![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15477 closed defect (can't reproduce)
Crash in Qt event loop in io_connect_method(), Intel Mac ChimeraX running on Mac M1
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.0.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Current thread 0x00000002003732c0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 58)
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{
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"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 1884,
"osVersion" : {
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"build" : "22A400",
"releaseType" : "User"
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"captureTime" : "2024-06-23 13:46:40.7122 +0200",
"incident" : "8DDE0B9E-851F-4D2B-82B0-EEA6AEA67905",
"pid" : 82186,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-06-22 23:49:38.0460 +0200",
"procStartAbsTime" : 2358824906804,
"procExitAbsTime" : 3347168165908,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"119C82FA-C5E3-5F0B-A592-754A83658024","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "02E04C25-79CA-2EF6-F248-C1774882463F",
"wakeTime" : 29,
"sleepWakeUUID" : "6D187058-9F0D-4131-9534-0DECEF8E8A3F",
"sip" : "enabled",
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"exception" : {"codes":"0x0000000000000002, 0x7900005455543870","rawCodes":[2,8718969240798115952],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x7900005455543870 -> 0x0000005455543870 (possible pointer authentication failure)"},
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"faultingThread" : 0,
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703326220288,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4816896,
"uuid" : "bca7763f-086a-3837-b278-2f8046e4e885",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.1"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703377190912,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16797687,
"uuid" : "817d572e-eb8c-3999-b7a0-68e1c4b47266",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703325126656,
"size" : 364532,
"uuid" : "06015868-b157-3745-889b-69e23c5034fd",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4556709888,
"size" : 66404352,
"uuid" : "7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
}
],
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000413
},
{
"rolloutId" : "61fd92db295c182621ececc3",
"factorPackIds" : {
},
"deploymentId" : 240000387
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "3dff9c91-a8fb-424e-a656-c8d6e6037574",
"experimentId" : "662152ede2d11d1408c4db33",
"deploymentId" : 400000014
}
]
},
"reportNotes" : [
"dyld_process_snapshot_create_for_process failed with 5"
]
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> open /Users/tjyang/Downloads/cryosparc_P34_J14_class_04_01600_volume.mrc
Opened cryosparc_P34_J14_class_04_01600_volume.mrc as #1, grid size
128,128,128, pixel 4.18, shown at level 3.38, step 1, values float32
> set bgColor white
> lighting soft
> close
> open /Users/tjyang/Downloads/cryosparc_P34_J16_001_volume_map(1).mrc
Opened cryosparc_P34_J16_001_volume_map(1).mrc as #1, grid size 160,160,160,
pixel 3.35, shown at level 2.55, step 1, values float32
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
Mismatch between Cocoa '\x0' and Carbon '\u3112' for virtual key 9 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> volume flip #1
Opened cryosparc_P34_J16_001_volume_map(1).mrc z flip as #2, grid size
160,160,160, pixel 3.35, shown at step 1, values float32
> close #1
> ui mousemode right zoom
> volume #2 level 1.837
> volume #2 level 2.628
> volume #2 level 0.2734
> ui tool show "Side View"
> volume #2 level 1.506
> volume #2 level 0.4206
> volume #2 level 0.1998
> volume #2 level 0.3838
> hide #!2 models
> show #!2 models
> volume #2 level 0.6229
> volume #2 level 0.9908
> open /Users/tjyang/Downloads/cryosparc_P34_J14_class_04_02000_volume.mrc
Opened cryosparc_P34_J14_class_04_02000_volume.mrc as #1, grid size
128,128,128, pixel 4.18, shown at level 3.35, step 1, values float32
> hide #!2 models
> volume #1 level 1.449
> volume #1 level 1.72
> volume #1 level 1.942
> close #1
> open /Users/tjyang/Downloads/cryosparc_P34_J14_class_02_02000_volume.mrc
Opened cryosparc_P34_J14_class_02_02000_volume.mrc as #1, grid size
128,128,128, pixel 4.18, shown at level 3.37, step 1, values float32
> volume #1 level 1.847
> close #1
> close #2
> open 7tut
Summary of feedback from opening 7tut fetched from pdb
---
warnings | Atom HO5' is not in the residue template for G /q:1
Atom HO5' is not in the residue template for G /u:1
Atom HO5' is not in the residue template for C /v:1
7tut title:
Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate
in complex with the multipass translocon [more info...]
Chain information for 7tut #1
---
Chain | Description | UniProt
1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476
2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96
3 | Protein transport protein Sec61 gamma |
4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483
5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106
6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224
7 | Nicalin | A0A8C0S144_CANLF -41-521
8 | Calcium load-activated calcium channel |
9 | Obligate partner of TMCO1 insertase |
A | uL2 | G1TT27_RABIT 1-257
B | Nascent chain |
C | uL4 | G1SVW5_RABIT 1-413
D | uL18 | G1SYJ6_RABIT 1-297
E | eL6 | G1SKF7_RABIT 1-291
F | uL30 | G1TUB1_RABIT 1-247
G | eL8 | G1STW0_RABIT 1-319
H | uL6 | G1SWI6_RABIT 1-192
I | uL16 | B7NZQ2_RABIT 1-214
J | uL5 | G1TUB8_RABIT 1-178
K | 28S ribosomal RNA |
L | eL13 | G1TPV0_RABIT 1-211
M | eL14 | G1SZ12_RABIT 1-218
N | eL15 | G1T0C1_RABIT 0-204
O | uL13 |
P | uL22 | G1TVT6_RABIT 1-184
Q | eL18 |
R | eL19 | G1TJR3_RABIT 1-196
S | eL20 |
T | eL21 | G1SHQ2_RABIT 1-160
U | eL22 | G1TSG1_RABIT 1-128
V | uL14 | G1T6D1_RABIT 1-140
W | eL24 | G1SE28_RABIT 1-157
X | eL23 | G1SE76_RABIT 1-156
Y | uL24 | G1SQH0_RABIT 1-145
Z | eL27 | G1TXF6_RABIT 1-136
a | uL15 | G1SNY0_RABIT 1-148
b | eL29 | G1SGR6_RABIT 1-226
c | eL30 | G1TDL2_RABIT 1-115
d | eL31 | G1SHG0_RABIT 1-125
e | eL32 | G1U437_RABIT 1-135
f | eL33 | G1SF08_RABIT 1-110
g | eL34 | G1U945_RABIT 1-116
h | eL35 | G1SIT5_RABIT 1-123
i | eL36 | G1TTQ5_RABIT 1-105
j | eL37 | U3KPD5_RABIT 1-97
k | eL38 | G1U001_RABIT 1-70
l | eL39 | G1TTN1_RABIT 1-51
m | eL40 | A0A2K5PSA0_CEBIM 10-102
n | eL41 | A0A087WNH4_RABIT 1-25
o | eL42 | G1U344_RABIT 1-106
p | eL43 | G1SY53_RABIT 1-92
q | P-site tRNA |
r | eL28 | G1U7L1_RABIT 1-137
u | 5S ribosomal RNA |
v | 5.8S ribosomal RNA |
w | uL3 | G1TL06_RABIT 2-403
Non-standard residues in 7tut #1
---
MG — magnesium ion
ZN — zinc ion
> close #1
> open emdb:21435
Opened emdb 21435 as #1, grid size 500,500,500, pixel 1.36, shown at level
0.0073, step 2, values float32, fit PDB 6w6l
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> volume #1 level 0.008496
> open 6w6l
Summary of feedback from opening 6w6l fetched from pdb
---
warning | Atom H1 is not in the residue template for UNK /y:1
6w6l title:
Cryo-EM structure of the human ribosome-TMCO1 translocon [more info...]
Chain information for 6w6l #2
---
Chain | Description | UniProt
1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_HUMAN 1-476
2 | Protein transport protein Sec61 subunit gamma | SC61G_HUMAN 1-68
3 | Protein transport protein Sec61 subunit beta | SC61B_HUMAN 1-96
4 | Transmembrane protein 147 | TM147_HUMAN 1-224
5 | Nicalin | NCLN_HUMAN 1-563
6 | Calcium load-activated calcium channel | TMCO1_HUMAN 1-188
7 | Coiled-coil domain-containing protein 47 | CCD47_HUMAN 1-483
A | 60S ribosomal protein L8 | RL8_HUMAN 1-257
B | 60S ribosomal protein L3 | RL3_HUMAN 1-403
C | 60S ribosomal protein L4 | RL4_HUMAN 1-427
D | 5.8S ribosomal RNA |
E | 5S ribosomal RNA |
F | 60S ribosomal protein L5 | RL5_HUMAN 1-297
G | 60S ribosomal protein L6 | RL6_HUMAN 1-288
H | 60S ribosomal protein L7 | RL7_HUMAN 1-248
I | 60S ribosomal protein L7a | RL7A_HUMAN 1-266
J | 60S ribosomal protein L9 | RL9_HUMAN 1-192
K | 60S ribosomal protein L10 | RL10_HUMAN 1-214
L | 60S ribosomal protein L11 | RL11_HUMAN 1-178
M | 60S ribosomal protein L13 | RL13_HUMAN 1-211
N | 60S ribosomal protein L14 | RL14_HUMAN 1-215
O | 60S ribosomal protein L15 | RL15_HUMAN 1-204
P | 60S ribosomal protein L13a | RL13A_HUMAN 1-203
Q | 60S ribosomal protein L17 | RL17_HUMAN 1-184
R | 60S ribosomal protein L18 | RL18_HUMAN 1-188
S | 60S ribosomal protein L19 | RL19_HUMAN 1-196
T | 60S ribosomal protein L18a | RL18A_HUMAN 1-176
U | 60S ribosomal protein L21 | RL21_HUMAN 1-160
V | 60S ribosomal protein L22 | RL22_HUMAN 1-128
W | 60S ribosomal protein L23 |
X | 60S ribosomal protein L24 | RL24_HUMAN 1-157
Y | 60S ribosomal protein L23a | RL23A_HUMAN 1-156
Z | 60S ribosomal protein L26 | RL26_HUMAN 1-145
a | 60S ribosomal protein L27 | RL27_HUMAN 1-136
b | 60S ribosomal protein L27a | RL27A_HUMAN 1-148
c | 60S ribosomal protein L29 | RL29_HUMAN 1-159
d | 60S ribosomal protein L30 | RL30_HUMAN 1-115
e | 60S ribosomal protein L31 |
f | 60S ribosomal protein L32 | RL32_HUMAN 1-135
g | 60S ribosomal protein L35a | RL35A_HUMAN 1-110
h | 60S ribosomal protein L34 | RL34_HUMAN 1-117
i | 60S ribosomal protein L35 | RL35_HUMAN 1-123
j | 60S ribosomal protein L36 | RL36_HUMAN 1-105
k | 60S ribosomal protein L37 | RL37_HUMAN 1-97
l | 60S ribosomal protein L38 | RL38_HUMAN 1-70
m | 60S ribosomal protein L39 | RL39_HUMAN 1-51
o | 60S ribosomal protein L41 | RL41_HUMAN 1-25
p | 60S ribosomal protein L36a | J3KQN4_HUMAN 1-106
q | 60S ribosomal protein L37a | RL37A_HUMAN 1-92
r | 60S ribosomal protein L28 | RL28_HUMAN 1-137
t | 28S ribosomal RNA |
u | tRNA |
v | tRNA |
y | Nascent chain mixture |
Non-standard residues in 6w6l #2
---
MG — magnesium ion
ZN — zinc ion
> select #2
259082 atoms, 270245 bonds, 3798 pseudobonds, 11953 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> volume #1 color #b2b2b280
> select clear
> close #1-2
> open EMDB:26133
Opened emdb 26133 as #1, grid size 412,412,412, pixel 1.34, shown at level
0.5, step 2, values float32, fit PDB 7tut
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> volume #1 step 1
> volume #1 level 0.6564
> open 7tut
Summary of feedback from opening 7tut fetched from pdb
---
warnings | Atom HO5' is not in the residue template for G /q:1
Atom HO5' is not in the residue template for G /u:1
Atom HO5' is not in the residue template for C /v:1
7tut title:
Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate
in complex with the multipass translocon [more info...]
Chain information for 7tut #2
---
Chain | Description | UniProt
1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476
2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96
3 | Protein transport protein Sec61 gamma |
4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483
5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106
6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224
7 | Nicalin | A0A8C0S144_CANLF -41-521
8 | Calcium load-activated calcium channel |
9 | Obligate partner of TMCO1 insertase |
A | uL2 | G1TT27_RABIT 1-257
B | Nascent chain |
C | uL4 | G1SVW5_RABIT 1-413
D | uL18 | G1SYJ6_RABIT 1-297
E | eL6 | G1SKF7_RABIT 1-291
F | uL30 | G1TUB1_RABIT 1-247
G | eL8 | G1STW0_RABIT 1-319
H | uL6 | G1SWI6_RABIT 1-192
I | uL16 | B7NZQ2_RABIT 1-214
J | uL5 | G1TUB8_RABIT 1-178
K | 28S ribosomal RNA |
L | eL13 | G1TPV0_RABIT 1-211
M | eL14 | G1SZ12_RABIT 1-218
N | eL15 | G1T0C1_RABIT 0-204
O | uL13 |
P | uL22 | G1TVT6_RABIT 1-184
Q | eL18 |
R | eL19 | G1TJR3_RABIT 1-196
S | eL20 |
T | eL21 | G1SHQ2_RABIT 1-160
U | eL22 | G1TSG1_RABIT 1-128
V | uL14 | G1T6D1_RABIT 1-140
W | eL24 | G1SE28_RABIT 1-157
X | eL23 | G1SE76_RABIT 1-156
Y | uL24 | G1SQH0_RABIT 1-145
Z | eL27 | G1TXF6_RABIT 1-136
a | uL15 | G1SNY0_RABIT 1-148
b | eL29 | G1SGR6_RABIT 1-226
c | eL30 | G1TDL2_RABIT 1-115
d | eL31 | G1SHG0_RABIT 1-125
e | eL32 | G1U437_RABIT 1-135
f | eL33 | G1SF08_RABIT 1-110
g | eL34 | G1U945_RABIT 1-116
h | eL35 | G1SIT5_RABIT 1-123
i | eL36 | G1TTQ5_RABIT 1-105
j | eL37 | U3KPD5_RABIT 1-97
k | eL38 | G1U001_RABIT 1-70
l | eL39 | G1TTN1_RABIT 1-51
m | eL40 | A0A2K5PSA0_CEBIM 10-102
n | eL41 | A0A087WNH4_RABIT 1-25
o | eL42 | G1U344_RABIT 1-106
p | eL43 | G1SY53_RABIT 1-92
q | P-site tRNA |
r | eL28 | G1U7L1_RABIT 1-137
u | 5S ribosomal RNA |
v | 5.8S ribosomal RNA |
w | uL3 | G1TL06_RABIT 2-403
Non-standard residues in 7tut #2
---
MG — magnesium ion
ZN — zinc ion
> select #2
267107 atoms, 278108 bonds, 4182 pseudobonds, 12662 residues, 4 models
selected
> hide sel atoms
> select #2/1-9
32434 atoms, 32776 bonds, 2025 residues, 1 model selected
> show sel cartoons
> select clear
> volume #1 level 0.5
> volume #1 level 0.6642
> volume #1 color #b2b2b280
> open /Users/tjyang/Downloads/cryosparc_P34_J16_001_volume_map(1).mrc
Opened cryosparc_P34_J16_001_volume_map(1).mrc as #3, grid size 160,160,160,
pixel 3.35, shown at level 2.55, step 1, values float32
> volume flip #3
Opened cryosparc_P34_J16_001_volume_map(1).mrc z flip as #4, grid size
160,160,160, pixel 3.35, shown at step 1, values float32
> close #3
> select add #4
2 models selected
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,78.459,0,1,0,-176.31,0,0,1,-57.318
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.88842,-0.3649,-0.27851,279.31,0.42165,0.88853,0.18088,-302.77,0.18146,-0.27814,0.94325,-14.059
> view matrix models
> #4,0.64154,-0.67449,-0.36537,452.33,0.23706,-0.27867,0.93067,-119.88,-0.72954,-0.68368,-0.01888,582.26
> view matrix models
> #4,0.67226,-0.51404,-0.53275,442,0.28693,-0.48246,0.82759,-50.663,-0.68245,-0.70922,-0.17684,616.71
> view matrix models
> #4,0.63939,-0.4983,-0.58556,459.67,0.38622,-0.45037,0.80498,-80.142,-0.66484,-0.74085,-0.09551,600.29
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.63939,-0.4983,-0.58556,388.44,0.38622,-0.45037,0.80498,103.47,-0.66484,-0.74085,-0.09551,666.09
> fitmap #4 inMap #1
Fit map cryosparc_P34_J16_001_volume_map(1).mrc z flip in map emdb 26133 using
40940 points
correlation = 0.9562, correlation about mean = 0.5321, overlap = 1.915e+05
steps = 272, shift = 17, angle = 28.1 degrees
Position of cryosparc_P34_J16_001_volume_map(1).mrc z flip (#4) relative to
emdb 26133 (#1) coordinates:
Matrix rotation and translation
0.27976532 -0.70296789 -0.65388648 559.71623510
0.20902266 -0.62014713 0.75612637 194.78282853
-0.93703837 -0.34821502 -0.02655944 628.25264255
Axis -0.75642098 0.19394549 0.62466987
Axis point 0.00000000 347.99237503 489.79100520
Rotation angle (degrees) 133.11544864
Shift along axis 6.84663922
> select clear
> ui mousemode right translate
> ui mousemode right zoom
> volume #4 level 0.15
> volume #4 level 0.4995
> hide #!4 models
> show #!4 models
> hide #!1 models
> hide #!2 models
> volume #4 level 0.1132
> hide #!4 models
> show #!1 models
> show #!2 models
> volume #1 level 0.6642
> hide #!1 models
> hide #!2 models
> show #!4 models
> volume #4 level 0.4075
> volume #4 level 0.3708
> hide #!4 models
> show #!1 models
> volume #1 color #b2b2b2
> lighting soft
> volume #1 level 0.5391
> hide #!1 models
> show #!4 models
> open
> /Users/tjyang/Downloads/cryosparc_P34_J15_class_01_00020_volume_sharp.mrc
Opened cryosparc_P34_J15_class_01_00020_volume_sharp.mrc as #3, grid size
128,128,128, pixel 4.18, shown at level 3.33, step 1, values float32
> hide #!4 models
> volume #3 level 0.6787
> volume #3 level 0.569
> volume #3 level 0.1849
> volume #3 level 0.4958
> volume #3 level 0.3312
> volume #3 level 1.685
> open /Users/tjyang/Downloads/cryosparc_P34_J16_002_volume_map.mrc
Opened cryosparc_P34_J16_002_volume_map.mrc as #5, grid size 160,160,160,
pixel 3.35, shown at level 2.54, step 1, values float32
> hide #!3 models
> volume #5 level 0.4151
> volume #5 level 0.6172
> volume #5 level 0.5364
> volume #5 level 0.2534
> open /Users/tjyang/Downloads/cryosparc_P34_J16_002_volume_map_sharp.mrc
Opened cryosparc_P34_J16_002_volume_map_sharp.mrc as #6, grid size
160,160,160, pixel 3.35, shown at level 3.03, step 1, values float32
> hide #!5 models
> volume #6 level 0.4088
> volume #6 level 0.6953
> hide #!6 models
> show #!5 models
> volume #5 level 0.3949
> hide #!5 models
> show #!6 models
> volume #6 level 0.5521
> volume #6 level 0.6953
> open /Users/tjyang/Downloads/fold_2024_05_14_09_26_model_0.cif
Chain information for fold_2024_05_14_09_26_model_0.cif #7
---
Chain | Description
A | .
B | .
C | .
D | .
> select add #7
7189 atoms, 7354 bonds, 915 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,233.09,0,1,0,362.25,0,0,1,182.83
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,296.27,0,1,0,350.43,0,0,1,124.89
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.73677,-0.48572,0.47036,290.77,0.32436,-0.35646,-0.8762,360.44,0.59326,0.79813,-0.10508,137.77
> select #7
7189 atoms, 7354 bonds, 915 residues, 1 model selected
> hide sel cartoons
> select #7/B
1465 atoms, 1492 bonds, 191 residues, 1 model selected
> show sel cartoons
> color #7 bychain
> color #6 darkgrey
> select clear
> select add #7
7189 atoms, 7354 bonds, 915 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.73677,-0.48572,0.47036,282.26,0.32436,-0.35646,-0.8762,353.41,0.59326,0.79813,-0.10508,115.88
> view matrix models
> #7,0.73677,-0.48572,0.47036,277.99,0.32436,-0.35646,-0.8762,342.22,0.59326,0.79813,-0.10508,108.8
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.73954,0.63264,-0.22988,280.18,0.18776,-0.52186,-0.83211,339.61,-0.64639,0.57222,-0.50472,87.538
> view matrix models
> #7,-0.33485,0.65229,-0.67999,262.51,0.29331,-0.61364,-0.73308,341.15,-0.89546,-0.44492,0.01415,81.289
> view matrix models
> #7,-0.74518,-0.46224,-0.48067,249.96,0.65203,-0.35384,-0.67057,348.43,0.13988,-0.8131,0.56507,96.524
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.74518,-0.46224,-0.48067,271.56,0.65203,-0.35384,-0.67057,355.08,0.13988,-0.8131,0.56507,157.81
> view matrix models
> #7,-0.74518,-0.46224,-0.48067,263.19,0.65203,-0.35384,-0.67057,353.75,0.13988,-0.8131,0.56507,161.88
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.8109,-0.54881,-0.20312,264.69,0.45439,-0.37179,-0.80951,349.7,0.36875,-0.74872,0.55086,165.04
> view matrix models
> #7,-0.80042,-0.56023,-0.21321,264.6,0.47903,-0.38399,-0.78936,350.11,0.36035,-0.73396,0.57572,165.34
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.80042,-0.56023,-0.21321,265.35,0.47903,-0.38399,-0.78936,350.28,0.36035,-0.73396,0.57572,164.14
> select #6
2 models selected
> view matrix models #6,1,0,0,0.070482,0,1,0,1.7356,0,0,1,0.38287
> select clear
> ui mousemode right zoom
> volume #6 color #a9a9a980
> select #7
7189 atoms, 7354 bonds, 915 residues, 1 model selected
> select #7/C
3578 atoms, 3657 bonds, 447 residues, 1 model selected
> show sel cartoons
> select #6
2 models selected
> select clear
> volume #6 color darkgrey
> volume #6 level 0.4088
> volume #6 color #a9a9a980
> ui mousemode right translate
> ui mousemode right zoom
> volume #6 level 0.5998
> volume #6 level 0.6953
> show #!2 models
> hide #!2 models
> volume #6 level 0.9818
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> show #!1 models
> volume #6 color darkgrey
> select add #6
2 models selected
> select add #7
7189 atoms, 7354 bonds, 915 residues, 3 models selected
> ui mousemode right "translate selected models"
> select add #5
7189 atoms, 7354 bonds, 915 residues, 5 models selected
> close #4
> view matrix models
> #5,1,0,0,139.39,0,1,0,-121.58,0,0,1,-150.74,#6,1,0,0,139.46,0,1,0,-119.84,0,0,1,-150.36,#7,-0.80042,-0.56023,-0.21321,404.74,0.47903,-0.38399,-0.78936,228.7,0.36035,-0.73396,0.57572,13.393
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.89136,-0.31226,0.32858,167.49,0.4524,0.65818,-0.60177,22.649,-0.028355,0.68505,0.72795,-261.26,#6,0.89136,-0.31226,0.32858,167.14,0.4524,0.65818,-0.60177,23.593,-0.028355,0.68505,0.72795,-259.8,#7,-0.74465,-0.62063,0.2456,348.57,-0.26368,-0.064511,-0.96245,274.47,0.61317,-0.78145,-0.11561,90.653
> view matrix models
> #5,-0.16048,0.38857,-0.90734,550.78,-0.35913,0.83326,0.42036,-92.921,0.91939,0.39331,0.0058216,-223.97,#6,-0.16048,0.38857,-0.90734,551.09,-0.35913,0.83326,0.42036,-91.339,0.91939,0.39331,0.0058216,-223.22,#7,-0.012371,0.60665,-0.79487,495.37,0.83809,-0.42729,-0.33915,172.65,-0.54539,-0.67037,-0.50314,158.71
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.16048,0.38857,-0.90734,440.11,-0.35913,0.83326,0.42036,37.267,0.91939,0.39331,0.0058216,-57.319,#6,-0.16048,0.38857,-0.90734,440.43,-0.35913,0.83326,0.42036,38.849,0.91939,0.39331,0.0058216,-56.569,#7,-0.012371,0.60665,-0.79487,384.71,0.83809,-0.42729,-0.33915,302.84,-0.54539,-0.67037,-0.50314,325.36
> fitmap #6 inMap #1
Fit map cryosparc_P34_J16_002_volume_map_sharp.mrc in map emdb 26133 using
92194 points
correlation = 0.8977, correlation about mean = 0.6195, overlap = 3.379e+05
steps = 308, shift = 25.9, angle = 24.2 degrees
Position of cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) relative to emdb
26133 (#1) coordinates:
Matrix rotation and translation
-0.32718154 0.67956357 -0.65661679 354.91883527
-0.24172322 0.61155440 0.75337316 -16.49084666
0.91352183 0.40520932 -0.03582302 -66.70997287
Axis -0.18784511 -0.84713812 -0.49706259
Axis point 209.67292814 0.00000000 111.13661725
Rotation angle (degrees) 112.06913452
Shift along axis -19.54071241
> select clear
> hide #!2 models
> hide #!1 models
> ui mousemode right zoom
> volume #6 level 0.7908
> select add #7
7189 atoms, 7354 bonds, 915 residues, 1 model selected
> volume #6 level 0.6476
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.012371,0.60665,-0.79487,395.9,0.83809,-0.42729,-0.33915,254.19,-0.54539,-0.67037,-0.50314,320.97
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.40154,0.27505,-0.87356,391.04,0.83556,-0.50055,0.22646,256.75,-0.37498,-0.82085,-0.43081,319.44
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.40154,0.27505,-0.87356,398.97,0.83556,-0.50055,0.22646,258.47,-0.37498,-0.82085,-0.43081,316.75
> view matrix models
> #7,0.40154,0.27505,-0.87356,398.56,0.83556,-0.50055,0.22646,262.52,-0.37498,-0.82085,-0.43081,318.93
> view matrix models
> #7,0.40154,0.27505,-0.87356,399.24,0.83556,-0.50055,0.22646,262.49,-0.37498,-0.82085,-0.43081,316.33
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.48809,0.28494,-0.82497,398.54,0.76515,-0.59443,0.24739,263.3,-0.41989,-0.75198,-0.50815,316.48
> view matrix models
> #7,0.47706,0.25411,-0.84133,398.57,0.75248,-0.6127,0.24161,263.4,-0.45409,-0.74834,-0.48351,316.96
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.47706,0.25411,-0.84133,398.71,0.75248,-0.6127,0.24161,262.68,-0.45409,-0.74834,-0.48351,312.26
> view matrix models
> #7,0.47706,0.25411,-0.84133,399.12,0.75248,-0.6127,0.24161,260.89,-0.45409,-0.74834,-0.48351,313.55
> select clear
> ui mousemode right "rotate selected models"
> select clear
> volume #6 level 0.8863
> hide #7 models
> volume #6 level 0.743
> show #7 models
> volume #6 level 0.7
> volume #6 level 0.6
> volume #6 color #a9a9a980
> ui mousemode right zoom
> show #!2 models
> select #2
267107 atoms, 278108 bonds, 4182 pseudobonds, 12662 residues, 4 models
selected
> hide sel cartoons
> log chains #2
Chain information for 7tut #2
---
Chain | Description | UniProt
1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476
2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96
3 | Protein transport protein Sec61 gamma |
4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483
5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106
6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224
7 | Nicalin | A0A8C0S144_CANLF -41-521
8 | Calcium load-activated calcium channel |
9 | Obligate partner of TMCO1 insertase |
A | uL2 | G1TT27_RABIT 1-257
B | Nascent chain |
C | uL4 | G1SVW5_RABIT 1-413
D | uL18 | G1SYJ6_RABIT 1-297
E | eL6 | G1SKF7_RABIT 1-291
F | uL30 | G1TUB1_RABIT 1-247
G | eL8 | G1STW0_RABIT 1-319
H | uL6 | G1SWI6_RABIT 1-192
I | uL16 | B7NZQ2_RABIT 1-214
J | uL5 | G1TUB8_RABIT 1-178
K | 28S ribosomal RNA |
L | eL13 | G1TPV0_RABIT 1-211
M | eL14 | G1SZ12_RABIT 1-218
N | eL15 | G1T0C1_RABIT 0-204
O | uL13 |
P | uL22 | G1TVT6_RABIT 1-184
Q | eL18 |
R | eL19 | G1TJR3_RABIT 1-196
S | eL20 |
T | eL21 | G1SHQ2_RABIT 1-160
U | eL22 | G1TSG1_RABIT 1-128
V | uL14 | G1T6D1_RABIT 1-140
W | eL24 | G1SE28_RABIT 1-157
X | eL23 | G1SE76_RABIT 1-156
Y | uL24 | G1SQH0_RABIT 1-145
Z | eL27 | G1TXF6_RABIT 1-136
a | uL15 | G1SNY0_RABIT 1-148
b | eL29 | G1SGR6_RABIT 1-226
c | eL30 | G1TDL2_RABIT 1-115
d | eL31 | G1SHG0_RABIT 1-125
e | eL32 | G1U437_RABIT 1-135
f | eL33 | G1SF08_RABIT 1-110
g | eL34 | G1U945_RABIT 1-116
h | eL35 | G1SIT5_RABIT 1-123
i | eL36 | G1TTQ5_RABIT 1-105
j | eL37 | U3KPD5_RABIT 1-97
k | eL38 | G1U001_RABIT 1-70
l | eL39 | G1TTN1_RABIT 1-51
m | eL40 | A0A2K5PSA0_CEBIM 10-102
n | eL41 | A0A087WNH4_RABIT 1-25
o | eL42 | G1U344_RABIT 1-106
p | eL43 | G1SY53_RABIT 1-92
q | P-site tRNA |
r | eL28 | G1U7L1_RABIT 1-137
u | 5S ribosomal RNA |
v | 5.8S ribosomal RNA |
w | uL3 | G1TL06_RABIT 2-403
> select #2/1-3
8915 atoms, 9011 bonds, 562 residues, 1 model selected
> show sel cartoons
> select clear
> volume #6 level 0.4568
> open 7tut
Summary of feedback from opening 7tut fetched from pdb
---
warnings | Atom HO5' is not in the residue template for G /q:1
Atom HO5' is not in the residue template for G /u:1
Atom HO5' is not in the residue template for C /v:1
7tut title:
Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate
in complex with the multipass translocon [more info...]
Chain information for 7tut #4
---
Chain | Description | UniProt
1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476
2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96
3 | Protein transport protein Sec61 gamma |
4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483
5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106
6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224
7 | Nicalin | A0A8C0S144_CANLF -41-521
8 | Calcium load-activated calcium channel |
9 | Obligate partner of TMCO1 insertase |
A | uL2 | G1TT27_RABIT 1-257
B | Nascent chain |
C | uL4 | G1SVW5_RABIT 1-413
D | uL18 | G1SYJ6_RABIT 1-297
E | eL6 | G1SKF7_RABIT 1-291
F | uL30 | G1TUB1_RABIT 1-247
G | eL8 | G1STW0_RABIT 1-319
H | uL6 | G1SWI6_RABIT 1-192
I | uL16 | B7NZQ2_RABIT 1-214
J | uL5 | G1TUB8_RABIT 1-178
K | 28S ribosomal RNA |
L | eL13 | G1TPV0_RABIT 1-211
M | eL14 | G1SZ12_RABIT 1-218
N | eL15 | G1T0C1_RABIT 0-204
O | uL13 |
P | uL22 | G1TVT6_RABIT 1-184
Q | eL18 |
R | eL19 | G1TJR3_RABIT 1-196
S | eL20 |
T | eL21 | G1SHQ2_RABIT 1-160
U | eL22 | G1TSG1_RABIT 1-128
V | uL14 | G1T6D1_RABIT 1-140
W | eL24 | G1SE28_RABIT 1-157
X | eL23 | G1SE76_RABIT 1-156
Y | uL24 | G1SQH0_RABIT 1-145
Z | eL27 | G1TXF6_RABIT 1-136
a | uL15 | G1SNY0_RABIT 1-148
b | eL29 | G1SGR6_RABIT 1-226
c | eL30 | G1TDL2_RABIT 1-115
d | eL31 | G1SHG0_RABIT 1-125
e | eL32 | G1U437_RABIT 1-135
f | eL33 | G1SF08_RABIT 1-110
g | eL34 | G1U945_RABIT 1-116
h | eL35 | G1SIT5_RABIT 1-123
i | eL36 | G1TTQ5_RABIT 1-105
j | eL37 | U3KPD5_RABIT 1-97
k | eL38 | G1U001_RABIT 1-70
l | eL39 | G1TTN1_RABIT 1-51
m | eL40 | A0A2K5PSA0_CEBIM 10-102
n | eL41 | A0A087WNH4_RABIT 1-25
o | eL42 | G1U344_RABIT 1-106
p | eL43 | G1SY53_RABIT 1-92
q | P-site tRNA |
r | eL28 | G1U7L1_RABIT 1-137
u | 5S ribosomal RNA |
v | 5.8S ribosomal RNA |
w | uL3 | G1TL06_RABIT 2-403
Non-standard residues in 7tut #4
---
MG — magnesium ion
ZN — zinc ion
> select #4
267107 atoms, 278108 bonds, 4182 pseudobonds, 12662 residues, 4 models
selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select #4/1-3
8915 atoms, 9011 bonds, 562 residues, 1 model selected
> show sel cartoons
> volume #6 level 0.791
> fitmap sel inMap #6
Fit molecule 7tut (#4) to map cryosparc_P34_J16_002_volume_map_sharp.mrc (#6)
using 8915 atoms
average map value = 0.8183, steps = 48
shifted from previous position = 2.05
rotated from previous position = 2.92 degrees
atoms outside contour = 4446, contour level = 0.79098
Position of 7tut (#4) relative to cryosparc_P34_J16_002_volume_map_sharp.mrc
(#6) coordinates:
Matrix rotation and translation
-0.35193617 -0.27357238 0.89515311 196.51973488
0.64800324 0.61889748 0.44391181 -206.52902182
-0.67545001 0.73629074 -0.04053662 256.09912553
Axis 0.15852788 0.85158114 0.49967838
Axis point 220.74112503 0.00000000 110.87713924
Rotation angle (degrees) 112.75476506
Shift along axis -16.75516713
> select clear
> hide #!2 models
> volume #6 level 0.1703
> volume #6 level 0.5523
> select #7/B
1465 atoms, 1492 bonds, 191 residues, 1 model selected
> select #7/B,C
5043 atoms, 5149 bonds, 638 residues, 1 model selected
> volume #6 level 0.6477
> volume #6 level 0.6
> open /Users/tjyang/Downloads/fold_2024_05_14_09_26_model_0.cif
Chain information for fold_2024_05_14_09_26_model_0.cif #8
---
Chain | Description
A | .
B | .
C | .
D | .
> mmaker #8 to #7
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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with
fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score =
2307.5
RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs:
0.000)
> color #8 bychain
> select clear
> hide #7 models
> select #8/B,C
5043 atoms, 5149 bonds, 638 residues, 1 model selected
> fitmap sel inMap #6
Fit molecule fold_2024_05_14_09_26_model_0.cif (#8) to map
cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) using 5043 atoms
average map value = 1.705, steps = 108
shifted from previous position = 34.3
rotated from previous position = 17.2 degrees
atoms outside contour = 1990, contour level = 0.6
Position of fold_2024_05_14_09_26_model_0.cif (#8) relative to
cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.90815609 -0.38320038 -0.16855258 280.53093727
0.40222756 -0.68711436 -0.60505109 332.61942350
0.11604091 -0.61727733 0.77814085 187.17954519
Axis -0.01463366 -0.34063150 0.94008299
Axis point 100.67849424 232.97883767 0.00000000
Rotation angle (degrees) 155.30776538
Shift along axis 58.55846017
> mmaker #8 to #7
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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with
fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score =
2307.5
RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs:
0.000)
> select #8/C inmap #6
Expected a keyword
> fitmap #8/C inMap #6
Fit molecule fold_2024_05_14_09_26_model_0.cif (#8) to map
cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) using 3578 atoms
average map value = 1.842, steps = 116
shifted from previous position = 39.5
rotated from previous position = 21.2 degrees
atoms outside contour = 1291, contour level = 0.6
Position of fold_2024_05_14_09_26_model_0.cif (#8) relative to
cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.91152941 -0.30352026 -0.27746997 287.30065986
0.41123301 -0.67480759 -0.61279859 333.11986580
-0.00124206 -0.67268875 0.73992451 189.77891996
Axis -0.07792012 -0.35938644 0.92993002
Axis point 114.48319125 234.38713212 0.00000000
Rotation angle (degrees) 157.39940731
Shift along axis 34.37585205
> select up
7189 atoms, 7354 bonds, 915 residues, 1 model selected
> mmaker #8 to #7
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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with
fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score =
2307.5
RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs:
0.000)
> select clear
> hide #8 models
> show #7 models
> show #8 models
> hide #7 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2/1-9
32434 atoms, 32776 bonds, 2025 residues, 1 model selected
> show sel cartoons
> select clear
> hide #8 models
> show #8 models
> hide #!6 models
> hide #!2 models
> show #7 models
> hide #8 models
> show #!1 models
> hide #!1 models
> show #!6 models
> volume #6 level 0.6477
> volume #6 color darkgrey
> hide #7 models
> hide #!6 models
> show #!5 models
> hide #!4 models
> show #!4 models
> show #!6 models
> fitmap #5 inMap #6
Fit map cryosparc_P34_J16_002_volume_map.mrc in map
cryosparc_P34_J16_002_volume_map_sharp.mrc using 138645 points
correlation = 0.9414, correlation about mean = 0.9112, overlap = 1.012e+06
steps = 136, shift = 26.1, angle = 24.2 degrees
Position of cryosparc_P34_J16_002_volume_map.mrc (#5) relative to
cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
1.00000000 -0.00001533 -0.00004860 0.00529735
0.00001533 1.00000000 0.00009606 -0.01009414
0.00004860 -0.00009606 0.99999999 0.03937849
Axis -0.88339006 -0.44693405 0.14096791
Axis point 0.00000000 402.03719382 80.05834663
Rotation angle (degrees) 0.00623025
Shift along axis 0.00538289
> select clear
> color #5 darkgrey
> select clear
> hide #!6 models
> volume #5 level 0.4757
> volume #5 color #a9a9a9b3
> show #7 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!5 models
> volume #6 level 1.125
> volume #5 level 0.496
> volume #5 level -0.009439
> volume #5 level 0.1523
> volume #5 level 0.4353
> show #8 models
> hide #7 models
> hide #8 models
> show #8 models
> hide #8 models
> show #7 models
> hide #!5 models
> show #!5 models
> show #8 models
> hide #!5 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #!4 models
> select #8/C:!-70
Expected an objects specifier or a keyword
> select #8/C:1-70
534 atoms, 552 bonds, 70 residues, 1 model selected
> hide sel cartoons
> select #8/C
3578 atoms, 3657 bonds, 447 residues, 1 model selected
> ~select #8:1-100
2805 atoms, 2860 bonds, 347 residues, 1 model selected
> show #!5 models
> select #8/C
3578 atoms, 3657 bonds, 447 residues, 1 model selected
> ~select #8:1-90
2883 atoms, 2939 bonds, 357 residues, 1 model selected
> fitmap sel inMap #5
Fit molecule fold_2024_05_14_09_26_model_0.cif (#8) to map
cryosparc_P34_J16_002_volume_map.mrc (#5) using 2883 atoms
average map value = 2.225, steps = 228
shifted from previous position = 50.3
rotated from previous position = 40 degrees
atoms outside contour = 410, contour level = 0.43531
Position of fold_2024_05_14_09_26_model_0.cif (#8) relative to
cryosparc_P34_J16_002_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
-0.55284171 -0.29334825 -0.77994413 288.88397895
0.83227870 -0.24040056 -0.49951949 316.13686704
-0.04096584 -0.92528610 0.37705095 208.66884110
Axis -0.30148467 -0.52326937 0.79705468
Axis point 113.62069640 294.74026807 0.00000000
Rotation angle (degrees) 135.08018356
Shift along axis -86.19835353
> mmaker #8 to #7
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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with
fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score =
2307.5
RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs:
0.000)
> select #8/B,C
5043 atoms, 5149 bonds, 638 residues, 1 model selected
> ~select #8:1-90
3654 atoms, 3724 bonds, 458 residues, 1 model selected
> fitmap sel inMap #5
Fit molecule fold_2024_05_14_09_26_model_0.cif (#8) to map
cryosparc_P34_J16_002_volume_map.mrc (#5) using 3654 atoms
average map value = 2.101, steps = 148
shifted from previous position = 48
rotated from previous position = 27.9 degrees
atoms outside contour = 557, contour level = 0.43531
Position of fold_2024_05_14_09_26_model_0.cif (#8) relative to
cryosparc_P34_J16_002_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
-0.68968697 -0.37002774 -0.62242377 290.11865428
0.71292906 -0.49745267 -0.49423980 324.30529604
-0.12674393 -0.78461475 0.60689015 198.58842110
Axis -0.23686827 -0.40434213 0.88340300
Axis point 110.74671265 262.70425652 0.00000000
Rotation angle (degrees) 142.19717065
Shift along axis -24.41658984
> mmaker #8 to #7
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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with
fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score =
2307.5
RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs:
0.000)
> volume #5 level 0.6375
> volume #5 level 0.3342
> volume #5 level 0.3949
> select clear
> hide #8 models
> show #7 models
> volume #6 level 1.364
> volume #6 level 0.6955
> hide #7 models
> volume #6 level 0.6
> volume #6 level 0.5
> hide #!6 models
> show #!5 models
> volume #5 color darkgrey
> volume #5 level 0.3342
> volume #5 level 0.2331
> volume #5 level 0.314
> volume #6 level 0.8342
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/tjyang/Desktop/movie21.mp4
Movie saved to /Users/tjyang/Desktop/movie21.mp4
> volume #6 level 1.121
> volume #5 level 0.6375
> volume #5 level 0.5364
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: Z11D000L9D/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.41.10
OS Loader Version: 8419.41.10
Software:
System Software Overview:
System Version: macOS 13.0.1 (22A400)
Kernel Version: Darwin 22.1.0
Time since boot: 2 days, 3 hours, 19 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 16 months ago
| Component: | Unassigned → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash setting volume contour level |
comment:2 by , 16 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash setting volume contour level → Crash in Qt event loop in io_connect_method(), Intel Mac ChimeraX running on Mac M1 |
Note:
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It isn't clear why ChimeraX crashed. It was in the Qt window toolkit event loop in a routine called io_connect_method().
What I'm wondering is how you managed to run Intel Mac ChimeraX on your M1 Mac? That requires ChimeraX to run under Rosetta Intel emulation which will be slower and possibly more prone to crashing. Did you choose the Intel Mac version from the ChimeraX download page? It should have shown you the universal Mac version and that would run native M1 Mac code. At any rate I suggest getting the ChimeraX M1 Mac version of ChimeraX univeral Mac version so your running native M1 code.