready-bin1.mrc 1 as #7.2, grid size 512,512,512, pixel 0.819,
shown at level 5.8, step 1, values float32
> hide #!7.1 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> color #5.2 #ff0f0081 models
> color #5.2 #ff0f0080 models
> move z 1
[Repeated 4 time(s)]
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> hide #!5 models
> move z 1
> show #!5 models
> hide #!5 models
> move z 1
> show #!5 models
> hide #!5 models
> move z 1
> show #!5 models
> hide #!5 models
> move z 1
> show #!5 models
> hide #!5 models
> move z 1
> show #!5 models
> hide #!5 models
> move z 1
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> move z 1
> show #!5 models
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> show #!5 models
> move z 1
> hide #!5 models
> move z 1
> show #!5 models
> close #5.1
> close #6.1
> close #7.1
> hide #!5 models
> hide #!6.2 models
> show #!6.2 models
> hide #!6 models
> hide #!7 models
> show #!4 models
> show #!1 models
> volume #4 level 3
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!7 models
> show #!5 models
> volume #7.2 level 3
> volume #6.2 level 3
> fitmap #7.2 inMap #5.2
Fit map class3-emready-bin1.mrc 1 in map class1-emready-bin1.mrc 1 using 22703
points
correlation = 0.9457, correlation about mean = 0.715, overlap = 9.559e+05
steps = 48, shift = 0.138, angle = 0.181 degrees
Position of class3-emready-bin1.mrc 1 (#7.2) relative to class1-emready-
bin1.mrc 1 (#5.2) coordinates:
Matrix rotation and translation
0.99969283 -0.02464239 -0.00264592 5.94674787
0.02463366 0.99969115 -0.00328442 -4.47932019
0.00272604 0.00321823 0.99999111 -1.44893223
Axis 0.13007195 -0.10745504 0.98566460
Axis point 185.60159232 239.92323134 0.00000000
Rotation angle (degrees) 1.43233486
Shift along axis -0.17333061
> fitmap #6.2 inMap #5.2
Fit map class2-emready-bin1.mrc 1 in map class1-emready-bin1.mrc 1 using 20843
points
correlation = 0.9506, correlation about mean = 0.7435, overlap = 1.006e+06
steps = 52, shift = 0.445, angle = 0.118 degrees
Position of class2-emready-bin1.mrc 1 (#6.2) relative to class1-emready-
bin1.mrc 1 (#5.2) coordinates:
Matrix rotation and translation
0.99995767 0.00290584 0.00873011 -1.84897125
-0.00289872 0.99999546 -0.00082787 0.94967124
-0.00873247 0.00080253 0.99996155 1.80592735
Axis 0.08825335 0.94524607 -0.31419933
Axis point 211.87280765 0.00000000 214.50876233
Rotation angle (degrees) 0.52925187
Shift along axis 0.16707393
> fitmap #6.2 inMap #7.2
Fit map class2-emready-bin1.mrc 1 in map class3-emready-bin1.mrc 1 using 20843
points
correlation = 0.9361, correlation about mean = 0.6471, overlap = 9.031e+05
steps = 40, shift = 0.0235, angle = 0.0659 degrees
Position of class2-emready-bin1.mrc 1 (#6.2) relative to class3-emready-
bin1.mrc 1 (#7.2) coordinates:
Matrix rotation and translation
0.99954826 0.02817140 0.01047112 -7.64003867
-0.02819583 0.99960001 0.00219347 5.70390243
-0.01040514 -0.00248772 0.99994277 3.12848992
Axis -0.07764341 0.34625874 -0.93492052
Axis point 202.76864893 275.43292028 0.00000000
Rotation angle (degrees) 1.72746961
Shift along axis -0.35666466
> hide #!5 models
> hide #!6.2 models
> hide #!7 models
> show #!2 models
> select add #2
201660 atoms, 214201 bonds, 1416 pseudobonds, 18543 residues, 3 models
selected
> select subtract #2
Nothing selected
> move z -10
> show #!3 models
> move z 2
[Repeated 2 time(s)]
> color #3 #00ff0088 models
> color #3 #00ff0074 models
> move z 2
[Repeated 5 time(s)]
> color #3 #00ff0039 models
> move z 2
[Repeated 3 time(s)]
> show #!1 models
> hide #!1 models
> move z 2
[Repeated 2 time(s)]
> move z -2
[Repeated 9 time(s)]
> move z 2
[Repeated 12 time(s)]
> move z -2
[Repeated 2 time(s)]
> move z 4
> move z
[Repeated 7 time(s)]
> move z 2
[Repeated 34 time(s)]
> move z -2
[Repeated 3 time(s)]
> move z 2
[Repeated 5 time(s)]
> show #!1 models
> hide #!1 models
> move z 2
[Repeated 10 time(s)]
> show #!1 models
> hide #!1 models
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display2
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display2
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display2
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display2
> move z -2
[Repeated 1 time(s)]
> move z 2
> select /M8
1441 atoms, 1465 bonds, 185 residues, 1 model selected
> color sel orange
> move z 2
[Repeated 11 time(s)]
> move z -2
[Repeated 2 time(s)]
> move z 2
[Repeated 4 time(s)]
> select /Q3:88
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
147 atoms, 146 bonds, 19 residues, 1 model selected
> select up
694 atoms, 701 bonds, 91 residues, 1 model selected
> select up
201660 atoms, 214201 bonds, 18543 residues, 1 model selected
> select down
694 atoms, 701 bonds, 91 residues, 1 model selected
> color sel yellow
> select clear
> move z -2
[Repeated 2 time(s)]
> show #!1 models
> hide #!2 models
> show #!2 models
> move z 2
> hide #!1 models
> move z 2
> show #!1 models
> hide #!1 models
> move z 2
[Repeated 4 time(s)]
> move z -2
[Repeated 1 time(s)]
> move z 2
[Repeated 38 time(s)]
> show #!1 models
> move z -6
> hide #!1 models
> show #!1 models
> hide #!1 models
> select /D4:47
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
119 atoms, 119 bonds, 14 residues, 1 model selected
> select up
1073 atoms, 1087 bonds, 134 residues, 1 model selected
> select up
201660 atoms, 214201 bonds, 18543 residues, 1 model selected
> select down
1073 atoms, 1087 bonds, 134 residues, 1 model selected
> color sel cyan
> select /S9:157
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
27 atoms, 27 bonds, 3 residues, 1 model selected
> select up
1494 atoms, 1519 bonds, 185 residues, 1 model selected
> select up
201660 atoms, 214201 bonds, 18543 residues, 1 model selected
> select down
1494 atoms, 1519 bonds, 185 residues, 1 model selected
> color sel white
> select clear
> move z -6
[Repeated 2 time(s)]
> show #!1 models
> hide #!1 models
> move z -6
> volume #3 level 3
> show #!1 models
> hide #!1 models
> move z 2
[Repeated 4 time(s)]
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> open /Users/kaizhou/Downloads/121224-ribo.pyc
Failed opening file /Users/kaizhou/Downloads/121224-ribo.pyc:
Python code was compiled for a different version of Python
> move z 2
> move z -2
> move z 2
[Repeated 20 time(s)]
> move z -150
> move z -70
> move z -50
> hide #!3 models
> show #!4 models
> color #4 #b285ff85 models
> color #4 #b285ff22 models
> color #4 #b285ff2e models
> color #4 #b2ffff2e models
> color #4 #b2ffdc2e models
> color #4 #b2ff6b2e models
> color #4 #b2ff7e2e models
> color #4 #58ff7e2e models
> color #4 #58ff7e00 models
> color #4 #58ff7e7d models
> color #4 #58ff7e4a models
> color #4 #58ff364a models
> color #4 #58ff362c models
> color #4 #58ff3639 models
> move z 2
[Repeated 4 time(s)]
> volume #4 step 1
> move z 2
[Repeated 5 time(s)]
> show #!1 models
> hide #!1 models
> move z 2
[Repeated 5 time(s)]
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> move z 2
[Repeated 39 time(s)]
> show #!1 models
> hide #!1 models
> show #!1 models
> move z -2
> hide #!5.2 models
> hide #!4 models
> show #!3 models
> hide #!1 models
> show #!4 models
> hide #!3 models
> move z -2
[Repeated 1 time(s)]
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> move z -2
[Repeated 5 time(s)]
> show #!3 models
> hide #!4 models
> show #!4 models
> show #!1 models
> hide #!3 models
> hide #!4 models
> hide #!1 models
> show #!4 models
> move z -2
[Repeated 2 time(s)]
> show #!1 models
> hide #!1 models
> move z -2
[Repeated 1 time(s)]
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> move z -2
> show #!1 models
> hide #!1 models
> move z -2
[Repeated 1 time(s)]
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> move z -2
[Repeated 1 time(s)]
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> move z -2
[Repeated 3 time(s)]
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> move z -2
[Repeated 3 time(s)]
> move z 20
> move z 2
[Repeated 10 time(s)]
> show #!1 models
> hide #!1 models
> move z 2
[Repeated 3 time(s)]
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> move z 2
[Repeated 14 time(s)]
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> move z 2
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> select clear
> select /N3:3
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
104 atoms, 104 bonds, 15 residues, 1 model selected
> select up
1003 atoms, 1018 bonds, 136 residues, 1 model selected
> select up
201660 atoms, 214201 bonds, 18543 residues, 1 model selected
> select down
1003 atoms, 1018 bonds, 136 residues, 1 model selected
> color sel lime
> select clear
> move z 2
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> move z 2
[Repeated 1 time(s)]
> show #!1 models
> hide #!1 models
> select /S6:23
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
57 atoms, 57 bonds, 6 residues, 1 model selected
> select up
1820 atoms, 1844 bonds, 226 residues, 1 model selected
> select up
201660 atoms, 214201 bonds, 18543 residues, 1 model selected
> select down
1820 atoms, 1844 bonds, 226 residues, 1 model selected
> color sel orange red
> select clear
> move z 2
[Repeated 4 time(s)]
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!4 models
> move z 2
[Repeated 4 time(s)]
> move z -2
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> move z -2
[Repeated 1 time(s)]
> move z 2
[Repeated 5 time(s)]
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> move z 2
[Repeated 1 time(s)]
> move z -52
> close #5-7#5.2#6.2#7.2
> save
> /Users/kaizhou/Desktop/Manuscript_project/Ribosome_protein_folding_plasticity/Dec18_35C_ribosome.cxs
> includeMaps true
——— End of log from Wed Dec 18 16:48:41 2024 ———
opened ChimeraX session
> select /Q1
233 atoms, 234 bonds, 25 residues, 1 model selected
> ui tool show "Side View"
> color sel blue
> select clear
> hide #!4 models
> select /Q1:13
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
225 atoms, 226 bonds, 24 residues, 1 model selected
> move z 2
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> select /P
146 atoms, 147 bonds, 15 residues, 1 model selected
> color sel cyan
> select clear
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> color #4 #58ff36ff models
> show #!3 models
> hide #!4 models
> color #3 lime models
> hide #!3 models
> show #!1 models
> color #1 #b2b2b2ff models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
225 atoms, 226 bonds, 24 residues, 1 model selected
> select /P:7
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /Q1:16
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
225 atoms, 226 bonds, 24 residues, 1 model selected
> select up
233 atoms, 234 bonds, 25 residues, 1 model selected
> open /Users/kaizhou/Downloads/4v52.cif
Summary of feedback from opening /Users/kaizhou/Downloads/4v52.cif
---
note | Fetching CCD NMY from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/NMY/NMY.cif
4v52.cif title:
Crystal structure of the bacterial ribosome from Escherichia coli in complex
with neomycin. [more info...]
Chain information for 4v52.cif #5
---
Chain | Description | UniProt
AA CA | 16S rRNA |
AB CB | 30S ribosomal protein S2 | RS2_ECOLI 1-240
AC CC | 30S ribosomal protein S3 | RS3_ECOLI 1-232
AD CD | 30S ribosomal protein S4 | RS4_ECOLI 1-205
AE CE | 30S ribosomal protein S5 | RS5_ECOLI 1-166
AF CF | 30S ribosomal protein S6 | RS6_ECOLI 1-135
AG CG | 30S ribosomal protein S7 | RS7_ECOLI 1-178
AH CH | 30S ribosomal protein S8 | RS8_ECOLI 1-129
AI CI | 30S ribosomal protein S9 | RS9_ECOLI 1-129
AJ CJ | 30S ribosomal protein S10 | RS10_ECOLI 1-103
AK CK | 30S ribosomal protein S11 | RS11_ECOLI 1-128
AL CL | 30S ribosomal protein S12 | RS12_ECOLI 1-123
AM CM | 30S ribosomal protein S13 | RS13_ECOLI 1-117
AN CN | 30S ribosomal protein S14 | RS14_ECOLI 1-100
AO CO | 30S ribosomal protein S15 | RS15_ECOLI 1-89
AP CP | 30S ribosomal protein S16 | RS16_ECOLI 1-82
AQ CQ | 30S ribosomal protein S17 | RS17_ECOLI 1-83
AR CR | 30S ribosomal protein S18 | RS18_ECOLI 1-74
AS CS | 30S ribosomal protein S19 | RS19_ECOLI 1-91
AT CT | 30S ribosomal protein S20 | RS20_ECOLI 1-86
AU CU | 30S ribosomal protein S21 | RS21_ECOLI 1-70
B0 D0 | 50S ribosomal protein L32 | RL32_ECOLI 1-56
B1 D1 | 50S ribosomal protein L33 | RL33_ECOLI 1-54
B2 D2 | 50S ribosomal protein L34 | RL34_ECOLI 1-46
B3 D3 | 50S ribosomal protein L35 | RL35_ECOLI 1-64
B4 D4 | 50S ribosomal protein L36 | RL36_ECOLI 1-38
BA DA | 5S rRNA |
BB DB | 23S rRNA |
BC DC | 50S ribosomal protein L2 | RL2_ECOLI 1-272
BD DD | 50S ribosomal protein L3 | RL3_ECOLI 1-209
BE DE | 50S ribosomal protein L4 | RL4_ECOLI 1-201
BF DF | 50S ribosomal protein L5 | RL5_ECOLI 1-178
BG DG | 50S ribosomal protein L6 | RL6_ECOLI 1-176
BH DH | 50S ribosomal protein L9 | RL9_ECOLI 1-149
BI DI | 50S ribosomal protein L11 | RL11_ECOLI 1-141
BJ DJ | 50S ribosomal protein L13 | RL13_ECOLI 1-142
BK DK | 50S ribosomal protein L14 | RL14_ECOLI 1-123
BL DL | 50S ribosomal protein L15 | RL15_ECOLI 1-144
BM DM | 50S ribosomal protein L16 | RL16_ECOLI 1-136
BN DN | 50S ribosomal protein L17 | RL17_ECOLI 1-127
BO DO | 50S ribosomal protein L18 | RL18_ECOLI 1-117
BP DP | 50S ribosomal protein L19 | RL19_ECOLI 1-114
BQ DQ | 50S ribosomal protein L20 | RL20_ECOLI 1-117
BR DR | 50S ribosomal protein L21 | RL21_ECOLI 1-103
BS DS | 50S ribosomal protein L22 | RL22_ECOLI 1-110
BT DT | 50S ribosomal protein L23 | RL23_ECOLI 1-100
BU DU | 50S ribosomal protein L24 | RL24_ECOLI 1-103
BV DV | 50S ribosomal protein L25 | RL25_ECOLI 1-94
BW DW | 50S ribosomal protein L27 | RL27_ECOLI 1-84
BX DX | 50S ribosomal protein L29 | RL29_ECOLI 1-63
BY DY | 50S ribosomal protein L30 | RL30_ECOLI 1-58
BZ DZ | 50S ribosomal protein L28 | RL28_ECOLI 1-78
Non-standard residues in 4v52.cif #5
---
MG — magnesium ion
NMY — neomycin (mycifradin; neomas; pimavecort; vonamycin)
ZN — zinc ion
4v52.cif mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> ui tool show "Render/Select by Attribute"
> ui tool show Matchmaker
> matchmaker #!5 to #2
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 class1-80S-fitting-using-8bn3.pdb, chain 1 (#2) with 4v52.cif,
chain BB (#5), sequence alignment score = 11119.3
RMSD between 699 pruned atom pairs is 1.048 angstroms; (across all 2733 pairs:
45.119)
> close #5
> open /Users/kaizhou/Downloads/4v52_ssu_nmy.pdb
Chain information for 4v52_ssu_nmy.pdb #5
---
Chain | Description
C | No description available
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #5 to #2
Using Nucleic matrix instead of BLOSUM-62 for matching
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | Nucleic
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 class1-80S-fitting-using-8bn3.pdb, chain 2 (#2) with
4v52_ssu_nmy.pdb, chain C (#5), sequence alignment score = 2489.4
RMSD between 354 pruned atom pairs is 1.083 angstroms; (across all 1472 pairs:
32.564)
> color sel white
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #5/C:1410
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
32831 atoms, 36762 bonds, 1530 residues, 1 model selected
> color sel light sea green
> select clear
> show #!2 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 42 atom styles
> style sel stick
Changed 42 atom styles
> style sel ball
Changed 42 atom styles
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
42 atoms, 45 bonds, 1 residue, 1 model selected
> style sel ball
Changed 42 atom styles
> show sel surfaces
> hide sel surfaces
> select clear
> move z 2
[Repeated 3 time(s)]
> show #!2 models
> hide #!2 models
> show #!2 models
> move z 2
[Repeated 3 time(s)]
> move z -2
[Repeated 4 time(s)]
> close #3-4
> close #1
> move z 2
[Repeated 1 time(s)]
> save
> /Users/kaizhou/Desktop/Manuscript_project/Ribosome_protein_folding_plasticity/L41_neomycin_sensitivity.cxs
——— End of log from Tue Dec 31 12:29:54 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Ultra
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac Pro
Model Identifier: Mac14,8
Enclosure: Tower
Model Number: Z1JZ000PZLL/A
Chip: Apple M2 Ultra
Total Number of Cores: 24 (16 performance and 8 efficiency)
Memory: 192 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 25 days, 6 hours, 7 minutes
Graphics/Displays:
Apple M2 Ultra:
Chipset Model: Apple M2 Ultra
Type: GPU
Bus: Built-In
Total Number of Cores: 60
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PG38UQ:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 144.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Television: Yes
PG38UQ:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 144.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: No
Television: Yes
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 , 4 weeks 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 , 4 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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