![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18239 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 (last modified by )
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 0x0000000209bf9f00 (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, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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, psutil._psutil_osx, psutil._psutil_posix, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.segment._segment (total: 63)
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"procRole" : "Background",
"version" : 2,
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"modelCode" : "MacBookPro18,3",
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"codeSigningMonitor" : 1,
"incident" : "72C825D6-E6E0-42E6-93F0-E8DA98CF316F",
"pid" : 45906,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
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"procLaunch" : "2025-07-17 08:54:25.7260 +0200",
"procStartAbsTime" : 29011033693088,
"procExitAbsTime" : 36528142095765,
"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"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4C8E28A8-55FD-C00A-23DC-2343A29F27E7",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["assetIsNotReady","siriAssetIsNotReady","notOptedIn"]},
"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" : "264C7EB5-08B7-4911-B949-B6DA6036DFE0",
"wakeTime" : 283073,
"sleepWakeUUID" : "FC13EE64-4579-4306-9DC7-998490E4CC80",
"sip" : "enabled",
"vmRegionInfo" : "0x169 is not in any region. Bytes before following region: 4365287063\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104310000-104314000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000169","rawCodes":[1,361],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000169"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":45906},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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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 /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/tRNA_coding.cxs
Opened cryosparc_P346_J194_003_volume_map.mrc as #1.1.1.1, grid size
384,384,384, pixel 1.19, shown at level 0.293, step 1, values float32
Log from Wed Jul 16 16:56:30 2025 Startup Messages
---
warning | Registration file '/Users/roan.groh/Library/Application Support/ChimeraX/registration' has expired
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 6sgc
Summary of feedback from opening 6sgc fetched from pdb
---
notes | Fetching compressed mmCIF 6sgc from http://files.rcsb.org/download/6sgc.cif
Fetching CCD 12A from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/12A/12A.cif
Fetching CCD 2MU from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/2MU/2MU.cif
Fetching CCD 70U from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/70U/70U.cif
Fetching CCD H2U from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/H2U/H2U.cif
6sgc title:
Rabbit 80S ribosome stalled on a poly(A) tail [more info...]
Chain information for 6sgc #1
---
Chain | Description | UniProt
23 33 | tRNA (Lys3) |
54 | 28S ribosomal RNA |
74 | 5S ribosomal RNA |
84 | 5.8S ribosomal RNA |
A1 | 18S ribosomal RNA |
A2 | Ribosomal protein L8 | G1TT27_RABIT 1-257
B | Ribosomal protein | G1SKZ8_RABIT 1-217
B1 | uS2 |
B2 | uL3 | G1TL06_RABIT 2-403
C1 | 40S ribosomal protein S3a | G1SS70_RABIT 1-264
C2 | uL4 |
D1 | uS5 |
D2 | 60S ribosomal protein L5 | G1SYJ6_RABIT 2-297
E1 | uS5 | G1TNM3_RABIT 1-243
E2 | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291
F1 | 40S ribosomal protein S4 | G1TK17_RABIT 1-263
F2 | uL30 | G1TUB1_RABIT 1-247
G1 | Ribosomal protein S5 | G1TFM5_RABIT 1-204
G2 | eL8 |
H1 | 40S ribosomal protein S6 | G1TM55_RABIT 1-249
H2 | uL6 | G1TX33_RABIT 1-192
I1 | 40S ribosomal protein S7 | G1SVB0_RABIT 1-194
I2 | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214
J1 | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208
J2 | Ribosomal protein L11 | G1TUB8_RABIT 1-178
K1 | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194
L1 | S10_plectin domain-ontaining protein | G1TPV3_RABIT 1-165
L2 | eL13 |
M1 | Ribosomal protein S11 | G1TRM4_RABIT 1-158
M2 | Ribosomal protein L14 | G1SZ12_RABIT 1-218
N1 | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132
N2 | Ribosomal protein L15 | G1T0C1_RABIT 1-204
O1 | Ribosomal_S13_N domain-containing protein | G1SP51_RABIT 1-151
O2 | uL13 |
P1 | uS11 |
P2 | uL22 | G1TVT6_RABIT 1-184
Q1 | uS19 | G1U0Q2_RABIT 1-145
Q2 | eL18 |
R1 | Ribosomal protein S16 | G1SGX4_RABIT 1-146
R2 | eL19 |
S1 | eS17 | G1TU13_RABIT 1-135
S2 | eL20 |
T1 | eS13 | G1TPG3_RABIT 1-152
T2 | eL21 | G1SHQ2_RABIT 1-160
U1 | eS19 | G1TN62_RABIT 1-145
U2 | eL22 |
V1 | Ribosomal_S10 domain-containing protein | G1SIZ2_RABIT 1-119
V2 | Ribosomal protein L23 | G1T6D1_RABIT 1-140
W1 | eS21 |
W2 | TRASH domain-containing protein | G1SE28_RABIT 1-157
X1 | Ribosomal protein S15a | G1TG89_RABIT 1-130
X2 | Ribosomal_L23eN domain-containing protein | G1SE76_RABIT 1-156
XX | poly-lysine nascent chain |
Y1 | uS12 |
Y2 | Ribosomal protein L26 | G1SQH0_RABIT 1-145
Z1 | eS24 |
Z2 | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136
a1 | eS25 | G1TDB3_RABIT 1-125
a2 | Ribosomal_L18e/L15P domain-containing protein | G1SNY0_RABIT 2-148
b1 | eS26 |
b2 | eL29 |
c1 | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84
c2 | Ribosomal_L7Ae domain-containing protein | G1TDL2_RABIT 1-115
d1 | Ribosomal protein S28 | G1TIB4_RABIT 1-69
d2 | eL31 | G1SHG0_RABIT 1-125
e1 | uS14 | G1U7M4_RABIT 1-56
e2 | eL32 | G1U437_RABIT 1-135
f1 | 40S ribosomal protein S30 | G1T8A2_RABIT 0-132
f2 | eL33 | G1SF08_RABIT 1-110
g1 | Ribosomal protein S27a | G1SK22_RABIT 1-156
g2 | eL34 | G1U945_RABIT 1-116
h1 | WD_REPEATS_REGION domain-containing protein | G1SJB4_RABIT 1-317
h2 | uL29 | G1SIT5_RABIT 1-123
i1 | polyA mRNA |
i2 | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105
j2 | Ribosomal protein L37 | U3KPD5_RABIT 1-97
k2 | eL38 | G1U001_RABIT 1-70
l2 | eL39 | G1TTN1_RABIT 1-51
m2 | eL40 |
n2 | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25
o2 | eL42 | G1U344_RABIT 1-106
p2 | eL43 | G1SY53_RABIT 1-92
r2 | Ribosomal_L28e domain-containing protein | G1U7L1_RABIT 1-137
s2 | uL10 |
t2 | Ribosomal protein L12 | G1SMR7_RABIT 1-165
Non-standard residues in 6sgc #1
---
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
> hide atoms
> show cartoons
> hide atoms
[Repeated 1 time(s)]
> hide cartoons
[deleted to fit within ticket limits]
> open /Users/roan.groh/Downloads/cryosparc_P346_J317_map_sharp.mrc
Opened cryosparc_P346_J317_map_sharp.mrc as #34, grid size 384,384,384, pixel
1.19, shown at level 0.00236, step 2, values float32
> volume #34 step 1
> volume #34 level 0.01397
> hide #!33 models
> volume #34 level 0.02848
> hide #!34 models
> open /Volumes/groups/dagdas/lab/Roan/01_Pollen-
> Project/Processing_Masks/60S_P618.mrc
Opened 60S_P618.mrc as #35, grid size 384,384,384, pixel 1.19, shown at level
0.152, step 2, values float32
> volume #35 step 1
> volume #35 level 0.0687
> volume #35 level 0.04648
> open /Users/roan.groh/Downloads/cryosparc_P346_J319_mask.mrc
Opened cryosparc_P346_J319_mask.mrc as #36, grid size 384,384,384, pixel 1.19,
shown at level 1, step 2, values float32
> volume #36 level 0.003747
> color #36 #ffb2b27f models
> color #36 #ffb2b280 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J259_004_volume_map.mrc
Opened cryosparc_P346_J259_004_volume_map.mrc as #37, grid size 384,384,384,
pixel 1.19, shown at level 0.164, step 2, values float32
> hide #!35 models
> volume #37 step 1
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P346_2023_Dehydrated/Dehyd_Processing/J183-188/cryosparc_P346_J188_class_03_00065_volume.mrc
Opened cryosparc_P346_J188_class_03_00065_volume.mrc as #38, grid size
96,96,96, pixel 4.76, shown at level 1.23, step 1, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P346_2023_Dehydrated/Dehyd_Processing/J183-188/cryosparc_P346_J188_class_08_00065_volume.mrc
Opened cryosparc_P346_J188_class_08_00065_volume.mrc as #39, grid size
96,96,96, pixel 4.76, shown at level 1.15, step 1, values float32
> hide #!37 models
> volume #38 level 0.3593
> volume #39 level 0.2868
> hide #!38 models
> hide #!36 models
> volume #39 level 0.2868
> ui tool show "Segment Map"
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 3 region surfaces
818 watershed regions, grouped to 3 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 3 regions, 3 surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 1 region surfaces
818 watershed regions, grouped to 1 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 1 regions, 1 surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 1 region surfaces
818 watershed regions, grouped to 1 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 1 regions, 1 surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Only showing 150 of 195 regions.
Showing 150 of 195 region surfaces
818 watershed regions, grouped to 195 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 195 regions, 150
surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 33 region surfaces
818 watershed regions, grouped to 33 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 33 regions, 33
surfaces
> select #40.1
1 model selected
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 56 region surfaces
818 watershed regions, grouped to 56 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 56 regions, 56
surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 59 region surfaces
818 watershed regions, grouped to 59 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 59 regions, 59
surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Only showing 150 of 273 regions.
Showing 150 of 273 region surfaces
818 watershed regions, grouped to 273 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 273 regions, 150
surfaces
Segmenting cryosparc_P346_J188_class_08_00065_volume.mrc, density threshold
0.286803
Showing 122 region surfaces
818 watershed regions, grouped to 122 regions
Showing cryosparc_P346_J188_class_08_00065_volume.seg - 122 regions, 122
surfaces
> select #40.111
1 model selected
> select #40.113
1 model selected
> select #40.116
1 model selected
> select add #40.111
2 models selected
> select add #40.113
3 models selected
> ui mousemode right select
Drag select of 1466, 3901 of 4548 triangles, 1461, 1486, 1476, 1467, 1487,
1474, 1464, 1473, 1462, 1485, 1484, 1463, 3367 of 3376 triangles, 1478, 3757
of 3852 triangles, 1489, 1480, 1468, 1465, 1477, 1481, 1490, 3555 of 3584
triangles, 1470, 1483, 1471, 1494, 1479, 2609 of 3336 triangles, 1482, 3086 of
3704 triangles, 1469, 1497, 1488, 1492, 1498, 1472, 1501, 1496, 1475, 2931 of
2948 triangles, 1493, 1509, 1503, 2163 of 3204 triangles, 1508, 1507, 1500,
1506, 1502, 1505, 1499, 1504, 1869 of 2480 triangles, 1495, 1491, 1512, 1510,
1514, 1583 of 1676 triangles, 1513, 1511, 1460, 1455, 726 of 812 triangles,
1055, 1289, 1458, 1358, 1337, 1346, 670, 420 of 544 triangles, 1335, 1088,
1089, 393, 777, 347, 104, 1128, 181, 210, 1361, 657, 76, 23, 710, 67, 44, 237,
717, 810, 428, 812, 100, 708, 405, 1163, 816, 83, 532, 397, 353, 815, 117,
814, 338, 39, 809, 391, 759, 640, 199, 370, 818, 98 of 100 triangles, 21, 143,
436, 413, 765, 396, 709, 672, 6 of 44 triangles, 817, 746, 745, 8, 713, 794,
39 cryosparc_P346_J188_class_08_00065_volume.mrc
> select #40.122
1 model selected
Drag select of 1466, 1461, 1486, 1476, 1467, 1487, 1474, 1464, 1473, 1462,
1485, 1484, 1463, 1478, 1489, 1480, 1468, 1465, 1477, 1481, 1490, 1470, 1483,
1471, 1494, 1479, 1482, 1469, 1497, 1488, 1492, 1498, 1472, 1501, 1496, 1475,
1493, 1509, 1503, 1508, 1507, 1500, 1506, 1502, 1505, 1499, 1504, 1495, 1491,
1512, 1510, 1514, 1513, 1511, 1460, 1455, 1055, 1289, 1458, 1358, 1337, 1346,
670, 1335, 1088, 1089, 393, 777, 347, 104, 1128, 181, 210, 1361, 657, 76, 23,
710, 67, 44, 237, 717, 810, 428, 812, 100, 708, 405, 1163, 816, 83, 532, 397,
353, 815, 117, 814, 338, 39, 809, 391, 759, 640, 199, 370, 818, 21, 143, 436,
413, 599, 765, 575, 32 of 44 triangles, 396, 709, 672, 817, 746, 745, 8, 713,
794, 39 cryosparc_P346_J188_class_08_00065_volume.mrc
> select #40.113
1 model selected
> select #40.111
1 model selected
Drag select of 1466, 1461, 1486, 1476, 1467, 1487, 1474, 1464, 1473, 1462,
1485, 1484, 1463, 1478, 1489, 1480, 1468, 1465, 1477, 1481, 1490, 1470, 1483,
1471, 1494, 1479, 1482, 1469, 1497, 1488, 1492, 1498, 1472, 1501, 1496, 1475,
1493, 1509, 1503, 1508, 1507, 1500, 1506, 1502, 1505, 1499, 1504, 1495, 1491,
1512, 1510, 1514, 1513, 1511, 1460, 1455, 1055, 1289, 1458, 1358, 1337, 1346,
670, 1335, 1088, 1089, 393, 777, 347, 104, 1128, 181, 210, 1361, 657, 76, 23,
710, 67, 44, 237, 717, 810, 428, 812, 100, 708, 405, 1163, 816, 83, 532, 397,
353, 815, 117, 814, 338, 39, 809, 391, 759, 640, 199, 370, 818, 21, 143, 436,
413, 599, 765, 575, 396, 709, 672, 817, 746, 745, 8, 713, 794, 39
cryosparc_P346_J188_class_08_00065_volume.mrc
> select #40.113
1 model selected
> ui mousemode right select
> select clear
> select #40.113
1 model selected
> select #40.111
1 model selected
> select add #40.113
2 models selected
> select add #40.116
3 models selected
> select add #40.121
4 models selected
> select add #40.119
5 models selected
> select add #40.112
6 models selected
> select add #40.118
7 models selected
> select add #40.122
8 models selected
> select add #40.120
9 models selected
> select add #40.109
10 models selected
> select add #40.110
11 models selected
> select add #40.115
12 models selected
> select add #40.114
13 models selected
> select add #40.117
14 models selected
> hide #!39 models
Drag select of 1466, 1461, 1486, 1476, 1467, 1487, 1474, 1464, 1473, 1462,
1485, 1484, 1463, 1478, 1489, 1480, 1468, 1465, 1477, 1481, 1490, 1470, 1483,
1471, 1494, 1479, 1482, 1469, 1497, 1488, 1492, 1498, 1472, 1501, 1496, 1475,
1493, 1509, 1503, 1508, 1507, 1500, 1506, 1502, 1505, 1499, 1504, 1495, 1491,
1512, 1510, 1514, 1513, 1511, 1460, 1455, 1055, 1289, 1458, 1358, 1337, 1346,
670, 1335, 1088, 1089, 393, 777, 347, 104, 1128, 181, 210, 1361, 657, 76, 23,
710, 67, 44, 237, 717, 810, 428, 812, 100, 708, 405, 1163, 816, 83, 532, 397,
353, 815, 117, 814, 338, 39, 809, 391, 759, 640, 199, 370, 818, 21, 143
Saving 108 regions to mrc file...
Opened P246_60S.mrc as #41, grid size 49,59,62, pixel 4.76, shown at step 1,
values float32
Wrote P246_60S.mrc
> colume resample #41 onGrid #20
Unknown command: colume resample #41 onGrid #20
> volume resample #41 onGrid #20
Opened P246_60S.mrc resampled as #42, grid size 384,384,384, pixel 1.19, shown
at step 1, values float32
> select add #40
123 models selected
> select subtract #40
Nothing selected
> hide #!40 models
> volume #42 level 0.09094
No map chosen to save
> save /Users/roan.groh/P346_60S.mrc models #42
> save /Users/roan.groh/Desktop/P346_60S_Mask.mrc models #42
> volume #42 level 0.0132
> open "/Users/roan.groh/Downloads/Unconfirmed 38399.crdownload.mrc"
Opened Unconfirmed 38399.crdownload.mrc as #43, grid size 384,384,384, pixel
1.19, shown at level 1, step 2, values float32
> volume #43 level 0.007055
> hide #!42 models
> color #43 #ffffb27b models
> color #43 #ffffb27a models
> show #!38 models
> show #!39 models
> show #!40 models
> close #19-43
> close #12-13
> rename #14 id #12
> rename #15 id #13
> rename #16 id #14
> rename #17 id #15
> rename #18 id #16
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P346_2023_Dehydrated/Dehyd_Processing/J183-188/cryosparc_P346_J188_class_03_00065_volume.mrc
Opened cryosparc_P346_J188_class_03_00065_volume.mrc as #17, grid size
96,96,96, pixel 4.76, shown at level 1.23, step 1, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/01_Experiments/01_Projects/04_Pollen/EM/Arabidopsis_Pollen/P346_2023_Dehydrated/Dehyd_Processing/J183-188/cryosparc_P346_J188_class_08_00065_volume.mrc
Opened cryosparc_P346_J188_class_08_00065_volume.mrc as #18, grid size
96,96,96, pixel 4.76, shown at level 1.15, step 1, values float32
> volume #17 level 0.3205
> volume #18 level 0.2658
> hide #!18 models
> show #!18 models
> hide #!17 models
> show #!17 models
> hide #!18 models
> show #!18 models
> hide #!17 models
> close #17-18
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J143_class_00_00040_volume.mrc
Opened cryosparc_P618_J143_class_00_00040_volume.mrc as #17, grid size
96,96,96, pixel 4.76, shown at level 1.52, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J143_class_01_00040_volume.mrc
Opened cryosparc_P618_J143_class_01_00040_volume.mrc as #18, grid size
96,96,96, pixel 4.76, shown at level 1.5, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J143_class_02_00040_volume.mrc
Opened cryosparc_P618_J143_class_02_00040_volume.mrc as #19, grid size
96,96,96, pixel 4.76, shown at level 1.48, step 1, values float32
> volume #17 level 0.3237
> volume #18 level 0.393
> volume #19 level 0.2151
Drag select of 17 cryosparc_P618_J143_class_00_00040_volume.mrc , 18
cryosparc_P618_J143_class_01_00040_volume.mrc , 19
cryosparc_P618_J143_class_02_00040_volume.mrc
> ui mousemode right zoom
> select subtract #17
4 models selected
> select subtract #19
2 models selected
> select subtract #18
Nothing selected
> hide #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> show #!18 models
> hide #!17 models
> hide #!19 models
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J144_class_00_00017_volume.mrc
Opened cryosparc_P618_J144_class_00_00017_volume.mrc as #20, grid size
160,160,160, pixel 2.85, shown at level 0.84, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J144_class_07_00017_volume.mrc
Opened cryosparc_P618_J144_class_07_00017_volume.mrc as #21, grid size
160,160,160, pixel 2.85, shown at level 0.816, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J144_class_08_00017_volume.mrc
Opened cryosparc_P618_J144_class_08_00017_volume.mrc as #22, grid size
160,160,160, pixel 2.85, shown at level 0.822, step 1, values float32
> hide #!18 models
> hide #!21 models
> hide #!22 models
> volume #20 level 0.3191
> volume #21 level 0.6088
> volume #22 level 0.4996
> volume #22 level 0.3522
> hide #!22 models
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J145_class_00_00019_volume.mrc
Opened cryosparc_P618_J145_class_00_00019_volume.mrc as #23, grid size
160,160,160, pixel 2.85, shown at level 0.716, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J145_class_02_00019_volume.mrc
Opened cryosparc_P618_J145_class_02_00019_volume.mrc as #24, grid size
160,160,160, pixel 2.85, shown at level 0.808, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J145_class_06_00019_volume.mrc
Opened cryosparc_P618_J145_class_06_00019_volume.mrc as #25, grid size
160,160,160, pixel 2.85, shown at level 0.829, step 1, values float32
> open
> /Users/roan.groh/Downloads/cryosparc_P618_J145_class_08_00019_volume.mrc
Opened cryosparc_P618_J145_class_08_00019_volume.mrc as #26, grid size
160,160,160, pixel 2.85, shown at level 0.821, step 1, values float32
> hide #!24 models
> hide #!25 models
> hide #!26 models
> volume #23 level 0.3597
> hide #!23 models
> show #!24 models
> volume #24 level 0.388
> hide #!24 models
> show #!25 models
> volume #25 level 0.4463
> volume #26 level 0.3024
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!24 models
> hide #!24 models
> show #!25 models
> hide #!25 models
> show #!25 models
> show #!24 models
> hide #!24 models
> hide #!26 models
> show #!20 models
> hide #!25 models
> show #!21 models
> hide #!20 models
> volume #21 level 0.3818
> hide #!21 models
> show #!22 models
> show #!23 models
> hide #!23 models
> show #!20 models
> hide #!20 models
> hide #!22 models
> show #!17 models
> show #!18 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> volume #17 level 0.1724
> show #!18 models
> hide #!17 models
> volume #18 level 0.7042
> volume #19 level 0.8178
> hide #!19 models
> save /Users/roan.groh/Desktop/Checking-Structure_TranslationalStates.cxs
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Structure_Comparison_F2A_V2.cxs
Opened cryosparc_P346_J219_map_sharp.mrc as #1, grid size 384,384,384, pixel
1.19, shown at level 0.112, step 2, values float32
Opened cryosparc_P346_J219_map_sharp.mrc gaussian as #2, grid size
384,384,384, pixel 1.19, shown at level 0.0803, step 1, values float32
Opened cryosparc_P618_J94_map_sharp.mrc as #3, grid size 384,384,384, pixel
1.19, shown at level 0.0968, step 2, values float32
Opened cryosparc_P618_J94_map_sharp.mrc gaussian as #4, grid size 384,384,384,
pixel 1.19, shown at level 0.0803, step 1, values float32
opened ChimeraX session
> close #1-4
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Structure_Comparison_F2A_V2.cxs
Opened cryosparc_P346_J219_map_sharp.mrc as #1, grid size 384,384,384, pixel
1.19, shown at level 0.112, step 2, values float32
Opened cryosparc_P346_J219_map_sharp.mrc gaussian as #2, grid size
384,384,384, pixel 1.19, shown at level 0.0803, step 1, values float32
Opened cryosparc_P618_J94_map_sharp.mrc as #3, grid size 384,384,384, pixel
1.19, shown at level 0.0968, step 2, values float32
Opened cryosparc_P618_J94_map_sharp.mrc gaussian as #4, grid size 384,384,384,
pixel 1.19, shown at level 0.0803, step 1, values float32
opened ChimeraX session
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Dehydrated/Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc
Opened Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc as #5, grid size
384,384,384, pixel 1.19, shown at level 0.226, step 2, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Dehydrated/Consensus-J311_cryosparc_P346_J311_map_sharp.mrc
Opened Consensus-J311_cryosparc_P346_J311_map_sharp.mrc as #6, grid size
384,384,384, pixel 1.19, shown at level 0.113, step 2, values float32
> close #1-4
> rename #5 id #1
> rename #6 id #2
> volume #1 step 1
> volume #2 step 1
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Germinated/Consensus-J132_cryosparc_P618_J132_004_volume_map.mrc
Opened Consensus-J132_cryosparc_P618_J132_004_volume_map.mrc as #3, grid size
384,384,384, pixel 1.19, shown at level 0.25, step 2, values float32
> open /Users/roan.groh/Library/CloudStorage/OneDrive-
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Germinated/Consensus-J133_cryosparc_P618_J133_map_sharp.mrc
Opened Consensus-J133_cryosparc_P618_J133_map_sharp.mrc as #4, grid size
384,384,384, pixel 1.19, shown at level 0.0979, step 2, values float32
> volume #3 step 1
> volume #4 step 1
> fitmap #2 inMap #1
Fit map Consensus-J311_cryosparc_P346_J311_map_sharp.mrc in map
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc using 565618 points
correlation = 0.9447, correlation about mean = 0.8277, overlap = 1.1e+05
steps = 48, shift = 0.0154, angle = 0.0177 degrees
Position of Consensus-J311_cryosparc_P346_J311_map_sharp.mrc (#2) relative to
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99999995 -0.00014916 -0.00027033 0.10006789
0.00014916 0.99999999 0.00000905 -0.02394076
0.00027033 -0.00000910 0.99999996 -0.06058140
Axis -0.02938043 -0.87518384 0.48289755
Axis point 204.06950091 0.00000000 368.90964158
Rotation angle (degrees) 0.01769778
Shift along axis -0.01124208
> fitmap #3 inMap #1
Fit map Consensus-J132_cryosparc_P618_J132_004_volume_map.mrc in map
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc using 564482 points
correlation = 0.9612, correlation about mean = 0.809, overlap = 1.225e+05
steps = 84, shift = 0.927, angle = 0.717 degrees
Position of Consensus-J132_cryosparc_P618_J132_004_volume_map.mrc (#3)
relative to Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.99999672 0.00163710 0.00196767 -0.32098861
-0.00166106 0.99992372 0.01223909 -2.38932597
-0.00194749 -0.01224232 0.99992316 3.98691864
Axis -0.97882912 0.15653804 -0.13186888
Axis point 0.00000000 318.16854857 189.71425335
Rotation angle (degrees) 0.71652878
Shift along axis -0.58557789
> fitmap #4 inMap #1
Fit map Consensus-J133_cryosparc_P618_J133_map_sharp.mrc in map
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc using 566625 points
correlation = 0.8877, correlation about mean = 0.6039, overlap = 8.032e+04
steps = 64, shift = 0.865, angle = 0.719 degrees
Position of Consensus-J133_cryosparc_P618_J133_map_sharp.mrc (#4) relative to
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99999701 0.00135613 0.00203377 -0.35347122
-0.00138107 0.99992326 0.01231113 -2.54732653
-0.00201692 -0.01231390 0.99992215 3.92029182
Axis -0.98085704 0.16134593 -0.10902733
Axis point 0.00000000 312.72975762 202.41759885
Rotation angle (degrees) 0.71924197
Shift along axis -0.49171499
> open 8b2l
Summary of feedback from opening 8b2l fetched from pdb
---
warning | Atom H1 is not in the residue template for UNK /l3:1
8b2l title:
Cryo-EM structure of the plant 80S ribosome [more info...]
Chain information for 8b2l #5
---
Chain | Description | UniProt
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264
A3 | 25S rRNA |
B1 | mRNA |
B3 | 5.8S rRNA |
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144
C3 | 5S rRNA |
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151
W2 i2 | tRNA |
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221
h1 | 18S rRNA |
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208
l3 | nascent chain |
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194
Non-standard residues in 8b2l #5
---
B8N —
(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic
acid
K — potassium ion
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!5 models
> hide atoms
> show cartoons
> select add #5
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.5994,0.19237,0.77699,-100.78,-0.66599,0.65835,0.35076,126.87,-0.44406,-0.72771,0.52273,307.1
> hide #!1 models
> view matrix models
> #5,-0.29109,-0.74227,0.60357,274.21,-0.74163,-0.22347,-0.63249,481.9,0.60436,-0.63174,-0.48544,270.15
> view matrix models
> #5,-0.43224,-0.80916,0.39802,355.15,-0.79985,0.1402,-0.58359,424.2,0.41642,-0.57061,-0.70781,342.96
> view matrix models
> #5,-0.67391,-0.73025,0.11219,448.7,-0.72053,0.61604,-0.31833,276.69,0.16335,-0.29537,-0.94132,396.09
> ui mousemode right "move picked models"
> show #!1 models
> view matrix models
> #5,-0.67391,-0.73025,0.11219,467.39,-0.72053,0.61604,-0.31833,307.24,0.16335,-0.29537,-0.94132,429.73
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.5894,-0.78166,0.20401,440.22,-0.77031,0.46771,-0.43344,364.83,0.24339,-0.41262,-0.87778,419.96
> fitmap #5 inMap #1
Fit molecule 8b2l (#5) to map
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1) using 361205 atoms
average map value = 0.1884, steps = 448
shifted from previous position = 31.2
rotated from previous position = 31.5 degrees
atoms outside contour = 237159, contour level = 0.22628
Position of 8b2l (#5) relative to
Consensus-J301_cryosparc_P346_J303_004_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
-0.21845575 -0.96565873 -0.14064239 494.28572978
-0.83164267 0.25963155 -0.49087870 424.51433350
0.51053651 0.00972894 -0.85980103 301.94011380
Axis 0.60152754 -0.78245318 0.16103301
Axis point 368.57912383 0.00000000 262.33622588
Rotation angle (degrees) 155.41053209
Shift along axis 13.78621289
> vop copy #5
> copy #5
Unknown command: copy #5
> vop copy #5
> hide #!1 models
> select subtract #5
Nothing selected
> show #!1 models
> copy model #5
Unknown command: copy model #5
> log metadata #5
Metadata for 8b2l #5
---
Title | Cryo-EM structure of the plant 80S ribosome
Citation | Smirnova, J., Loerke, J., Kleinau, G., Schmidt, A., Burger, J., Meyer, E.H., Mielke, T., Scheerer, P., Bock, R., Spahn, C.M.T., Zoschke, R. (2023). Structure of the actively translating plant 80S ribosome at 2.2 angstrom resolution. Nat.Plants, 9, 987-1000. PMID: 37156858. DOI: 10.1038/s41477-023-01407-y
Non-standard residues | B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid
K — potassium ion
MG — magnesium ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
UY1 — 2'-O-methylpseudouridine-5'-monophosphate
ZN — zinc ion
Sources (natural) | Nicotiana tabacum (common tobacco)
Nicotiana tabacum
CryoEM Map | EMDB 15806 — open map
Experimental method | Electron microscopy
Resolution | 2.20Å
> log chains #5
Chain information for 8b2l #5
---
Chain | Description | UniProt
A1 | 40S ribosomal protein S4 | A0A1S4DQ51_TOBAC 1-264
A3 | 25S rRNA |
B1 | mRNA |
B3 | 5.8S rRNA |
C1 | 40S ribosomal protein S12 | A0A1S4B129_TOBAC 1-144
C3 | 5S rRNA |
D1 | 40S ribosomal protein S17-like | A0A1S3Z9G2_TOBAC 1-149
D3 | 60S ribosomal protein L13 | A0A1S4CSN1_TOBAC 1-206
E1 | 40S ribosomal protein S19-3 | A0A1S3Y949_TOBAC 1-143
E3 | 60S ribosomal protein L14-1 | A0A1S4A807_TOBAC 1-134
F1 | 40S ribosomal protein S3a | RS3A_TOBAC 1-261
F3 | Ribosomal protein L15 | A0A1S4D5P7_TOBAC 1-204
G1 | 40S ribosomal protein S21 | A0A1S4A3T4_TOBAC 1-83
G3 | 60S ribosomal protein L18-2-like | A0A1S4DF55_TOBAC 1-187
H1 | 40S ribosomal protein S24 | A0A1S3ZXI6_TOBAC 1-133
H3 | Ribosomal protein L19 | A0A1S3X0I4_TOBAC 1-214
I1 | 40S ribosomal protein S25 | A0A076L2E2_TOBAC 1-107
I3 | 60S ribosomal protein L18a | A0A1S4CP52_TOBAC 1-178
J1 | 40S ribosomal protein S26 | A0A1S4CWI7_TOBAC 1-127
J3 | 60S ribosomal protein L21-1-like | A0A1S3XCW6_TOBAC 1-164
K1 | 40S ribosomal protein S27 | A0A1S3XJK0_TOBAC 1-86
K3 | 60S ribosomal protein L22-2-like | A0A1S4BSU3_TOBAC 1-127
L1 | 40S ribosomal protein S28 | A0A1S4AS05_TOBAC 1-65
L3 | 60S ribosomal protein L24-like | A0A1S4BHF2_TOBAC 1-164
M1 | 40S ribosomal protein S30 | A0A1S3XGJ0_TOBAC 1-62
M3 | eL27 (60S ribosomal protein L27) | A0A1S4AEL0_TOBAC 1-135
N1 | ubiquitin-40S ribosomal protein S27a-like | A0A1S4C0C1_TOBAC 1-156
N3 | eL28 (60S ribosomal protein L28) | A0A1S4D1U6_TOBAC 1-143
O1 | 40S ribosomal protein S7 | A0A1S3Z906_TOBAC 1-191
O3 | 60S ribosomal protein L29 | A0A1S3YR12_TOBAC 1-61
P1 | 40S ribosomal protein S8 | A0A1S4CZK3_TOBAC 1-224
P3 | 60S ribosomal protein L30-like | A0A1S3WZ09_TOBAC 1-113
Q1 | guanine nucleotide-binding protein subunit beta-like protein | A0A1S4ABX7_TOBAC 1-329
Q3 | eL31 (60S ribosomal protein L31) | A0A1S3Y3V5_TOBAC 1-120
R1 | 40S ribosomal protein S20-2 | A0A1S3XHL0_TOBAC 1-122
R3 | 60S ribosomal protein L32-1 | A0A1S3Z2X4_TOBAC 1-133
S1 | 40S ribosomal protein S14-2 | A0A1S3XAN1_TOBAC 1-150
S3 | eL33 (60S ribosomal protein L35a) | A0A1S3XU79_TOBAC 1-112
T1 | 40S ribosomal protein S23 | A0A1S4C879_TOBAC 1-142
T3 | 60S ribosomal protein L34 | RL34_TOBAC 1-120
U1 | 40S ribosomal protein S18 | A0A1S3YM01_TOBAC 1-152
U3 | eL36 (60S ribosomal protein L36) | A0A1S4D2I2_TOBAC 1-110
V1 | 40S ribosomal protein S29 | A0A1S4DPT4_TOBAC 1-56
V3 | Ribosomal protein L37 | A0A1S4DN51_TOBAC 1-95
W1 | 30S ribosomal protein S15, chloroplastic | A0A1S3ZRI7_TOBAC 1-151
W2 i2 | tRNA |
W3 | 60S ribosomal protein L38 | A0A1S4C4G8_TOBAC 1-69
X1 | 40S ribosomal protein S11-like | A0A1S4BW10_TOBAC 1-159
X3 | 60S ribosomal protein L39-3 | A0A1S3YR32_TOBAC 1-51
Y1 | 40S ribosomal protein S15-like | A0A1S4DFI4_TOBAC 1-152
Y3 | ubiquitin-60S ribosomal protein L40 | A0A1S3X011_TOBAC 1-128
Z1 | 40S ribosomal protein SA | A0A1S3Y4M0_TOBAC 1-336
Z3 | 60S ribosomal protein L44 | A0A1S4AVP7_TOBAC 1-105
a1 | 40S ribosomal protein S3-2-like | A0A1S4BXU2_TOBAC 1-248
a3 | 60S ribosomal protein L37a | A0A1S3X5Y9_TOBAC 1-92
b1 | 40S ribosomal protein S9-2-like | A0A1S4B907_TOBAC 1-197
b3 | eL6 (60S ribosomal protein L6) | A0A1S4B0G2_TOBAC 1-230
c1 | 40S ribosomal protein S2-3-like | A0A1S3XAX8_TOBAC 1-280
c3 | 60S ribosomal protein L7a | A0A1S4D668_TOBAC 1-258
d1 | 40S ribosomal protein S5-like | A0A1S4BXT5_TOBAC 1-210
d3 | uL13 (60S ribosomal protein L13a) | A0A1S4DN49_TOBAC 1-206
e1 | 40S ribosomal protein S15a-1 | A0A1S4DBQ8_TOBAC 1-130
e3 | 60S ribosomal protein L23 | A0A1S3XSQ1_TOBAC 1-140
f1 | 40S ribosomal protein S16 | A0A1S4AU23_TOBAC 4-150
f3 | uL15 (60S ribosomal protein L27a) | A0A1S4BFD5_TOBAC 1-148
g3 | uL16 (60S ribosomal protein L10) | A0A1S3Z2D7_TOBAC 1-221
h1 | 18S rRNA |
h3 | 60S ribosomal protein L5-like | A0A1S3XE16_TOBAC 1-301
j3 | 50S ribosomal protein L22, chloroplastic | A0A1S4CCH0_TOBAC 1-175
k1 | 40S ribosomal protein S6 | A0A1S3Z3Y7_TOBAC 1-249
k3 | 60S ribosomal protein L23a | RL23A_TOBAC 1-154
l1 | 40S ribosomal protein S10-1-like | A0A1S4DHU6_TOBAC 1-208
l3 | nascent chain |
m3 | uL24 (60S ribosomal protein L26) | A0A1S4DPM5_TOBAC 1-146
n3 | 60S ribosomal protein L35-like | A0A1S3WY31_TOBAC 1-123
o3 | uL2 (60S ribosomal protein L8) | A0A1S3XXQ5_TOBAC 1-260
p3 | 60S ribosomal protein L41 | RL41_TOBAC 1-25
q3 | 60S ribosomal protein L7-4-like | A0A1S4A5Z2_TOBAC 1-242
r3 | uL3 (60S ribosomal protein L3) | A0A1S3ZLI9_TOBAC 1-389
s3 | uL4 (60S ribosomal protein L4) | A0A1S3X0M5_TOBAC 1-405
t3 | uL5 (60S ribosomal protein L11) | A0A1S3XAW1_TOBAC 1-181
u3 | uL6 (60S ribosomal protein L9) | A0A1S4C068_TOBAC 1-194
> color #5 #275c70
> select #9/54,74,84,A1
Nothing selected
> select #5/54,74,84,A1
4261 atoms, 4294 bonds, 266 residues, 1 model selected
> hide #!1 models
> select #5/54,74,84,A1
4261 atoms, 4294 bonds, 266 residues, 1 model selected
> select #5/A1,A3,B3,C3
120359 atoms, 125472 bonds, 4063 pseudobonds, 7520 residues, 4 models selected
> select add #5
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> select subtract #5
Nothing selected
> select #5/A1,A3,B3,C3,h1
174913 atoms, 181978 bonds, 6097 pseudobonds, 11304 residues, 4 models
selected
> color sel #B7C9CF
> select add #5
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> select subtract #5
Nothing selected
> show #!4 models
> show #!3 models
> color zone #3,4 near #5 distance 6
> color #3,4 #275c70
> color zone #3,4 near #5 distance 6
> hide #!5 models
> hide #!4 models
> volume #3 level 0.1958
> color #1,2,5 #e1b74d
> hide #!4 models
> show #!5 models
> select #5/A1,A3,B3,C3,h1
174913 atoms, 181978 bonds, 6097 pseudobonds, 11304 residues, 4 models
selected
> color sel #F5E7C4
> color zone #1,2 near #5 distance 6
> show #!1 models
> show #!2 models
> select add #5
361205 atoms, 369089 bonds, 6486 pseudobonds, 23567 residues, 4 models
selected
> hide #!5 models
> select subtract #5
Nothing selected
> show #!3 models
> show #!4 models
> hide #!1 models
> hide #!3 models
> volume #4 level 0.113
> ui mousemode right translate
> save "/Users/roan.groh/Documents/OneDrive -
> VBC/02_Presentations/06_Paper/02_Pollen_Paper/Figure_2/F2C_V2/Structure_Comparison_F2A_V2.cxs"
> hide #!4 models
> open /Users/roan.groh/Desktop/Checking-Structure_TranslationalStates.cxs
Opened cryosparc_P618_J51_003_volume_map.mrc as #1, grid size 384,384,384,
pixel 1.19, shown at level 0.254, step 1, values float32
Opened cryosparc_P618_J52_004_volume_map.mrc as #2, grid size 384,384,384,
pixel 1.19, shown at level 0.273, step 1, values float32
Opened cryosparc_P618_J53_003_volume_map.mrc as #3, grid size 384,384,384,
pixel 1.19, shown at level 0.275, step 1, values float32
Opened cryosparc_P618_J51_003_volume_map.mrc gaussian as #4, grid size
384,384,384, pixel 1.19, shown at level 0.121, step 1, values float32
Opened cryosparc_P618_J52_004_volume_map.mrc gaussian as #5, grid size
384,384,384, pixel 1.19, shown at level 0.131, step 1, values float32
Opened cryosparc_P618_J53_003_volume_map.mrc gaussian as #6, grid size
384,384,384, pixel 1.19, shown at level 0.129, step 1, values float32
Opened Classic_emdb 15872 as #7, grid size 348,348,348, pixel 1.72, shown at
level 0.0016, step 1, values float32
Opened Rot-1_emdb 15874 as #8, grid size 348,348,348, pixel 1.72, shown at
level 0.0032, step 1, values float32
Opened Rot-2_emdb 15876 as #9, grid size 348,348,348, pixel 1.72, shown at
level 0.0016, step 1, values float32
Opened Translocation_emdb 15877 as #10, grid size 348,348,348, pixel 1.72,
shown at level 0.0035, step 1, values float32
Opened Post_emdb 15878 as #11, grid size 348,348,348, pixel 1.72, shown at
level 0.0028, step 2, values float32
Opened Classic_emdb 15872 gaussian as #12, grid size 348,348,348, pixel 1.72,
shown at level 0.00124, step 1, values float32
Opened Rot-1_emdb 15874 gaussian as #13, grid size 348,348,348, pixel 1.72,
shown at level 0.00305, step 1, values float32
Opened Rot-2_emdb 15876 gaussian as #14, grid size 348,348,348, pixel 1.72,
shown at level 0.00125, step 1, values float32
Opened Translocation_emdb 15877 gaussian as #15, grid size 348,348,348, pixel
1.72, shown at level 0.00388, step 1, values float32
Opened Post_emdb 15878 gaussian as #16, grid size 348,348,348, pixel 1.72,
shown at level 0.00347, step 1, values float32
Opened cryosparc_P618_J143_class_00_00040_volume.mrc as #17, grid size
96,96,96, pixel 4.76, shown at level 0.172, step 1, values float32
Opened cryosparc_P618_J143_class_01_00040_volume.mrc as #18, grid size
96,96,96, pixel 4.76, shown at level 0.704, step 1, values float32
Opened cryosparc_P618_J143_class_02_00040_volume.mrc as #19, grid size
96,96,96, pixel 4.76, shown at level 0.818, step 1, values float32
Opened cryosparc_P618_J144_class_00_00017_volume.mrc as #20, grid size
160,160,160, pixel 2.85, shown at level 0.319, step 1, values float32
Opened cryosparc_P618_J144_class_07_00017_volume.mrc as #21, grid size
160,160,160, pixel 2.85, shown at level 0.382, step 1, values float32
Opened cryosparc_P618_J144_class_08_00017_volume.mrc as #22, grid size
160,160,160, pixel 2.85, shown at level 0.352, step 1, values float32
Opened cryosparc_P618_J145_class_00_00019_volume.mrc as #23, grid size
160,160,160, pixel 2.85, shown at level 0.36, step 1, values float32
Opened cryosparc_P618_J145_class_02_00019_volume.mrc as #24, grid size
160,160,160, pixel 2.85, shown at level 0.388, step 1, values float32
Opened cryosparc_P618_J145_class_06_00019_volume.mrc as #25, grid size
160,160,160, pixel 2.85, shown at level 0.446, step 1, values float32
Opened cryosparc_P618_J145_class_08_00019_volume.mrc as #26, grid size
160,160,160, pixel 2.85, shown at level 0.302, step 1, values float32
opened ChimeraX session
> open /Users/roan.groh/Downloads/cryosparc_P618_J148_004_volume_map.mrc
Opened cryosparc_P618_J148_004_volume_map.mrc as #27, grid size 384,384,384,
pixel 1.19, shown at level 0.272, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J147_003_volume_map.mrc
Opened cryosparc_P618_J147_003_volume_map.mrc as #28, grid size 384,384,384,
pixel 1.19, shown at level 0.244, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J146_004_volume_map.mrc
Opened cryosparc_P618_J146_004_volume_map.mrc as #29, grid size 384,384,384,
pixel 1.19, shown at level 0.273, step 2, values float32
> volume #27 step 1
> volume #28 step 1
> volume #29 step 1
> ui mousemode right zoom
> close #27-29
> hide #!26 models
> open /Users/roan.groh/Downloads/cryosparc_P618_J151_004_volume_map.mrc
Opened cryosparc_P618_J151_004_volume_map.mrc as #27, grid size 384,384,384,
pixel 1.19, shown at level 0.279, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J150_003_volume_map.mrc
Opened cryosparc_P618_J150_003_volume_map.mrc as #28, grid size 384,384,384,
pixel 1.19, shown at level 0.28, step 2, values float32
> open /Users/roan.groh/Downloads/cryosparc_P618_J149_003_volume_map.mrc
Opened cryosparc_P618_J149_003_volume_map.mrc as #29, grid size 384,384,384,
pixel 1.19, shown at level 0.257, step 2, values float32
> volume #27 step 1
> volume #28 step 1
> volume #29 step 1
> hide #!28 models
> hide #!29 models
> show #!28 models
> hide #!27 models
> show #!29 models
> hide #!28 models
> open /Users/roan.groh/Downloads/cryosparc_P346_J321_004_volume_map.mrc
Opened cryosparc_P346_J321_004_volume_map.mrc as #30, grid size 384,384,384,
pixel 1.19, shown at level 0.179, step 2, values float32
> hide #!29 models
> volume #30 step 1
> open /Users/roan.groh/Downloads/cryosparc_P346_J320_004_volume_map.mrc
Opened cryosparc_P346_J320_004_volume_map.mrc as #31, grid size 384,384,384,
pixel 1.19, shown at level 0.181, step 2, values float32
> hide #!30 models
> volume #31 step 1
===== Log before crash end =====
Log:
Startup Messages
---
warning | Registration file '/Users/roan.groh/Library/Application Support/ChimeraX/registration' has expired
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
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
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: MacBook Pro
Model Identifier: MacBookPro18,3
Model Number: MKGT3D/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 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, 1 hour, 24 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 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
HP ENVY 27s:
Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
UI Looks like: 2560 x 1440 @ 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
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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
more-itertools: 10.3.0
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
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
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
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
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: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 3 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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