![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9596 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 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 0x00007ff850901700 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
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{
"uptime" : 650000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 29557,
"osVersion" : {
"train" : "macOS 13.5",
"build" : "22G74",
"releaseType" : "User"
},
"captureTime" : "2023-08-17 00:01:29.0035 +0200",
"incident" : "FF85DC01-52F8-43EE-8584-419CD39FCC33",
"pid" : 83438,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-08-16 16:45:52.5821 +0200",
"procStartAbsTime" : 635216170973013,
"procExitAbsTime" : 656436675524308,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"1B621CC7-A08E-58E5-A30C-B64306F232D4","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5A8EFE95-C9B8-50CB-3111-3AE68D059CBA",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 2,
"bridgeVersion" : {"build":"20P6072","train":"7.6"},
"sleepWakeUUID" : "7E43A03C-6243-4EE3-95FF-CDC43B020D9D",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737488183272\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffd6000-7ffffffd7000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":83438},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737488183272\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffd6000-7ffffffd7000 [ 4K] r-x\/r-x SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Processing_1-202208/Refinement-
> March/Anas refinement/monosome_P-site_no-H_RS-R_50.pdb" format pdb
Summary of feedback from opening
/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/KI/Jurkat_monosome_project/Processing_1-202208/Refinement-
March/Anas refinement/monosome_P-site_no-H_RS-R_50.pdb
---
warnings | Ignored bad PDB record found on line 12
SSBOND 1 CYS A2 45 CYS A2 76
Cannot find LINK/SSBOND residue FES (7099121)
Cannot find LINK/SSBOND residue FES (7099121)
Cannot find LINK/SSBOND residue FES (8965361)
Cannot find LINK/SSBOND residue FES (8965361)
Cannot find LINK/SSBOND residue FES (7099121)
4 messages similar to the above omitted
Chain information for monosome_P-site_no-H_RS-R_50.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
8 | No description available
9 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
AA | No description available
AB | No description available
AC | No description available
AD | No description available
AE | No description available
AF | No description available
AG | No description available
AH | No description available
AI | No description available
AJ | No description available
AK | No description available
AL | No description available
AM | No description available
AN | No description available
AO | No description available
AP | No description available
AQ | No description available
AR | No description available
AS | No description available
AT | No description available
AU | No description available
AV | No description available
AW | No description available
AX | No description available
AY | No description available
AZ | No description available
Ax | No description available
Ay | No description available
Az | No description available
B | No description available
D | No description available
E | No description available
F | No description available
H | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
l | No description available
m | No description available
o | No description available
p | No description available
q | No description available
r | No description available
s | No description available
t | No description available
u | No description available
z | No description available
> open 6spf format mmcif fromDatabase pdb
6spf title:
Pseudomonas aeruginosa 70s ribosome from an aminoglycoside resistant clinical
isolate [more info...]
Chain information for 6spf #2
---
Chain | Description | UniProt
1 | 50S ribosomal protein L31 | A0A072ZJG4_PSEAI 2-32
2 | 50S ribosomal protein L32 | A0A069QB25_PSEAI 2-54
3 | 50S ribosomal protein L33 | A0A140SG33_PSEAI 2-51
4 | 50S ribosomal protein L34 | A0A087L9L7_PSEAI 1-44
5 | 50S ribosomal protein L35 | A0A069QC44_PSEAI 2-64
6 | 50S ribosomal protein L36 | E2RXU2_PSEAI 1-38
A | Pseudomonas aeruginosa strain PAO1 23S ribosomal RNA |
B | 5S rRNA |
C | 50S ribosomal protein L2 | A0A241XHA2_PSEAI 3-273
D | 50S ribosomal protein L3 | A0A072ZBZ2_PSEAI 3-209
E | 50S ribosomal protein L4 | A0A241XH26_PSEAI 2-200
F | 50S ribosomal protein L5 | A0A072ZMU2_PSEAI 3-176
G | 50S ribosomal protein L6 | A0A2V3F3S9_PSEAI 2-170
H | 50S ribosomal protein L9 | A0A072ZKF0_PSEAI 2-79
I | 50S ribosomal protein L11 | A0A2V3GYK0_PSEAI 3-142
J | 50S ribosomal protein L13 | A0A071L356_PSEAI 2-142
K | 50S ribosomal protein L14 | E2RXT6_PSEAI 1-120
L | 50S ribosomal protein L15 | A0A2V3D5Z8_PSEAI 1-144
M | 50S ribosomal protein L16 | A0A069QEB6_PSEAI 1-136
N | 50S ribosomal protein L17 | A0A072ZCA1_PSEAI 1-120
O | 50S ribosomal protein L18 | E2RXU0_PSEAI 2-116
P | 50S ribosomal protein L19 | A0A263PZC6_PSEAI 2-115
Q | 50S ribosomal protein L20 | A0A069QEE3_PSEAI 2-118
R | 50S ribosomal protein L21 | A0A072ZDZ0_PSEAI 1-102
S | 50S ribosomal protein L22 | A0A1C7BCP0_PSEAI 1-110
T | 50S ribosomal protein L23 | E2RXT1_PSEAI 1-94
U | 50S ribosomal protein L24 | E2RXT7_PSEAI 1-103
V | 50S ribosomal protein L25 | A0A072ZBM5_PSEAI 4-191
W | 50S ribosomal protein L27 | A0A071LFT4_PSEAI 10-85
X | 50S ribosomal protein L28 | A0A072ZIQ9_PSEAI 2-78
Y | Ribosomal protein uL29 |
Z | 50S ribosomal protein L30 | E2RXU1_PSEAI 2-58
a | 16S rRNA |
b | 30S ribosomal protein S2 | A0A072ZPV8_PSEAI 3-228
c | 30S ribosomal protein S3 | A0A140S919_PSEAI 5-207
d | 30S ribosomal protein S4 | A0A072ZDF7_PSEAI 3-206
e | 30S ribosomal protein S5 | A0A241XG65_PSEAI 11-159
f | 30S ribosomal protein S6 | A0A069Q263_PSEAI 2-101
g | 30S ribosomal protein S7 | A0A2V3F2U6_PSEAI 3-156
h | 30S ribosomal protein S8 | E2RXT9_PSEAI 2-130
i | 30S ribosomal protein S9 | A0A069PXX1_PSEAI 3-128
j | 30S ribosomal protein S10 | E2RXT0_PSEAI 8-103
k | 30S ribosomal protein S11 | E2RXU4_PSEAI 14-128
l | 30S ribosomal protein S12 | A0A071L394_PSEAI 2-121
m | 30S ribosomal protein S13 | E2RXU3_PSEAI 3-112
n | 30S ribosomal protein S14 | E2RXT8_PSEAI 3-100
o | 30S ribosomal protein S15 | A0A071L3R7_PSEAI 2-88
p | 30S ribosomal protein S16 | A0A2V4FRZ2_PSEAI 1-78
q | 30S ribosomal protein S17 | E2RXT5_PSEAI 9-84
r | 30S ribosomal protein S18 | A0A2V3DLV3_PSEAI 19-74
s | 30S ribosomal protein S19 | E2RXT2_PSEAI 2-81
t | 30S ribosomal protein S20 | A0A072ZDZ9_PSEAI 2-87
u | 30S ribosomal protein S21 | A0A069QC99_PSEAI 34-67
> open 7m4v format mmcif fromDatabase pdb
7m4v title:
A. baumannii Ribosome-Eravacycline complex: 50S [more info...]
Chain information for 7m4v #3
---
Chain | Description | UniProt
0 | 50S ribosomal protein L33 | A0A062FI44_ACIBA 1-51
1 | 50S ribosomal protein L34 | A0A1J6Y3G0_9GAMM 1-44
2 | 50S ribosomal protein L35 | RL35_ACIB5 1-64
3 | 50S ribosomal protein L36 | A0A372FJT1_9GAMM 1-38
A | 23s ribosomal RNA |
B | 5s ribosomal RNA |
C | 50S ribosomal protein L2 | RL2_ACIB5 1-274
D | 50S ribosomal protein L3 | RL3_ACIB5 1-212
E | 50S ribosomal protein L4 | RL4_ACIB5 1-200
F | 50S ribosomal protein L5 | RL5_ACIB5 1-178
G | 50S ribosomal protein L6 | RL6_ACIB5 1-177
H | 50S ribosomal protein L9 | RL9_ACIB5 1-148
I | 50S ribosomal protein L13 | RL13_ACIB5 1-142
J | 50S ribosomal protein L14 | N8SHC6_9GAMM 1-122
K | 50S ribosomal protein L15 | RL15_ACIB5 1-146
L | 50S ribosomal protein L16 | RL16_ACIB5 1-137
M | 50S ribosomal protein L17 | RL17_ACIB5 1-125
N | 50S ribosomal protein L18 | RL18_ACIB5 1-116
O | 50S ribosomal protein L19 | RL19_ACIB5 1-122
P | 50S ribosomal protein L20 | V5VGC9_ACIBA 1-119
Q | 50S ribosomal protein L21 | RL21_ACIB5 1-103
R | 50S ribosomal protein L22 | A0A009I821_ACIB9 1-109
S | 50S ribosomal protein L23 | RL23_ACIB5 1-106
T | 50S ribosomal protein L24 | RL24_ACIB5 1-105
U | 50S ribosomal protein L25 | RL25_ACIB5 1-98
V | 50S ribosomal protein L27 | RL27_ACIB5 1-85
W | 50S ribosomal protein L28 | N9N7A0_9GAMM 1-78
X | 50S ribosomal protein L29 | RL29_ACIB5 1-65
Y | 50S ribosomal protein L30 | A0A062FG91_ACIBA 1-58
Z | 50S ribosomal protein L32 | RL32_ACIB5 1-61
Non-standard residues in 7m4v #3
---
MG — magnesium ion
YQM — Eravacycline
ZN — zinc ion
> open 7qi4 format mmcif fromDatabase pdb
Summary of feedback from opening 7qi4 fetched from pdb
---
warnings | Atom H is not in the residue template for PRO /s:135
Atom HN10 is not in the residue template for SPM /AA:1702
Atom H103 is not in the residue template for SPD /AA:1703
Atom H103 is not in the residue template for SPD /A:3301
Atom H103 is not in the residue template for SPD /A:3302
Atom H103 is not in the residue template for SPD /A:3303
Atom HN13 is not in the residue template for PUT /A:3304
Atom H1 is not in the residue template for VAL /B:101
7qi4 title:
Human mitochondrial ribosome at 2.2 A resolution [more info...]
Chain information for 7qi4 #4
---
Chain | Description | UniProt
0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | 16S mitochondrial rRNA |
A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 2-218
A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 |
CHCH1_HUMAN 1-118
A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial |
PTCD3_HUMAN 1-689
AA | 12S mitochondrial rRNA |
AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
AQ | MRPS21 isoform 1 | A0A2J8VEN6_PONAB 1-87
AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
Aw | A/A-tRNA |
Ax | P/P-tRNA |
Ay | E/E-tRNA |
Az | mRNA |
B | mitochondrial tRNAVal |
D | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
E | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
F | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
H | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
I | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
J | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-192
K | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
L | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
M | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
N | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
O | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
P | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 1-180
Q | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
R | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
S | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
T | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 1-206
U | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
V | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
W | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
X | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
Y | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
Z | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215
c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 1-306
e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212
g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123
k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-128
o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 |
G45IP_HUMAN 1-222
r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439
t u v w x y | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN 1-198
z | 39S ribosomal protein L1, mitochondrial | RM01_HUMAN 1-325
Non-standard residues in 7qi4 #4
---
5F0 — (3~{S})-3-azanyl-4-methoxy-4-oxidanylidene-butanoic acid
ATP — adenosine-5'-triphosphate
FES — FE2/S2 (inorganic) cluster
GDP — guanosine-5'-diphosphate
K — potassium ion
MG — magnesium ion
NAD — nicotinamide-adenine-dinucleotide
PUT — 1,4-diaminobutane (putrescine)
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
VAL — valine
ZN — zinc ion
> open 8crx format mmcif fromDatabase pdb
Summary of feedback from opening 8crx fetched from pdb
---
warning | Atom O3' has no neighbors to form bonds with according to residue
template for U /a:1730
8crx title:
Cutibacterium acnes 70S ribosome with mRNA, P-site tRNA and Sarecycline bound
[more info...]
Chain information for 8crx #5
---
Chain | Description | UniProt
0 | 50S ribosomal protein L33 | A0A2C6LJM0_CUTAC 1-56
1 | 50S ribosomal protein L34 | A0A2B7IDI8_CUTAC 1-44
2 | 50S ribosomal protein L35 | A0A371N4N9_CUTAC 1-68
3 | 50S ribosomal protein L36 | A0A2B7JN22_CUTAC 1-37
4 | 50S ribosomal protein L31 | A0A2B7JUW7_CUTAC 1-69
A | RNA (1537-MER) |
B | 30S ribosomal protein S2 | A0A2B7I756_CUTAC 1-283
C | P-site initiator tRNA |
D | 30S ribosomal protein S4 | A0A2B7JMY9_CUTAC 1-201
E | 30S ribosomal protein S5 | A0A2B7I5L8_CUTAC 1-215
F | 30S ribosomal protein S6 | A0A2C6L3A1_CUTAC 1-96
G | 30S ribosomal protein S3 | A0A2B7I5Y3_CUTAC 1-269
H | 30S ribosomal protein S8 | A0A2B7ITQ7_CUTAC 1-135
I | 30S ribosomal protein S7 | A0A2B7ITZ4_CUTAC 1-156
J | 30S ribosomal protein S9 | A0A2B7JN42_CUTAC 1-173
K | 30S ribosomal protein S11 | A0A2B7I645_CUTAC 1-135
L | 30S ribosomal protein S12 | A0A2C6LJN0_CUTAC 1-123
M | 30S ribosomal protein S10 | A0A085B5E4_CUTAC 1-103
N | 30S ribosomal protein S13 | A0A2C6LKT6_CUTAC 1-123
O | 30S ribosomal protein S15 | A0A2B7I743_CUTAC 1-87
P | 30S ribosomal protein S16 | A0A2B7IXM7_CUTAC 1-147
Q | 30S ribosomal protein S17 | A0A2B7JMS7_CUTAC 1-90
R | 30S ribosomal protein S18 | A0A2C6LI71_CUTAC -3-75
S | 30S ribosomal protein S14 type Z | A0A2B7JMX1_CUTAC 1-61
T | 30S ribosomal protein S20 | A0A2B7I592_CUTAC 1-88
U | 30S ribosomal protein S19 | A0A2B7ITR7_CUTAC 1-93
V | 50S ribosomal protein bL37 |
X | 30S ribosomal protein bS22 | A0A533INE0_CUTAC 1-33
Y | 32MF mRNA |
a | 23S ribosomal RNA |
b | 5S ribosomal RNA |
c | 50S ribosomal protein L2 | A0A2B7JMV5_CUTAC 1-278
d | 50S ribosomal protein L3 | A0A1G9KW65_CUTAC 1-223
e | 50S ribosomal protein L4 | A0A2B7I5M5_CUTAC 1-301
f | 50S ribosomal protein L5 | A0A3E2DDM1_CUTAC 1-210
g | 50S ribosomal protein L6 | A0A2B7I5S3_CUTAC 1-180
i | 50S ribosomal protein L13 | A0A2B7I6I7_CUTAC 1-147
j | 50S ribosomal protein L14 | A0A2B7JMZ8_CUTAC 1-122
k | 50S ribosomal protein L15 | A0A2B7IUA0_CUTAC 1-146
l | 50S ribosomal protein L16 | A0A2B7I5M8_CUTAC 1-139
m | 50S ribosomal protein L17 | A0A085AZY3_CUTAC 1-187
n | 50S ribosomal protein L18 | A0A2B7JN02_CUTAC 1-127
o | 50S ribosomal protein L19 | A0A2C6LKT3_CUTAC 1-117
p | 50S ribosomal protein L20 | A0A2B7I6V3_CUTAC 1-123
q | 50S ribosomal protein L21 | A0A085B4N9_CUTAC 1-102
r | 50S ribosomal protein L22 | A0A2B7ITY5_CUTAC 1-153
s | 50S ribosomal protein L23 | A0A2C6LEQ5_CUTAC 1-102
t | 50S ribosomal protein L24 | A0A085B5D2_CUTAC 1-122
u | 50S ribosomal protein L25 | A0A2B7IYF8_CUTAC 1-205
v | 50S ribosomal protein L27 | A0A2B7IGT1_CUTAC 1-89
w | 50S ribosomal protein L28 | A0A2B7I7B7_CUTAC 1-61
x | 50S ribosomal protein L29 | A0A2B7JB12_CUTAC 1-77
y | 50S ribosomal protein L30 | A0A2B7I5Y4_CUTAC 2-61
z | 50S ribosomal protein L32 | A0A2B7I771_CUTAC 1-63
Non-standard residues in 8crx #5
---
MG — magnesium ion
V7A — Sarecycline
ZN — zinc ion
> hide atoms
> show cartoons
> lighting soft
> ui tool show Matchmaker
> matchmaker #!2-5 to #1
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 monosome_P-site_no-H_RS-R_50.pdb, chain A (#1) with 6spf, chain A
(#2), sequence alignment score = 5975.7
RMSD between 382 pruned atom pairs is 0.903 angstroms; (across all 1547 pairs:
67.816)
Matchmaker monosome_P-site_no-H_RS-R_50.pdb, chain A (#1) with 7m4v, chain A
(#3), sequence alignment score = 5875.2
RMSD between 450 pruned atom pairs is 1.236 angstroms; (across all 1538 pairs:
49.351)
Matchmaker monosome_P-site_no-H_RS-R_50.pdb, chain A (#1) with 7qi4, chain A
(#4), sequence alignment score = 9157.7
RMSD between 1467 pruned atom pairs is 0.481 angstroms; (across all 1556
pairs: 0.995)
Matchmaker monosome_P-site_no-H_RS-R_50.pdb, chain A (#1) with 8crx, chain a
(#5), sequence alignment score = 5770.9
RMSD between 361 pruned atom pairs is 0.913 angstroms; (across all 1492 pairs:
70.485)
> hide #!2 models
> hide #!3 models
> hide #!5 models
> hide #!1 models
> open /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
> KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tige-LSU-1.pdb
Summary of feedback from opening
/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive-
KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tige-LSU-1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LEU D 184
ALA D 186 1 3
Start residue of secondary structure not found: HELIX 2 2 HIS D 252 LYS D 254
1 3
Start residue of secondary structure not found: HELIX 3 3 ALA D 260 ARG D 262
1 3
Start residue of secondary structure not found: HELIX 4 4 ASN D 263 TRP D 265
1 3
Start residue of secondary structure not found: HELIX 5 5 ASN E 57 LEU E 73 1
17
996 messages similar to the above omitted
Cannot find LINK/SSBOND residue FES (201 )
Cannot find LINK/SSBOND residue FES (201 )
> select #4/A:3078
31 atoms, 32 bonds, 1 residue, 1 model selected
> select up
49872 atoms, 53804 bonds, 1558 residues, 1 model selected
> cartoon style width 1.5 thickness 1
> lighting flat
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
> lighting soft
> set bgColor white
> ui tool show "Side View"
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 872908 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1968.140.7.0.0 (iBridge: 20.16.6072.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.5 (22G74)
Kernel Version: Darwin 22.6.0
Time since boot: 10 days, 18 hours, 55 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
B277U:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 70.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: TDBEE003853B
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.21.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Duc,
--Eric