![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18307 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.8 (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: Segmentation fault
Current thread 0x0000000200bbdf00 (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, lxml._elementpath, lxml.etree, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, PIL._imagingmath, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix (total: 57)
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{
"uptime" : 100000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1274628220,
"deployVersion" : 210,
"modelCode" : "Mac16,8",
"coalitionID" : 16625,
"osVersion" : {
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"build" : "24F74",
"releaseType" : "User"
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"captureTime" : "2025-07-29 10:37:56.0501 +0200",
"codeSigningMonitor" : 2,
"incident" : "80A52606-FC50-412F-A032-5EAD0FCE45DF",
"pid" : 65987,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-28 19:53:27.4807 +0200",
"procStartAbsTime" : 2474620286970,
"procExitAbsTime" : 2576440694830,
"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":"0F9A9603-E1C1-549F-8715-AAEA2C742E8A","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2EB47986-06CB-2ABF-673C-EC337EFF8F17",
"appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn","siriAssetIsNotReady","assetIsNotReady"]},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"codeSigningAuxiliaryInfo" : 0,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "EC7216E5-FF2A-44D0-B842-C0F4D671326B",
"wakeTime" : 2218,
"sleepWakeUUID" : "01C07DA5-2CB1-48DC-8E21-327D8C5B1D53",
"sip" : "enabled",
"vmRegionInfo" : "0x64bce3e5d088 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
"exception" : {"codes":"0x0000000000000001, 0x0000e4bce3e5d088","rawCodes":[1,251499928473736],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000e4bce3e5d088 -> 0x000064bce3e5d088 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":65987},
"vmregioninfo" : "0x64bce3e5d088 is not in any region. \n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n UNUSED SPACE AT END",
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"faultingThread" : 0,
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"source" : "P",
"arch" : "arm64e",
"base" : 6755864576,
"size" : 31568,
"uuid" : "519f3220-7499-334a-96d6-ccf3dc28f986",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6822580224,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21568640,
"uuid" : "5d0da1bd-412c-3ed8-84e9-40ca62fe7b42",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.60.5"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6751813632,
"size" : 636112,
"uuid" : "9cf0401a-a938-389e-a77d-9e9608076ccf",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6756093952,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5500928,
"uuid" : "df489a59-b4f6-32b8-9bb4-9b832960aa52",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "3502.1.401"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6754668544,
"size" : 577528,
"uuid" : "875203a1-087b-33a6-93a5-928bb7e9114c",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
"base" : 6750978048,
"size" : 5047205888,
"uuid" : "d7397d7f-8df9-3920-81a7-c0a144be9c51"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=9.4G written=5192K(0%) resident=5192K(0%) swapped_out=0K(0%) unallocated=9.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 576K 27 \nColorSync 656K 33 \nCoreAnimation 1760K 108 \nCoreGraphics 48K 3 \nCoreUI image data 5904K 51 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 8.7G 181 \nMALLOC guard page 288K 18 \nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 848K 53 \nStack 170.9M 54 \nStack Guard 56.0M 1 \nVM_ALLOCATE 322.9M 201 \nVM_ALLOCATE (reserved) 256.0M 2 reserved VM address space (unallocated)\n__AUTH 5521K 697 \n__AUTH_CONST 77.4M 944 \n__CTF 824 1 \n__DATA 34.3M 1087 \n__DATA_CONST 36.9M 1103 \n__DATA_DIRTY 2778K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 647.0M 153 \n__OBJC_RO 61.4M 1 \n__OBJC_RW 2396K 1 \n__TEXT 1.3G 1123 \n__TPRO_CONST 128K 2 \ndyld private memory 800K 8 \nmapped file 289.5M 61 \npage table in kernel 5192K 1 \nshared memory 3744K 26 \n=========== ======= ======= \nTOTAL 11.9G 6298 \nTOTAL, minus reserved VM space 11.7G 6298 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "9d2e6a3fb7cc2b480554b18eb93ad1c9b8090fb6",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "67d07cd6a7affa169ae21f45",
"factorPackIds" : {
},
"deploymentId" : 240000002
},
{
"rolloutId" : "6425c75e4327780c10cc4252",
"factorPackIds" : {
"SIRI_HOME_AUTOMATION_INTENT_SELECTION_CACHE" : "642600a457e7664b1698eb32"
},
"deploymentId" : 240000004
}
],
"experiments" : [
]
}
}
===== 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
> open 9guq
9guq title:
30S PIC (Pre-Initiation complex) [more info...]
Chain information for 9guq #1
---
Chain | Description | UniProt
A | 16S ribosomal RNA |
B | 30S ribosomal protein S1 | RS1_ECOLI 1-557
C | 30S ribosomal protein S2 | RS2_ECOLI 1-241
D | Small ribosomal subunit protein uS3 | RS3_ECOLI 1-233
E | Small ribosomal subunit protein uS4 | RS4_ECOLI 1-206
F | 30S ribosomal protein S5 | RS5_ECOLI 10-165
G | Small ribosomal subunit protein bS6, non-modified isoform | RS6_ECOLI 1-131
H | 30S ribosomal protein S7 | RS7_ECOLI 1-156
I | 30S ribosomal protein S8 | RS8_ECOLI 1-130
J | 30S ribosomal protein S9 | RS9_ECOLI 1-130
K | 30S ribosomal protein S10 | RS10_ECOLI 1-103
L | 30S ribosomal protein S11 | RS11_ECOLI 1-129
M | 30S ribosomal protein S12 | RS12_ECOLI 1-124
N | 30S ribosomal protein S13 | RS13_ECOLI 1-118
O | 30S ribosomal protein S14 | RS14_ECOLI 1-101
P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89
Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82
R | 30S ribosomal protein S17 | RS17_ECOLI 1-84
S | 30S ribosomal protein S18 | RS18_ECOLI 1-75
T | 30S ribosomal protein S19 | RS19_ECOLI 1-92
U | 30S ribosomal protein S20 | RS20_ECOLI 1-87
V | 30S ribosomal protein S21 | RS21_ECOLI 1-71
W | tRNA(fmet) P-site |
X | mRNA |
Non-standard residues in 9guq #1
---
2MG — 2N-methylguanosine-5'-monophosphate
4OC — 4N,O2'-methylcytidine-5'-monophosphate
4SU — 4-thiouridine-5'-monophosphate
5MC — 5-methylcytidine-5'-monophosphate
5MU — 5-methyluridine 5'-monophosphate
D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid
G7M — N7-methyl-guanosine-5'-monophosphate
H2U — 5,6-dihydrouridine-5'-monophosphate
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
OMC — O2'-methylycytidine-5'-monophosphate
UR3 — 3-methyluridine-5'-monophoshate
> open 9guS
9gus title:
30S mRNA delivery complex TEC resolved (30S only) [more info...]
Chain information for 9gus #2
---
Chain | Description | UniProt
A | 16S ribosomal RNA |
B | 30S ribosomal protein S1 | RS1_ECOLI 1-557
C | 30S ribosomal protein S2 | RS2_ECOLI 1-241
D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233
E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206
F | 30S ribosomal protein S5 | RS5_ECOLI 10-165
G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131
H | 30S ribosomal protein S7 | RS7_ECOLI 1-156
I | 30S ribosomal protein S8 | RS8_ECOLI 1-130
J | 30S ribosomal protein S9 | RS9_ECOLI 1-130
K | 30S ribosomal protein S10 | RS10_ECOLI 1-103
L | 30S ribosomal protein S11 | RS11_ECOLI 1-129
M | 30S ribosomal protein S12 | RS12_ECOLI 1-124
N | 30S ribosomal protein S13 | RS13_ECOLI 1-118
O | 30S ribosomal protein S14 | RS14_ECOLI 1-101
P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89
Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82
R | 30S ribosomal protein S17 | RS17_ECOLI 1-84
S | 30S ribosomal protein S18 | RS18_ECOLI 1-75
T | 30S ribosomal protein S19 | RS19_ECOLI 1-92
U | 30S ribosomal protein S20 | RS20_ECOLI 1-87
V | 30S ribosomal protein S21 | RS21_ECOLI 1-71
W | tRNA(fmet) P-site |
X | mRNA |
Non-standard residues in 9gus #2
---
2MG — 2N-methylguanosine-5'-monophosphate
4OC — 4N,O2'-methylcytidine-5'-monophosphate
4SU — 4-thiouridine-5'-monophosphate
5MC — 5-methylcytidine-5'-monophosphate
5MU — 5-methyluridine 5'-monophosphate
D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid
G7M — N7-methyl-guanosine-5'-monophosphate
H2U — 5,6-dihydrouridine-5'-monophosphate
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
OMC — O2'-methylycytidine-5'-monophosphate
UR3 — 3-methyluridine-5'-monophoshate
> open 9gup
Summary of feedback from opening 9gup fetched from pdb
---
note | Fetching compressed mmCIF 9gup from http://files.rcsb.org/download/9gup.cif
9gup title:
30S mRNA delivery complex (open head) [more info...]
Chain information for 9gup #3
---
Chain | Description | UniProt
A | 16S ribosomal RNA |
B | 30S ribosomal protein S1 | RS1_ECOLI 1-557
C | 30S ribosomal protein S2 | RS2_ECOLI 1-241
D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233
E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206
F | 30S ribosomal protein S5 | RS5_ECOLI 10-165
G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131
H | 30S ribosomal protein S7 | RS7_ECOLI 1-156
I | 30S ribosomal protein S8 | RS8_ECOLI 1-130
J | 30S ribosomal protein S9 | RS9_ECOLI 1-130
K | 30S ribosomal protein S10 | RS10_ECOLI 1-103
L | 30S ribosomal protein S11 | RS11_ECOLI 1-129
M | 30S ribosomal protein S12 | RS12_ECOLI 1-124
N | 30S ribosomal protein S13 | RS13_ECOLI 1-118
O | 30S ribosomal protein S14 | RS14_ECOLI 1-101
P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89
Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82
R | 30S ribosomal protein S17 | RS17_ECOLI 1-84
S | 30S ribosomal protein S18 | RS18_ECOLI 1-75
T | 30S ribosomal protein S19 | RS19_ECOLI 1-92
U | 30S ribosomal protein S20 | RS20_ECOLI 1-87
V | 30S ribosomal protein S21 | RS21_ECOLI 1-71
X | mRNA |
Non-standard residues in 9gup #3
---
2MG — 2N-methylguanosine-5'-monophosphate
4OC — 4N,O2'-methylcytidine-5'-monophosphate
5MC — 5-methylcytidine-5'-monophosphate
D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid
G7M — N7-methyl-guanosine-5'-monophosphate
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
UR3 — 3-methyluridine-5'-monophoshate
> open 9guw
Summary of feedback from opening 9guw fetched from pdb
---
warnings | Atom OP1 has no neighbors to form bonds with according to residue template for A /X:38
Atom OP2 has no neighbors to form bonds with according to residue template for
A /X:38
9guw title:
30S-TEC (TEC in expressome position) Inactive state 2 [more info...]
Chain information for 9guw #4
---
Chain | Description | UniProt
1 2 | DNA-directed RNA polymerase subunit alpha | RPOA_ECOLI 1-329
3 | DNA-directed RNA polymerase subunit beta | RPOB_ECOLI 1-1342
4 | DNA-directed RNA polymerase subunit beta' | RPOC_ECO57 1-1406
5 | DNA-directed RNA polymerase subunit omega | RPOZ_ECOLI 1-91
6 | Non-Template DNA strand |
7 | Template DNA strand |
A | 16S ribosomal RNA |
B | 30S ribosomal protein S1 | RS1_ECOLI 1-557
C | 30S ribosomal protein S2 | RS2_ECOLI 1-241
D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233
E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206
F | 30S ribosomal protein S5 | RS5_ECOLI 10-166
G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131
H | 30S ribosomal protein S7 | RS7_ECOLI 1-156
I | 30S ribosomal protein S8 | RS8_ECOLI 1-130
J | 30S ribosomal protein S9 | RS9_ECOLI 1-130
K | 30S ribosomal protein S10 | RS10_ECOLI 1-103
L | 30S ribosomal protein S11 | RS11_ECOLI 1-129
M | 30S ribosomal protein S12 | RS12_ECOLI 1-124
N | 30S ribosomal protein S13 | RS13_ECOLI 1-118
O | 30S ribosomal protein S14 | RS14_ECOLI 1-101
P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89
Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82
R | 30S ribosomal protein S17 | RS17_ECOLI 1-84
S | 30S ribosomal protein S18 | RS18_ECOLI 1-75
T | 30S ribosomal protein S19 | RS19_ECOLI 1-92
U | 30S ribosomal protein S20 | RS20_ECOLI 1-87
X | mRNA |
Z | Transcription termination/antitermination protein NusG | NUSG_ECOLI 1-181
Non-standard residues in 9guw #4
---
2MG — 2N-methylguanosine-5'-monophosphate
5MC — 5-methylcytidine-5'-monophosphate
D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid
G7M — N7-methyl-guanosine-5'-monophosphate
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
ZN — zinc ion
> open 9guv
9guv title:
30S mRNA delivery complex (closed-head) [more info...]
Chain information for 9guv #5
---
Chain | Description | UniProt
A | 16S ribosomal RNA |
B | 30S ribosomal protein S1 | RS1_ECOLI 1-557
C | 30S ribosomal protein S2 | RS2_ECOLI 1-241
D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233
E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206
F | Small ribosomal subunit protein uS5 | C3SR27_ECOLX 1-165
G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131
H | 30S ribosomal protein S7 | RS7_ECOLI 1-156
I | 30S ribosomal protein S8 | RS8_ECOLI 1-130
J | 30S ribosomal protein S9 | RS9_ECOLI 1-130
K | 30S ribosomal protein S10 | RS10_ECOLI 1-103
L | 30S ribosomal protein S11 | RS11_ECOLI 1-129
M | 30S ribosomal protein S12 | RS12_ECOLI 1-124
N | 30S ribosomal protein S13 | RS13_ECOLI 1-118
O | 30S ribosomal protein S14 | RS14_ECOLI 1-101
P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89
Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82
R | 30S ribosomal protein S17 | RS17_ECOLI 1-84
S | 30S ribosomal protein S18 | RS18_ECOLI 1-75
T | 30S ribosomal protein S19 | RS19_ECOLI 1-92
U | 30S ribosomal protein S20 | RS20_ECOLI 1-87
V | 30S ribosomal protein S21 | RS21_ECOLI 1-71
W | tRNA(fmet) P-site |
X | mRNA |
Non-standard residues in 9guv #5
---
2MG — 2N-methylguanosine-5'-monophosphate
4OC — 4N,O2'-methylcytidine-5'-monophosphate
4SU — 4-thiouridine-5'-monophosphate
5MC — 5-methylcytidine-5'-monophosphate
5MU — 5-methyluridine 5'-monophosphate
D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid
G7M — N7-methyl-guanosine-5'-monophosphate
H2U — 5,6-dihydrouridine-5'-monophosphate
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
OMC — O2'-methylycytidine-5'-monophosphate
UR3 — 3-methyluridine-5'-monophoshate
> hide #!4 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> hide #!5 models
> hide #!4 models
> show #!5 models
> close #5
> open 9gux
9gux title:
30S-TEC (TEC in expressome position) Inactive state 1 [more info...]
Chain information for 9gux #5
---
Chain | Description | UniProt
1 2 | DNA-directed RNA polymerase subunit alpha | RPOA_ECOLI 1-329
3 | DNA-directed RNA polymerase subunit beta | RPOB_ECOLI 1-1342
4 | DNA-directed RNA polymerase subunit beta' | RPOC_ECO57 1-1406
5 | DNA-directed RNA polymerase subunit omega | RPOZ_ECOLI 1-91
6 | Non-Template DNA strand |
7 | Template DNA strand |
A | 16S ribosomal RNA |
B | 30S ribosomal protein S1 | RS1_ECOLI 1-557
C | 30S ribosomal protein S2 | RS2_ECOLI 1-241
D | Small ribosomal subunit protein uS3 | C3SQX2_ECOLX 1-233
E | Small ribosomal subunit protein uS4 | RS4_ECOBW 1-206
F | 30S ribosomal protein S5 | RS5_ECOLI 10-166
G | Small ribosomal subunit protein bS6 | W8T6F0_ECOLX 1-131
H | 30S ribosomal protein S7 | RS7_ECOLI 1-156
I | 30S ribosomal protein S8 | RS8_ECOLI 1-130
J | 30S ribosomal protein S9 | RS9_ECOLI 1-130
K | 30S ribosomal protein S10 | RS10_ECOLI 1-103
L | 30S ribosomal protein S11 | RS11_ECOLI 1-129
M | 30S ribosomal protein S12 | RS12_ECOLI 1-124
N | 30S ribosomal protein S13 | RS13_ECOLI 1-118
O | 30S ribosomal protein S14 | RS14_ECOLI 1-101
P | Small ribosomal subunit protein uS15 | RS15_ECOLI 1-89
Q | 30S ribosomal protein S16 | RS16_ECOLI 1-82
R | 30S ribosomal protein S17 | RS17_ECOLI 1-84
S | 30S ribosomal protein S18 | RS18_ECOLI 1-75
T | 30S ribosomal protein S19 | RS19_ECOLI 1-92
U | 30S ribosomal protein S20 | RS20_ECOLI 1-87
V | 30S ribosomal protein S21 | RS21_ECOLI 1-71
X | mRNA |
Z | Transcription termination/antitermination protein NusG | NUSG_ECOLI 1-180
Non-standard residues in 9gux #5
---
2MG — 2N-methylguanosine-5'-monophosphate
5MC — 5-methylcytidine-5'-monophosphate
D2T — (3R)-3-(methylsulfanyl)-L-aspartic acid
G7M — N7-methyl-guanosine-5'-monophosphate
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
ZN — zinc ion
> open "/Volumes/LaCie/P147/Final MAps/cryosparc_P147_J438_008_volume_map.mrc"
Opened cryosparc_P147_J438_008_volume_map.mrc as #6, grid size 360,360,360,
pixel 0.731, shown at level 0.0504, step 2, values float32
> close #1-4
> close #5
> surface dust #6 size 7.31
> volume #6 step 1
> volume #6 level 0.1029
> volume #6 level 0.06193
> volume #6 level 0.03989
> volume #6 level 0.09446
> volume #6 level 0.04724
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view
> ui tool show "Side View"
> view
> lighting simple
> ui tool show "Volume Viewer"
> volume #6 level 0.07788
> volume #6 level 0.05195
> volume #6 level 0.06373
> volume #6 level 0.04959
> volume #6 level 0.05431
> open 1iw7
Summary of feedback from opening 1iw7 fetched from pdb
---
notes | Fetching compressed mmCIF 1iw7 from http://files.rcsb.org/download/1iw7.cif
Fetching CCD PB from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/PB/PB.cif
1iw7 title:
Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus
at 2.6A resolution [more info...]
Chain information for 1iw7 #1
---
Chain | Description | UniProt
A B K L | RNA polymerase alpha subunit | RPOA_THETH 1-315
C M | RNA polymerase beta subunit |
D N | RNA polymerase beta subunit |
E O | RNA polymerase omega subunit |
F P | RNA polymerase sigma-70 subunit |
Non-standard residues in 1iw7 #1
---
MG — magnesium ion
PB — lead (II) ion
1iw7 mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> hide atoms
> show cartoons
> ui tool show "Model Panel"
> close #1
> open 1907
Fetching url http://files.rcsb.org/download/1907.cif failed:
HTTP Error 404: Not Found
> open 1907
Fetching url http://files.rcsb.org/download/1907.cif failed:
HTTP Error 404: Not Found
> view
> open /Volumes/LaCie/30S_IFs/Maps/cryosparc_P1_J470_008_volume_map.mrc
Opened cryosparc_P1_J470_008_volume_map.mrc as #1, grid size 600,600,600,
pixel 0.729, shown at level 0.0663, step 4, values float32
> open /Volumes/LaCie/30S_IFs/cryosparc_P1_J472_007_volume_map.mrc
Opened cryosparc_P1_J472_007_volume_map.mrc as #2, grid size 600,600,600,
pixel 0.729, shown at level 0.0503, step 4, values float32
> open /Volumes/LaCie/30S_IFs/cryosparc_P1_J476_008_volume_map.mrc
Opened cryosparc_P1_J476_008_volume_map.mrc as #3, grid size 600,600,600,
pixel 0.729, shown at level 0.0609, step 4, values float32
> surface dust #1 size 7.29
> surface dust #2 size 7.29
> surface dust #3 size 7.29
> open /Volumes/LaCie/30S_IFs/cryosparc_P1_J498_010_volume_map.mrc
Opened cryosparc_P1_J498_010_volume_map.mrc as #4, grid size 600,600,600,
pixel 0.729, shown at level 0.0583, step 4, values float32
> select add #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,3.8846,0,1,0,9.0861,0,0,1,-0.25038
> view matrix models
> #4,-0.98939,0.10777,0.097446,391.6,-0.10521,-0.99396,0.031094,464.23,0.10021,0.020512,0.99475,-25.361
> view matrix models
> #4,-0.98939,0.10777,0.097446,384.99,-0.10521,-0.99396,0.031094,452.43,0.10021,0.020512,0.99475,-18.659
> select subtract #4
Nothing selected
> surface dust #1 size 7.29
> surface dust #2 size 7.29
> surface dust #3 size 7.29
> surface dust #4 size 7.29
> open /Volumes/LaCie/30S_IFs/cryosparc_P1_J499_008_volume_map.mrc
Opened cryosparc_P1_J499_008_volume_map.mrc as #5, grid size 600,600,600,
pixel 0.729, shown at level 0.0486, step 4, values float32
> open /Volumes/LaCie/30S_IFs/cryosparc_P1_J500_008_volume_map.mrc
Opened cryosparc_P1_J500_008_volume_map.mrc as #7, grid size 600,600,600,
pixel 0.729, shown at level 0.0511, step 4, values float32
> open /Volumes/LaCie/30S_IFs/cryosparc_P1_J501_004_volume_map.mrc
Opened cryosparc_P1_J501_004_volume_map.mrc as #8, grid size 600,600,600,
pixel 0.729, shown at level 0.0492, step 4, values float32
> surface dust #1 size 7.29
> surface dust #2 size 7.29
> surface dust #3 size 7.29
> surface dust #4 size 7.29
> surface dust #5 size 7.29
> surface dust #7 size 7.29
> surface dust #8 size 7.29
===== 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 - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac16,8
Model Number: Z1FE001RUFN/A
Chip: Apple M4 Pro
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 48 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 4 days, 19 hours, 31 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
BE27A:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
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 , 3 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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