![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 7 months ago
Closed 7 months ago
#17199 closed defect (can't reproduce)
Crash in graphics driver during Qt drawing
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00000001e9284f40 (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, chimerax.pdb_lib._load_libs, 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, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 58)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,4",
"coalitionID" : 46696,
"osVersion" : {
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"build" : "23H124",
"releaseType" : "User"
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"captureTime" : "2025-03-26 17:15:21.3052 +0800",
"codeSigningMonitor" : 1,
"incident" : "D5A380BC-9F93-44A4-9944-16DF4A6D83D8",
"pid" : 11053,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-26 17:13:04.8887 +0800",
"procStartAbsTime" : 6520694870321,
"procExitAbsTime" : 6523922485160,
"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":"7422D222-3F6E-58D3-BEB3-4BCAD5990DB0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "3C91DD76-F011-CF79-E711-B18951BB4CF1",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 928,
"sleepWakeUUID" : "C8411CA6-743B-4386-9AB2-16787BCA367F",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":11053},
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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/phonghoa/Desktop/L24 human vs yeast.cxs"
Log from Wed Mar 26 17:09:16 2025 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 4ug0 fromDatabase pdb format mmcif
Summary of feedback from opening 4ug0 fetched from pdb
---
note | Fetching compressed mmCIF 4ug0 from http://files.rcsb.org/download/4ug0.cif
4ug0 title:
Structure of the human 80S ribosome [more info...]
Chain information for 4ug0 #1
---
Chain | Description | UniProt
L5 | 28S ribosomal RNA |
L7 | 5S ribosomal RNA |
L8 | 5.8S ribosomal RNA |
LA | 60S RIBOSOMAL PROTEIN L8 | RL8_HUMAN 1-257
LB | 60S RIBOSOMAL PROTEIN L3 | RL3_HUMAN 1-403
LC | 60S RIBOSOMAL PROTEIN L4 | RL4_HUMAN 1-427
LD | 60S RIBOSOMAL PROTEIN L5 | RL5_HUMAN 1-297
LE | 60S RIBOSOMAL PROTEIN L6 | RL6_HUMAN 1-288
LF | 60S RIBOSOMAL PROTEIN L7 | RL7_HUMAN 1-248
LG | 60S RIBOSOMAL PROTEIN L7A | RL7A_HUMAN 1-266
LH | 60S RIBOSOMAL PROTEIN L9 | RL9_HUMAN 1-192
LI | 60S RIBOSOMAL PROTEIN L10-LIKE | RL10L_HUMAN 1-214
LJ | 60S RIBOSOMAL PROTEIN L11 | RL11_HUMAN 1-178
LL | 60S RIBOSOMAL PROTEIN L13 | RL13_HUMAN 1-211
LM | 60S RIBOSOMAL PROTEIN L14 | RL14_HUMAN 1-215
LN | 60S RIBOSOMAL PROTEIN L15 | RL15_HUMAN 1-204
LO | 60S RIBOSOMAL PROTEIN L13A | RL13A_HUMAN 1-203
LP | 60S RIBOSOMAL PROTEIN L17 | RL17_HUMAN 1-184
LQ | 60S RIBOSOMAL PROTEIN L18 | RL18_HUMAN 1-188
LR | 60S RIBOSOMAL PROTEIN L19 | RL19_HUMAN 1-196
LS | 60S RIBOSOMAL PROTEIN L18A | RL18A_HUMAN 1-176
LT | 60S RIBOSOMAL PROTEIN L21 | RL21_HUMAN 1-160
LU | 60S RIBOSOMAL PROTEIN L22 | RL22_HUMAN 1-128
LV | 60S RIBOSOMAL PROTEIN L23 | RL23_HUMAN 1-140
LW | 60S RIBOSOMAL PROTEIN L24 | RL24_HUMAN 1-157
LX | 60S RIBOSOMAL PROTEIN L23A | RL23A_HUMAN 1-156
LY | 60S RIBOSOMAL PROTEIN L26 | RL26_HUMAN 1-145
LZ | 60S RIBOSOMAL PROTEIN L27 | RL27_HUMAN 1-136
La | 60S RIBOSOMAL PROTEIN L27A | RL27A_HUMAN 1-148
Lb | 60S RIBOSOMAL PROTEIN L29 | RL29_HUMAN 1-159
Lc | 60S RIBOSOMAL PROTEIN L30 | RL30_HUMAN 1-115
Ld | 60S RIBOSOMAL PROTEIN L31 | RL31_HUMAN 1-125
Le | 60S RIBOSOMAL PROTEIN L32 | RL32_HUMAN 1-135
Lf | 60S RIBOSOMAL PROTEIN L35A | RL35A_HUMAN 1-110
Lg | 60S RIBOSOMAL PROTEIN L34 | RL34_HUMAN 1-117
Lh | 60S RIBOSOMAL PROTEIN L35 | RL35_HUMAN 1-123
Li | 60S RIBOSOMAL PROTEIN L36 | RL36_HUMAN 1-105
Lj | 60S RIBOSOMAL PROTEIN L37 | RL37_HUMAN 1-97
Lk | 60S RIBOSOMAL PROTEIN L38 | RL38_HUMAN 1-70
Ll | 60S RIBOSOMAL PROTEIN L39 | RL39_HUMAN 1-51
Lm | UBIQUITIN-60S RIBOSOMAL PROTEIN L40 | RL40_HUMAN 1-128
Ln | 60S RIBOSOMAL PROTEIN L41 | RL41_HUMAN 1-25
Lo | 60S RIBOSOMAL PROTEIN L36A | RL36A_HUMAN 1-106
Lp | 60S RIBOSOMAL PROTEIN L37A | RL37A_HUMAN 1-92
Lr | 60S RIBOSOMAL PROTEIN L28 | RL28_HUMAN 1-137
Lz | 60S RIBOSOMAL PROTEIN L10A | RL10A_HUMAN 1-217
S2 | 18S ribosomal RNA |
S6 | HUMAN INITIATOR MET-TRNA-I |
SA | 40S RIBOSOMAL PROTEIN SA | RSSA_HUMAN 1-295
SB | 40S RIBOSOMAL PROTEIN S3A | RS3A_HUMAN 1-264
SC | 40S RIBOSOMAL PROTEIN S2 | RS2_HUMAN 1-293
SD | 40S RIBOSOMAL PROTEIN S3 | RS3_HUMAN 1-243
SE | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | RS4X_HUMAN 1-263
SF | 40S RIBOSOMAL PROTEIN S5 | RS5_HUMAN 1-204
SG | 40S RIBOSOMAL PROTEIN S6 | RS6_HUMAN 1-249
SH | 40S RIBOSOMAL PROTEIN S7 | RS7_HUMAN 1-194
SI | 40S RIBOSOMAL PROTEIN S8 | RS8_HUMAN 1-208
SJ | 40S RIBOSOMAL PROTEIN S9 | RS9_HUMAN 1-194
SK | 40S RIBOSOMAL PROTEIN S10 | RS10_HUMAN 1-165
SL | 40S RIBOSOMAL PROTEIN S11 | RS11_HUMAN 1-158
SM | 40S RIBOSOMAL PROTEIN |
SN | 40S RIBOSOMAL PROTEIN S13 | RS13_HUMAN 1-151
SO | 40S RIBOSOMAL PROTEIN S14 | RS14_HUMAN 1-151
SP | 40S RIBOSOMAL PROTEIN S15 | RS15_HUMAN 1-145
SQ | 40S RIBOSOMAL PROTEIN S16 | RS16_HUMAN 1-146
SR | 40S RIBOSOMAL PROTEIN S17-LIKE | RS17L_HUMAN 1-135
SS | 40S RIBOSOMAL PROTEIN S18 | RS18_HUMAN 1-152
ST | 40S RIBOSOMAL PROTEIN S19 | RS19_HUMAN 1-145
SU | 40S RIBOSOMAL PROTEIN S20 | RS20_HUMAN 1-119
SV | 40S RIBOSOMAL PROTEIN S21 | RS21_HUMAN 1-83
SW | 40S RIBOSOMAL PROTEIN S15A | RS15A_HUMAN 1-130
SX | 40S RIBOSOMAL PROTEIN S23 | RS23_HUMAN 1-143
SY | 40S RIBOSOMAL PROTEIN S24 | RS24_HUMAN 1-133
SZ | 40S RIBOSOMAL PROTEIN S25 | RS25_HUMAN 1-125
Sa | 40S RIBOSOMAL PROTEIN S26 | RS26_HUMAN 1-115
Sb | 40S RIBOSOMAL PROTEIN S27 | RS27_HUMAN 1-84
Sc | 40S RIBOSOMAL PROTEIN S28 | RS28_HUMAN 1-69
Sd | 40S RIBOSOMAL PROTEIN S29 | RS29_HUMAN 1-56
Se | 40S RIBOSOMAL PROTEIN S30 | RS30_HUMAN 1-59
Sf | UBIQUITIN-40S RIBOSOMAL PROTEIN S27A | RS27A_HUMAN 1-156
Sg | GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 | GBLP_HUMAN 1-317
Non-standard residues in 4ug0 #1
---
MG — magnesium ion
ZN — zinc ion
> sequence chain #1/LW
Alignment identifier is 1/LW
> select /LW:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /LW
1015 atoms, 1030 bonds, 124 residues, 1 model selected
> color sel red
> sequence chain #1/SG
Alignment identifier is 1/SG
> select /SG:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /SG
1923 atoms, 1946 bonds, 237 residues, 1 model selected
> color sel blue
> select add #1
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> select subtract #1
Nothing selected
> select add #1
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> select subtract #1
Nothing selected
> open 3j77 fromDatabase pdb format mmcif
3j77 title:
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated
conformations (Class II - rotated ribosome with 1 tRNA) [more info...]
Chain information for 3j77 #2
---
Chain | Description | UniProt
10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105
11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156
12 | 40S ribosomal protein S12 | RS12_YEAST 1-143
13 | 40S ribosomal protein S13 | RS13_YEAST 1-151
14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137
15 | 40S ribosomal protein S15 | RS15_YEAST 1-142
16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143
17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136
18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146
19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144
1S | 18S ribosomal RNA |
20 | 40S ribosomal protein S20 | RS20_YEAST 1-121
21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87
22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130
23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145
24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135
25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108
26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119
27 | 40S ribosomal protein S27 | RS27_YEAST 1-82
28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67
29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56
2S | 25S ribosomal RNA |
30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63
31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152
5S | 5S ribosomal RNA |
60 | 60S ribosomal protein L10 | RL10_YEAST 1-221
61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174
62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165
63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199
64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138
65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204
66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199
67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184
68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186
69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189
70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172
71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160
72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121
73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137
74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155
75 | 60S ribosomal protein L25 | RL25_YEAST 1-142
76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127
77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136
78 | 60S ribosomal protein L28 | RL28_YEAST 1-149
79 | 60S ribosomal protein L29 | RL29_YEAST 1-59
80 | 60S ribosomal protein L30 | RL30_YEAST 1-105
81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113
82 | 60S ribosomal protein L32 | RL32_YEAST 1-130
83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107
84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121
85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120
86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100
87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88
88 | 60S ribosomal protein L38 | RL38_YEAST 1-78
89 | 60S ribosomal protein L39 | RL39_YEAST 1-51
8S | 5.8S ribosomal RNA |
90 | 60S ribosomal protein L40 | RL401_YEAST 1-128
91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25
92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106
93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92
L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217
L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254
L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387
L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362
L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297
L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176
L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244
L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256
L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191
MR | messenger RNA |
P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312
PT | P/E-site initiator transfer RNAfMet |
RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319
S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252
S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255
S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254
S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240
S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261
S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225
S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236
S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190
S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200
S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197
> select add #2
207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected
> hide sel atoms
> show sel cartoons
> select subtract #2
Nothing selected
> ui tool show Matchmaker
> matchmaker #!2 to #1
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 4ug0, chain L5 (#1) with 3j77, chain 2S (#2), sequence alignment
score = 15359
RMSD between 2164 pruned atom pairs is 1.046 angstroms; (across all 3168
pairs: 14.499)
> sequence chain #2/74
Alignment identifier is 2/74
> select clear
> select #2/74
1089 atoms, 1103 bonds, 135 residues, 1 model selected
> color sel magenta
> select add #2
207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected
> select subtract #2
Nothing selected
> sequence chain #2/S6
Alignment identifier is 2/S6
> select clear
> select #2/S6
1820 atoms, 1844 bonds, 226 residues, 1 model selected
> color sel cornflower blue
> select add #2
207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected
> select subtract #2
Nothing selected
> save "/Users/phonghoa/Desktop/human vs yeast 80s )L24=.cxs"
> sequence chain #2/L5
Alignment identifier is 2/L5
> select #2/L5:297
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/L5
2376 atoms, 2426 bonds, 296 residues, 1 model selected
> color sel orange
> select add #2
207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected
> select subtract #2
Nothing selected
> sequence chain #1/LD
Alignment identifier is 1/LD
> select clear
> select #1/LD
2382 atoms, 2428 bonds, 293 residues, 1 model selected
> color sel orange red
> select add #1
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> select subtract #1
Nothing selected
> save "/Users/phonghoa/Desktop/L24 human vs yeast.cxs"
——— End of log from Wed Mar 26 17:09:16 2025 ———
opened ChimeraX session
> save /Users/phonghoa/Desktop/image1.png supersample 3
> volume appearance airways
No volumes specified
Alignment identifier is 1/L5
Alignment identifier is 1/L7
Alignment identifier is 1/L8
Alignment identifier is 1/LA
Alignment identifier is 1/LB
Alignment identifier is 1/LC
Alignment identifier is 1/LD
Alignment identifier is 1/LE
Alignment identifier is 1/LF
Alignment identifier is 1/LG
Alignment identifier is 1/LH
Alignment identifier is 1/LI
Alignment identifier is 1/LJ
Alignment identifier is 1/LL
Alignment identifier is 1/LM
Alignment identifier is 1/LN
Alignment identifier is 1/LO
Alignment identifier is 1/LP
Alignment identifier is 1/LQ
Alignment identifier is 1/LR
Alignment identifier is 1/LS
Alignment identifier is 1/LT
Alignment identifier is 1/LU
Alignment identifier is 1/LV
Alignment identifier is 1/LW
Alignment identifier is 1/LX
Alignment identifier is 1/LY
Alignment identifier is 1/LZ
Alignment identifier is 1/La
Alignment identifier is 1/Lb
Alignment identifier is 1/Lc
Alignment identifier is 1/Ld
Alignment identifier is 1/Le
Alignment identifier is 1/Lf
Alignment identifier is 1/Lg
Alignment identifier is 1/Lh
Alignment identifier is 1/Li
Alignment identifier is 1/Lj
Alignment identifier is 1/Lk
Alignment identifier is 1/Ll
Alignment identifier is 1/Lm
Alignment identifier is 1/Ln
Alignment identifier is 1/Lo
Alignment identifier is 1/Lp
Alignment identifier is 1/Lr
Alignment identifier is 1/Lz
Alignment identifier is 1/S2
Alignment identifier is 1/S6
Alignment identifier is 1/SA
Alignment identifier is 1/SB
Alignment identifier is 1/SD
Alignment identifier is 1/SE
Alignment identifier is 1/SF
Alignment identifier is 1/SH
Alignment identifier is 1/SI
Alignment identifier is 1/SK
Alignment identifier is 1/SL
Alignment identifier is 1/SP
Alignment identifier is 1/SQ
Alignment identifier is 1/SR
Alignment identifier is 1/SS
Alignment identifier is 1/ST
Alignment identifier is 1/SU
Alignment identifier is 1/SV
Alignment identifier is 1/SX
Alignment identifier is 1/Sa
Alignment identifier is 1/Sc
Alignment identifier is 1/Sd
Alignment identifier is 1/Sf
Alignment identifier is 1/Sg
Alignment identifier is 1/SC
Alignment identifier is 1/SG
Alignment identifier is 1/SJ
Alignment identifier is 1/SM
Alignment identifier is 1/SN
Alignment identifier is 1/SO
Alignment identifier is 1/SW
Alignment identifier is 1/SY
Alignment identifier is 1/SZ
Alignment identifier is 1/Sb
Alignment identifier is 1/Se
Alignment identifier is 2/L1
Alignment identifier is 2/L2
Alignment identifier is 2/L3
Alignment identifier is 2/L4
Alignment identifier is 2/L5
Alignment identifier is 2/L6
Alignment identifier is 2/L7
Alignment identifier is 2/L8
Alignment identifier is 2/L9
Alignment identifier is 2/60
Alignment identifier is 2/61
Alignment identifier is 2/62
Alignment identifier is 2/63
Alignment identifier is 2/64
Alignment identifier is 2/65
Alignment identifier is 2/66
Alignment identifier is 2/67
Alignment identifier is 2/68
Alignment identifier is 2/69
Alignment identifier is 2/70
Alignment identifier is 2/71
Alignment identifier is 2/72
Alignment identifier is 2/73
Alignment identifier is 2/74
Alignment identifier is 2/75
Alignment identifier is 2/76
Alignment identifier is 2/77
Alignment identifier is 2/78
Alignment identifier is 2/79
Alignment identifier is 2/80
Alignment identifier is 2/81
Alignment identifier is 2/82
Alignment identifier is 2/83
Alignment identifier is 2/84
Alignment identifier is 2/85
Alignment identifier is 2/86
Alignment identifier is 2/87
Alignment identifier is 2/88
Alignment identifier is 2/89
Alignment identifier is 2/90
Alignment identifier is 2/91
Alignment identifier is 2/92
Alignment identifier is 2/93
Alignment identifier is 2/P0
Alignment identifier is 2/RC
Alignment identifier is 2/S0
Alignment identifier is 2/S1
Alignment identifier is 2/S2
Alignment identifier is 2/S3
Alignment identifier is 2/S4
Alignment identifier is 2/S5
Alignment identifier is 2/S6
Alignment identifier is 2/S7
Alignment identifier is 2/S8
Alignment identifier is 2/S9
Alignment identifier is 2/10
Alignment identifier is 2/11
Alignment identifier is 2/12
Alignment identifier is 2/13
Alignment identifier is 2/14
Alignment identifier is 2/15
Alignment identifier is 2/16
Alignment identifier is 2/17
Alignment identifier is 2/18
Alignment identifier is 2/19
Alignment identifier is 2/20
Alignment identifier is 2/21
Alignment identifier is 2/22
Alignment identifier is 2/23
Alignment identifier is 2/24
Alignment identifier is 2/25
Alignment identifier is 2/26
Alignment identifier is 2/27
Alignment identifier is 2/28
Alignment identifier is 2/29
Alignment identifier is 2/30
Alignment identifier is 2/31
Alignment identifier is 2/1S
Alignment identifier is 2/2S
Alignment identifier is 2/8S
Alignment identifier is 2/5S
Alignment identifier is 2/MR
Alignment identifier is 2/PT
===== 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 "/Users/phonghoa/Desktop/L24 human vs yeast.cxs"
Log from Wed Mar 26 17:09:16 2025 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 4ug0 fromDatabase pdb format mmcif
Summary of feedback from opening 4ug0 fetched from pdb
---
note | Fetching compressed mmCIF 4ug0 from http://files.rcsb.org/download/4ug0.cif
4ug0 title:
Structure of the human 80S ribosome [more info...]
Chain information for 4ug0 #1
---
Chain | Description | UniProt
L5 | 28S ribosomal RNA |
L7 | 5S ribosomal RNA |
L8 | 5.8S ribosomal RNA |
LA | 60S RIBOSOMAL PROTEIN L8 | RL8_HUMAN 1-257
LB | 60S RIBOSOMAL PROTEIN L3 | RL3_HUMAN 1-403
LC | 60S RIBOSOMAL PROTEIN L4 | RL4_HUMAN 1-427
LD | 60S RIBOSOMAL PROTEIN L5 | RL5_HUMAN 1-297
LE | 60S RIBOSOMAL PROTEIN L6 | RL6_HUMAN 1-288
LF | 60S RIBOSOMAL PROTEIN L7 | RL7_HUMAN 1-248
LG | 60S RIBOSOMAL PROTEIN L7A | RL7A_HUMAN 1-266
LH | 60S RIBOSOMAL PROTEIN L9 | RL9_HUMAN 1-192
LI | 60S RIBOSOMAL PROTEIN L10-LIKE | RL10L_HUMAN 1-214
LJ | 60S RIBOSOMAL PROTEIN L11 | RL11_HUMAN 1-178
LL | 60S RIBOSOMAL PROTEIN L13 | RL13_HUMAN 1-211
LM | 60S RIBOSOMAL PROTEIN L14 | RL14_HUMAN 1-215
LN | 60S RIBOSOMAL PROTEIN L15 | RL15_HUMAN 1-204
LO | 60S RIBOSOMAL PROTEIN L13A | RL13A_HUMAN 1-203
LP | 60S RIBOSOMAL PROTEIN L17 | RL17_HUMAN 1-184
LQ | 60S RIBOSOMAL PROTEIN L18 | RL18_HUMAN 1-188
LR | 60S RIBOSOMAL PROTEIN L19 | RL19_HUMAN 1-196
LS | 60S RIBOSOMAL PROTEIN L18A | RL18A_HUMAN 1-176
LT | 60S RIBOSOMAL PROTEIN L21 | RL21_HUMAN 1-160
LU | 60S RIBOSOMAL PROTEIN L22 | RL22_HUMAN 1-128
LV | 60S RIBOSOMAL PROTEIN L23 | RL23_HUMAN 1-140
LW | 60S RIBOSOMAL PROTEIN L24 | RL24_HUMAN 1-157
LX | 60S RIBOSOMAL PROTEIN L23A | RL23A_HUMAN 1-156
LY | 60S RIBOSOMAL PROTEIN L26 | RL26_HUMAN 1-145
LZ | 60S RIBOSOMAL PROTEIN L27 | RL27_HUMAN 1-136
La | 60S RIBOSOMAL PROTEIN L27A | RL27A_HUMAN 1-148
Lb | 60S RIBOSOMAL PROTEIN L29 | RL29_HUMAN 1-159
Lc | 60S RIBOSOMAL PROTEIN L30 | RL30_HUMAN 1-115
Ld | 60S RIBOSOMAL PROTEIN L31 | RL31_HUMAN 1-125
Le | 60S RIBOSOMAL PROTEIN L32 | RL32_HUMAN 1-135
Lf | 60S RIBOSOMAL PROTEIN L35A | RL35A_HUMAN 1-110
Lg | 60S RIBOSOMAL PROTEIN L34 | RL34_HUMAN 1-117
Lh | 60S RIBOSOMAL PROTEIN L35 | RL35_HUMAN 1-123
Li | 60S RIBOSOMAL PROTEIN L36 | RL36_HUMAN 1-105
Lj | 60S RIBOSOMAL PROTEIN L37 | RL37_HUMAN 1-97
Lk | 60S RIBOSOMAL PROTEIN L38 | RL38_HUMAN 1-70
Ll | 60S RIBOSOMAL PROTEIN L39 | RL39_HUMAN 1-51
Lm | UBIQUITIN-60S RIBOSOMAL PROTEIN L40 | RL40_HUMAN 1-128
Ln | 60S RIBOSOMAL PROTEIN L41 | RL41_HUMAN 1-25
Lo | 60S RIBOSOMAL PROTEIN L36A | RL36A_HUMAN 1-106
Lp | 60S RIBOSOMAL PROTEIN L37A | RL37A_HUMAN 1-92
Lr | 60S RIBOSOMAL PROTEIN L28 | RL28_HUMAN 1-137
Lz | 60S RIBOSOMAL PROTEIN L10A | RL10A_HUMAN 1-217
S2 | 18S ribosomal RNA |
S6 | HUMAN INITIATOR MET-TRNA-I |
SA | 40S RIBOSOMAL PROTEIN SA | RSSA_HUMAN 1-295
SB | 40S RIBOSOMAL PROTEIN S3A | RS3A_HUMAN 1-264
SC | 40S RIBOSOMAL PROTEIN S2 | RS2_HUMAN 1-293
SD | 40S RIBOSOMAL PROTEIN S3 | RS3_HUMAN 1-243
SE | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | RS4X_HUMAN 1-263
SF | 40S RIBOSOMAL PROTEIN S5 | RS5_HUMAN 1-204
SG | 40S RIBOSOMAL PROTEIN S6 | RS6_HUMAN 1-249
SH | 40S RIBOSOMAL PROTEIN S7 | RS7_HUMAN 1-194
SI | 40S RIBOSOMAL PROTEIN S8 | RS8_HUMAN 1-208
SJ | 40S RIBOSOMAL PROTEIN S9 | RS9_HUMAN 1-194
SK | 40S RIBOSOMAL PROTEIN S10 | RS10_HUMAN 1-165
SL | 40S RIBOSOMAL PROTEIN S11 | RS11_HUMAN 1-158
SM | 40S RIBOSOMAL PROTEIN |
SN | 40S RIBOSOMAL PROTEIN S13 | RS13_HUMAN 1-151
SO | 40S RIBOSOMAL PROTEIN S14 | RS14_HUMAN 1-151
SP | 40S RIBOSOMAL PROTEIN S15 | RS15_HUMAN 1-145
SQ | 40S RIBOSOMAL PROTEIN S16 | RS16_HUMAN 1-146
SR | 40S RIBOSOMAL PROTEIN S17-LIKE | RS17L_HUMAN 1-135
SS | 40S RIBOSOMAL PROTEIN S18 | RS18_HUMAN 1-152
ST | 40S RIBOSOMAL PROTEIN S19 | RS19_HUMAN 1-145
SU | 40S RIBOSOMAL PROTEIN S20 | RS20_HUMAN 1-119
SV | 40S RIBOSOMAL PROTEIN S21 | RS21_HUMAN 1-83
SW | 40S RIBOSOMAL PROTEIN S15A | RS15A_HUMAN 1-130
SX | 40S RIBOSOMAL PROTEIN S23 | RS23_HUMAN 1-143
SY | 40S RIBOSOMAL PROTEIN S24 | RS24_HUMAN 1-133
SZ | 40S RIBOSOMAL PROTEIN S25 | RS25_HUMAN 1-125
Sa | 40S RIBOSOMAL PROTEIN S26 | RS26_HUMAN 1-115
Sb | 40S RIBOSOMAL PROTEIN S27 | RS27_HUMAN 1-84
Sc | 40S RIBOSOMAL PROTEIN S28 | RS28_HUMAN 1-69
Sd | 40S RIBOSOMAL PROTEIN S29 | RS29_HUMAN 1-56
Se | 40S RIBOSOMAL PROTEIN S30 | RS30_HUMAN 1-59
Sf | UBIQUITIN-40S RIBOSOMAL PROTEIN S27A | RS27A_HUMAN 1-156
Sg | GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 | GBLP_HUMAN 1-317
Non-standard residues in 4ug0 #1
---
MG — magnesium ion
ZN — zinc ion
> sequence chain #1/LW
Alignment identifier is 1/LW
> select /LW:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /LW
1015 atoms, 1030 bonds, 124 residues, 1 model selected
> color sel red
> sequence chain #1/SG
Alignment identifier is 1/SG
> select /SG:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /SG
1923 atoms, 1946 bonds, 237 residues, 1 model selected
> color sel blue
> select add #1
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> select subtract #1
Nothing selected
> select add #1
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> select subtract #1
Nothing selected
> open 3j77 fromDatabase pdb format mmcif
3j77 title:
Structures of yeast 80S ribosome-tRNA complexes in the rotated and non-rotated
conformations (Class II - rotated ribosome with 1 tRNA) [more info...]
Chain information for 3j77 #2
---
Chain | Description | UniProt
10 | 40S ribosomal protein S10 | RS10A_YEAST 1-105
11 | 40S ribosomal protein S11 | RS11A_YEAST 1-156
12 | 40S ribosomal protein S12 | RS12_YEAST 1-143
13 | 40S ribosomal protein S13 | RS13_YEAST 1-151
14 | 40S ribosomal protein S14 | RS14A_YEAST 1-137
15 | 40S ribosomal protein S15 | RS15_YEAST 1-142
16 | 40S ribosomal protein S16 | RS16A_YEAST 1-143
17 | 40S ribosomal protein S17 | RS17A_YEAST 1-136
18 | 40S ribosomal protein S18 | RS18A_YEAST 1-146
19 | 40S ribosomal protein S19 | RS19A_YEAST 1-144
1S | 18S ribosomal RNA |
20 | 40S ribosomal protein S20 | RS20_YEAST 1-121
21 | 40S ribosomal protein S21 | RS21A_YEAST 1-87
22 | 40S ribosomal protein S22 | RS22A_YEAST 1-130
23 | 40S ribosomal protein S23 | RS23A_YEAST 1-145
24 | 40S ribosomal protein S24 | RS24A_YEAST 1-135
25 | 40S ribosomal protein S25 | RS25A_YEAST 1-108
26 | 40S ribosomal protein S26 | RS26A_YEAST 1-119
27 | 40S ribosomal protein S27 | RS27_YEAST 1-82
28 | 40S ribosomal protein S28 | RS28A_YEAST 1-67
29 | 40S ribosomal protein S29 | RS29A_YEAST 1-56
2S | 25S ribosomal RNA |
30 | 40S ribosomal protein S30 | RS30A_YEAST 1-63
31 | 40S ribosomal protein S31 | RS27A_YEAST 1-152
5S | 5S ribosomal RNA |
60 | 60S ribosomal protein L10 | RL10_YEAST 1-221
61 | 60S ribosomal protein L11 | RL11A_YEAST 1-174
62 | 60S ribosomal protein L12 | RL12A_YEAST 1-165
63 | 60S ribosomal protein L13 | RL13A_YEAST 1-199
64 | 60S ribosomal protein L14 | RL14A_YEAST 1-138
65 | 60S ribosomal protein L15 | RL15A_YEAST 1-204
66 | 60S ribosomal protein L16 | RL16A_YEAST 1-199
67 | 60S ribosomal protein L17 | RL17A_YEAST 1-184
68 | 60S ribosomal protein L18 | RL18A_YEAST 1-186
69 | 60S ribosomal protein L19 | RL19A_YEAST 1-189
70 | 60S ribosomal protein L20 | RL20A_YEAST 1-172
71 | 60S ribosomal protein L21 | RL21A_YEAST 1-160
72 | 60S ribosomal protein L22 | RL22A_YEAST 1-121
73 | 60S ribosomal protein L23 | RL23A_YEAST 1-137
74 | 60S ribosomal protein L24 | RL24A_YEAST 1-155
75 | 60S ribosomal protein L25 | RL25_YEAST 1-142
76 | 60S ribosomal protein L26 | RL26A_YEAST 1-127
77 | 60S ribosomal protein L27 | RL27A_YEAST 1-136
78 | 60S ribosomal protein L28 | RL28_YEAST 1-149
79 | 60S ribosomal protein L29 | RL29_YEAST 1-59
80 | 60S ribosomal protein L30 | RL30_YEAST 1-105
81 | 60S ribosomal protein L31 | RL31A_YEAST 1-113
82 | 60S ribosomal protein L32 | RL32_YEAST 1-130
83 | 60S ribosomal protein L33 | RL33A_YEAST 1-107
84 | 60S ribosomal protein L34 | RL34A_YEAST 1-121
85 | 60S ribosomal protein L35 | RL35A_YEAST 1-120
86 | 60S ribosomal protein L36 | RL36A_YEAST 1-100
87 | 60S ribosomal protein L37 | RL37A_YEAST 1-88
88 | 60S ribosomal protein L38 | RL38_YEAST 1-78
89 | 60S ribosomal protein L39 | RL39_YEAST 1-51
8S | 5.8S ribosomal RNA |
90 | 60S ribosomal protein L40 | RL401_YEAST 1-128
91 | 60S ribosomal protein L41 | RL41A_YEAST 1-25
92 | 60S ribosomal protein L42 | RL44A_YEAST 1-106
93 | 60S ribosomal protein L43 | RL43A_YEAST 1-92
L1 | 60S ribosomal protein L1 | RL1A_YEAST 1-217
L2 | 60S ribosomal protein L2 | RL2A_YEAST 1-254
L3 | 60S ribosomal protein L3 | RL3_YEAST 1-387
L4 | 60S ribosomal protein L4 | RL4A_YEAST 1-362
L5 | 60S ribosomal protein L5 | RL5_YEAST 1-297
L6 | 60S ribosomal protein L6 | RL6A_YEAST 1-176
L7 | 60S ribosomal protein L7 | RL7A_YEAST 1-244
L8 | 60S ribosomal protein L8 | RL8A_YEAST 1-256
L9 | 60S ribosomal protein L9 | RL9A_YEAST 1-191
MR | messenger RNA |
P0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312
PT | P/E-site initiator transfer RNAfMet |
RC | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319
S0 | 40S ribosomal protein S0 | RSSA1_YEAST 1-252
S1 | 40S ribosomal protein S1 | RS3A1_YEAST 1-255
S2 | 40S ribosomal protein S2 | RS2_YEAST 1-254
S3 | 40S ribosomal protein S3 | RS3_YEAST 1-240
S4 | 40S ribosomal protein S4 | RS4A_YEAST 1-261
S5 | 40S ribosomal protein S5 | RS5_YEAST 1-225
S6 | 40S ribosomal protein S6 | RS6A_YEAST 1-236
S7 | 40S ribosomal protein S7 | RS7A_YEAST 1-190
S8 | 40S ribosomal protein S8 | RS8A_YEAST 1-200
S9 | 40S ribosomal protein S9 | RS9A_YEAST 1-197
> select add #2
207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected
> hide sel atoms
> show sel cartoons
> select subtract #2
Nothing selected
> ui tool show Matchmaker
> matchmaker #!2 to #1
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 4ug0, chain L5 (#1) with 3j77, chain 2S (#2), sequence alignment
score = 15359
RMSD between 2164 pruned atom pairs is 1.046 angstroms; (across all 3168
pairs: 14.499)
> sequence chain #2/74
Alignment identifier is 2/74
> select clear
> select #2/74
1089 atoms, 1103 bonds, 135 residues, 1 model selected
> color sel magenta
> select add #2
207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected
> select subtract #2
Nothing selected
> sequence chain #2/S6
Alignment identifier is 2/S6
> select clear
> select #2/S6
1820 atoms, 1844 bonds, 226 residues, 1 model selected
> color sel cornflower blue
> select add #2
207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected
> select subtract #2
Nothing selected
> save "/Users/phonghoa/Desktop/human vs yeast 80s )L24=.cxs"
> sequence chain #2/L5
Alignment identifier is 2/L5
> select #2/L5:297
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #2/L5
2376 atoms, 2426 bonds, 296 residues, 1 model selected
> color sel orange
> select add #2
207751 atoms, 223107 bonds, 4428 pseudobonds, 17064 residues, 3 models
selected
> select subtract #2
Nothing selected
> sequence chain #1/LD
Alignment identifier is 1/LD
> select clear
> select #1/LD
2382 atoms, 2428 bonds, 293 residues, 1 model selected
> color sel orange red
> select add #1
218776 atoms, 234864 bonds, 4237 pseudobonds, 17789 residues, 4 models
selected
> select subtract #1
Nothing selected
> save "/Users/phonghoa/Desktop/L24 human vs yeast.cxs"
——— End of log from Wed Mar 26 17:09:16 2025 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: Mac15,4
Model Number: Z1950004VZP/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 11881.1.1
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7 (23H124)
Kernel Version: Darwin 23.6.0
Time since boot: 8 days, 6 hours, 35 minutes
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in graphics driver during Qt drawing |
comment:2 by , 7 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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