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Opened 18 months ago
Closed 18 months ago
#15104 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4-arm64-arm-64bit
ChimeraX Version: 1.6rc202304252053 (2023-04-25 20:53:05 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 0x00000001efee5e00 (most recent call first):
File "/Applications/ChimeraX-1.6-rc2023.04.25.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-rc2023.04.25.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-rc2023.04.25.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-rc2023.04.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6-rc2023.04.25.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" : 390000,
"procRole" : "Background",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 23847,
"osVersion" : {
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"build" : "22F66",
"releaseType" : "User"
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"captureTime" : "2024-04-29 16:33:46.7545 -0400",
"incident" : "513D6C63-B7A5-4337-A4A8-52D9A3DAF0EC",
"pid" : 46087,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-25 16:04:55.2687 -0400",
"procStartAbsTime" : 8117922785634,
"procExitAbsTime" : 9393364879568,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6-rc2023.04.25.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4C23F015-FEA2-97D2-0E0F-B6A4AD618697",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 3002,
"sleepWakeUUID" : "D5200120-4CAE-4793-9442-57E28F154E88",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 105557813886952\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600118000000-600120000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6792146944,
"size" : 520184,
"uuid" : "95a70e20-1df3-3ddf-900c-315ed0b2c067",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6793801728,
"size" : 28668,
"uuid" : "f80c6971-c080-31f5-ab6e-be01311154af",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6794014720,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5087232,
"uuid" : "203e4401-8c2e-3157-a24b-92f52551d43e",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1977"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6810374144,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 10248192,
"uuid" : "d5337cc6-a075-3ca0-b5bf-b49da8878337",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "1977"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6846861312,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15790080,
"uuid" : "041c7d21-21cc-3eea-ae53-d39f5ca6a24e",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.60.124"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6954016768,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3358720,
"uuid" : "d800278b-4e6c-3032-b56f-027a938a51d6",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6886203392,
"CFBundleShortVersionString" : "1.22",
"CFBundleIdentifier" : "com.apple.HIServices",
"size" : 409600,
"uuid" : "ab1464a5-20e6-3c95-8548-1c03866fb283",
"path" : "\/System\/Library\/Frameworks\/ApplicationServices.framework\/Versions\/A\/Frameworks\/HIServices.framework\/Versions\/A\/HIServices",
"name" : "HIServices"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6874255360,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 4374528,
"uuid" : "96676a53-b1e0-3d7e-b98b-b73873cd1880",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6791839744,
"size" : 294912,
"uuid" : "c2fd3094-b465-39a4-b774-16583ff53c4b",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6790094848,
"size" : 582996,
"uuid" : "bd993f39-c902-37d6-8bd8-6d827c7f121e",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6949109760,
"CFBundleShortVersionString" : "306.7.4",
"CFBundleIdentifier" : "com.apple.Metal",
"size" : 2002944,
"uuid" : "2bab169c-42da-36e3-955a-f30b709ec2ad",
"path" : "\/System\/Library\/Frameworks\/Metal.framework\/Versions\/A\/Metal",
"name" : "Metal",
"CFBundleVersion" : "306.7.4"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"sharedCache" : {
"base" : 6789431296,
"size" : 3551805440,
"uuid" : "7d9faa84-5c6b-3ef4-9379-faba64346673"
},
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "ef45c3c799d687e7c3aadbc0025924581155042f",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62fe74515312cd4599bd3c80",
"factorPackIds" : {
"MYRIAD_BOOSTS" : "62fe74805312cd4599bd3c81"
},
"deploymentId" : 240000006
},
{
"rolloutId" : "60da5e84ab0ca017dace9abf",
"factorPackIds" : {
},
"deploymentId" : 240000008
}
],
"experiments" : [
{
"treatmentId" : "5d51a80d-93ec-47e1-9027-675002e78e4a",
"experimentId" : "6384d56b96e8d228551ec182",
"deploymentId" : 400000023
}
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202304252053 (2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Feb 23 15:56:32 2024UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Tue Jan 30 16:17:55 2024UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Nov 3 09:32:22 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Oct 20 15:54:08 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Oct 20 15:24:47 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Oct 20 15:08:11 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Oct 20 14:52:35 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/stefhed/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/6elz 2.cif"
6elz 2.cif title:
State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar
pre-60S ribosomes [more info...]
Chain information for 6elz 2.cif #1
---
Chain | Description | UniProt
1 | 25S ribosomal RNA |
2 | 5.8S ribosomal RNA |
6 | Internal transcribed spacer 2 |
A | Ribosome biogenesis protein BRX1 | BRX1_YEAST 1-291
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | ATP-dependent RNA helicase HAS1 | HAS1_YEAST 1-505
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
I | Nucleolar complex-associated protein 3 | NOC3_YEAST 1-663
J | rRNA-processing protein EBP2 | EBP2_YEAST 1-427
K | Proteasome-interacting protein CIC1 | CIC1_YEAST 1-376
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosome subunit biogenesis protein NIP7 | NIP7_YEAST 1-181
m | Ribosome biogenesis protein ERB1 | ERB1_YEAST 1-807
n | Pescadillo homolog | PESC_YEAS7 1-605
o | Ribosome biogenesis protein 15 | NOP15_YEAST 1-220
p | Ribosome biogenesis protein YTM1 | YTM1_YEAS7 1-460
q | 25S rRNA (cytosine(2870)-C(5))-methyltransferase | NOP2_YEAST 1-618
r | Ribosome biogenesis protein NSA2 | NSA2_YEAS7 1-261
s | Nuclear GTP-binding protein NUG1 | NUG1_YEAST 1-520
t | Ribosome biogenesis protein RLP7 | RLP7_YEAST 1-322
u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v | Nucleolar protein 16 | NOP16_YEAST 1-231
w | 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase | SPB1_YEAST 1-841
y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
z | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 6elz 2.cif #1
---
ZN — zinc ion
> select all
134887 atoms, 143091 bonds, 2452 pseudobonds, 12372 residues, 4 models
selected
> hide sel
> show nucleic
> hide sel surfaces
> show sel cartoons
> hide sel surfaces
> hide surfaces
> select all
134887 atoms, 143091 bonds, 2452 pseudobonds, 12372 residues, 4 models
selected
> hide all
> select clear
> select #1:I, y, s, K, W, A, r, u, t, p, z
29269 atoms, 32087 bonds, 715 pseudobonds, 1392 residues, 3 models selected
> hide sel
> hide sel cartoons
> hide sel surfaces
> select #1:K
Nothing selected
> select #1/K
2073 atoms, 2107 bonds, 1 pseudobond, 257 residues, 2 models selected
> hide sel
> hide sel cartoons
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> hide sel cartoons
> select #1/y, s, K, W, A, r, u, t, p, z
15075 atoms, 15315 bonds, 10 pseudobonds, 1883 residues, 2 models selected
> hide sel cartoons
> select nucleic
57318 atoms, 64137 bonds, 2412 pseudobonds, 2680 residues, 3 models selected
> show sel cartoons
> ladder nucleotides
Unknown command: ladder nucleotides
> show nucleotides ladder
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> nucleotides sel ladder
[Repeated 2 time(s)]
> select #1/A-Z
38689 atoms, 39375 bonds, 15 pseudobonds, 4848 residues, 2 models selected
> hide sel
> hide sel cartoons
> select #1/a, c-k
7802 atoms, 7921 bonds, 4 pseudobonds, 981 residues, 2 models selected
> hide sel cartoons
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
> show sel surfaces
> hide sel cartoons
> color sel yellow
> select #1/D
1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected
> select #1/D
1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> color sel red
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
> hide sel cartoons
> show sel surfaces
> select #1/o
1107 atoms, 1129 bonds, 133 residues, 1 model selected
> hide sel cartoons
> show sel surfaces
> color sel blue
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> show sel surfaces
> color sel light green
> select #1/w
3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> color sel orange
> select clear
> select #1/b
3410 atoms, 3474 bonds, 3 pseudobonds, 421 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> color sel light blue
> select clear
> select #1/n
3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected
> hide sel cartoons
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> select #1/:42-635
Expected an objects specifier or a keyword
> select #1/1:42-635
11543 atoms, 12934 bonds, 447 pseudobonds, 537 residues, 3 models selected
> color sel lightblue red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel red
> color sel lightred
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel lightblue red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #1/1:662-1435
14182 atoms, 15879 bonds, 569 pseudobonds, 661 residues, 3 models selected
> color sel orange
> select #1/1:1452-1878
8891 atoms, 9946 bonds, 390 pseudobonds, 416 residues, 3 models selected
> color sel yellow
> select up
52595 atoms, 58864 bonds, 390 pseudobonds, 2457 residues, 3 models selected
> select up
134887 atoms, 143091 bonds, 2448 pseudobonds, 12372 residues, 3 models
selected
> select #1/1:1911-2332
902 atoms, 1007 bonds, 48 pseudobonds, 42 residues, 3 models selected
> color sel light green
> color sel forest green
> select #1/1:2400-2980
4471 atoms, 4995 bonds, 172 pseudobonds, 210 residues, 3 models selected
> color sel medium blue
> select #1/1:2995-3396
8560 atoms, 9569 bonds, 344 pseudobonds, 402 residues, 2 models selected
> color sel lightblue purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel purple
> color medium purple
> color sel medium purple
> select #1/2
3353 atoms, 3746 bonds, 83 pseudobonds, 158 residues, 2 models selected
> color sel pink
> color sel hot pink
> select clear
> sequence chain #1/D
Alignment identifier is 1/D
> select #1/D
1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select /I:132-601
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select /I:132-601
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> sequence chain #1/I
Alignment identifier is 1/I
> select /I:132-133
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /I:132-133
18 atoms, 17 bonds, 2 residues, 1 model selected
> color sel white
> select clear
Alignment identifier is 1/1
Alignment identifier is 1/2
Alignment identifier is 1/6
Alignment identifier is 1/L
Alignment identifier is 1/N
Alignment identifier is 1/Q
Alignment identifier is 1/R
Alignment identifier is 1/S
Alignment identifier is 1/T
Alignment identifier is 1/U
Alignment identifier is 1/Z
Alignment identifier is 1/c
Alignment identifier is 1/d
Alignment identifier is 1/e
Alignment identifier is 1/f
Alignment identifier is 1/g
Alignment identifier is 1/i
Alignment identifier is 1/j
Alignment identifier is 1/k
Alignment identifier is 1/O
Alignment identifier is 1/V
Alignment identifier is 1/a
Alignment identifier is 1/P
Alignment identifier is 1/X
Alignment identifier is 1/Y
Alignment identifier is 1/h
Alignment identifier is 1/F
Alignment identifier is 1/B
Alignment identifier is 1/C
Alignment identifier is 1/H
Alignment identifier is 1/A
Alignment identifier is 1/K
Alignment identifier is 1/m
Alignment identifier is 1/D
Alignment identifier is 1/W
Alignment identifier is 1/l
Alignment identifier is 1/b
Alignment identifier is 1/o
Alignment identifier is 1/n
Alignment identifier is 1/r
Alignment identifier is 1/s
Alignment identifier is 1/t
Alignment identifier is 1/y
Alignment identifier is 1/z
Alignment identifier is 1/p
Alignment identifier is 1/q
Alignment identifier is 1/u
Alignment identifier is 1/v
Alignment identifier is 1/w
Destroying pre-existing alignment with identifier 1/I
Alignment identifier is 1/I
Alignment identifier is 1/J
Alignment identifier is 1/E
Alignment identifier is 1/G
Alignment identifier is 1/M
Window position QRect(2176,1854 100x30) outside any known screen, using
primary screen
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
Alignment identifier is 1/J
> select /J:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /J:196-197
16 atoms, 15 bonds, 2 residues, 1 model selected
> color sel white
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
> select /J:339
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /J:339-340
14 atoms, 13 bonds, 2 residues, 1 model selected
> color sel white
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
Alignment identifier is 1/m
> select /m:125
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /m:125-126
18 atoms, 18 bonds, 2 residues, 1 model selected
> color sel white
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
> select #1/o
1107 atoms, 1129 bonds, 133 residues, 1 model selected
Alignment identifier is 1/o
> select /o:88-89
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /o:88-89
21 atoms, 21 bonds, 2 residues, 1 model selected
> color sel white
> select #1/o
1107 atoms, 1129 bonds, 133 residues, 1 model selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
Alignment identifier is 1/q
> select /q:227
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /q:227-229
27 atoms, 27 bonds, 3 residues, 1 model selected
> color sel white
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select /q:549
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /q:549-550
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel white
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
Alignment identifier is 1/v
> select /v:65
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /v:65-66
13 atoms, 12 bonds, 2 residues, 1 model selected
> color sel white
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
> select /v:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /v:155-156
16 atoms, 15 bonds, 2 residues, 1 model selected
> color sel white
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
> select #1/w
3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected
Alignment identifier is 1/w
> select /w:328
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /w:328-329
16 atoms, 15 bonds, 2 residues, 1 model selected
> color sel white
> select #1/w
3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected
> select /w:639-640
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /w:639-640
15 atoms, 14 bonds, 2 residues, 1 model selected
> color sel white
> select clear
> ui mousemode right "move markers"
[Repeated 1 time(s)]
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> set bgColor gray
> set bgColor black
> set bgColor white
> set bgColor black
> select clear
> ui tool show "Side View"
> view orient
> ui mousemode right "mark maximum"
> ui mousemode right "mark plane"
> ui mousemode right "mark surface"
> ui mousemode right "mark center"
> ui mousemode right "mark point"
> ui mousemode right "link markers"
> ui mousemode right "move markers"
> ui mousemode right "resize markers"
> select /D:267-481
1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected
Alignment identifier is 1/D
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting soft
> select clear
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
Alignment identifier is 1/I
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
Alignment identifier is 1/v
> select /v:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /v:3-45
352 atoms, 355 bonds, 43 residues, 1 model selected
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Oct 20 14:52:35 2023 ———
opened ChimeraX session
> lighting simple
> lighting soft
> lighting full
> lighting soft
> select /L
998 atoms, 1017 bonds, 122 residues, 1 model selected
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/3jct-nog2state1.cif"
3jct-nog2state1.cif title:
Cryo-em structure of eukaryotic pre-60S ribosomal subunits [more info...]
Chain information for 3jct-nog2state1.cif #2
---
Chain | Description | UniProt
1 | RDN25-1 rRNA |
2 | RDN58-1 rRNA |
3 | RDN5-2 rRNA |
4 | Probable metalloprotease ARX1 | Q03862 1-593
5 | rRNA-processing protein CGR1 | P53188 1-120
6 | ITS2-1 miscRNA |
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
I | Bud site selection protein 20 | BUD20_YEAST 1-166
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | Proteasome-interacting protein CIC1 | CIC1_YEAST 1-376
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
n | Pescadillo homolog | PESC_YEAST 1-605
o | Ribosome biogenesis protein 15 | NOP15_YEAST 1-220
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome biogenesis protein NOP53 | NOP53_YEAST 1-455
r | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
s | Nuclear GTP-binding protein NUG1 | NUG1_YEAST 1-520
t | Ribosome biogenesis protein RLP7 | RLP7_YEAST 1-322
u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v | Ribosome biogenesis protein RPF2 | RPF2_YEAST 1-344
w | Regulator of ribosome biosynthesis | RRS1_YEAST 1-203
x | Ribosome assembly protein 4 | NLE1_YEAST 1-515
y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
z | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 3jct-nog2state1.cif #2
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> hide all
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Oct 20 15:08:11 2023 ———
opened ChimeraX session
> select #1/A
1623 atoms, 1663 bonds, 2 pseudobonds, 198 residues, 2 models selected
> show sel surfaces
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
Alignment identifier is 1/m
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Oct 20 15:24:47 2023 ———
opened ChimeraX session
> select #1/m:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/m:156-169
105 atoms, 107 bonds, 14 residues, 1 model selected
> select #1/m:125
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/m:125-155
246 atoms, 250 bonds, 31 residues, 1 model selected
> color sel lightblue orange
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color (#!1 & sel) #fff125ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffd00bff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffb80cff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffdc10ff
[Repeated 1 time(s)]
> color (#!1 & sel) #fff612ff
> color (#!1 & sel) #fff613ff
> color (#!1 & sel) #ffdd16ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffd617ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffcf13ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffbc13ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffa50aff
> select clear
> select #1/m:125
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/m:125-155
246 atoms, 250 bonds, 31 residues, 1 model selected
> color (#!1 & sel) #ffb51dff
> color (#!1 & sel) #ffbf40ff
> color (#!1 & sel) #ffd8aeff
> color (#!1 & sel) #ffdbb2ff
> color (#!1 & sel) #ffe0b5ff
> color (#!1 & sel) #ffe5bbff
> color (#!1 & sel) #fff2c7ff
> color (#!1 & sel) #ffe2b1ff
> select clear
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
> select #1/m:125
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/m:125-126
18 atoms, 18 bonds, 2 residues, 1 model selected
> color sel white
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Oct 20 15:54:08 2023 ———
opened ChimeraX session
> select #1/n
3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected
> show sel surfaces
Alignment identifier is 1/n
> select clear
> color sel red
[Repeated 1 time(s)]
> select #1/n
3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected
> select #1/n:594
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/n:591-594
31 atoms, 30 bonds, 4 residues, 1 model selected
> color sel red
> select clear
> select #1/u
976 atoms, 996 bonds, 116 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select #1/l
1377 atoms, 1408 bonds, 174 residues, 1 model selected
> hide sel
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
Alignment identifier is 1/I
> select clear
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Nov 3 09:32:22 2023 ———
opened ChimeraX session
> hide #!2 models
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
Alignment identifier is 1/q
> color (#!1 & sel) red
> undo
> color (#!1 & sel) red
> undo
> select #1/I:562,564,599,605
27 atoms, 25 bonds, 3 residues, 1 model selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/w:562,564,599,605
Nothing selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select clear
> select #1/q:562,564,599,605
Nothing selected
> color #1 red
> undo
> select clear
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select clear
> select #1/q:562,564,599,605
Nothing selected
> select #1/q :562,564,599,605
Nothing selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select clear
> select #1/q: 562, 564, 599, 605
Nothing selected
> select #1/ q:562, 564, 599, 605
Nothing selected
> select #1/ q: 562, 564, 599, 605
Nothing selected
> select #1/q: 562, 564, 599, 605
Nothing selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select clear
> color #1 red
> undo
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/q: 388, 392, 449, 482, 510
39 atoms, 35 bonds, 5 residues, 1 model selected
> color (#!1 & sel) red
> select clear
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Tue Jan 30 16:17:55 2024 ———
opened ChimeraX session
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select #1/l
1377 atoms, 1408 bonds, 174 residues, 1 model selected
Alignment identifier is 1/l
> select #1/G
1438 atoms, 1463 bonds, 1 pseudobond, 184 residues, 2 models selected
> show sel cartoons
> select #1/P
1442 atoms, 1465 bonds, 183 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/s
301 atoms, 301 bonds, 36 residues, 1 model selected
> show sel cartoons
> select #1/W
1870 atoms, 1902 bonds, 232 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/z
444 atoms, 445 bonds, 55 residues, 1 model selected
> show sel cartoons
> select #1/r
1438 atoms, 1462 bonds, 2 pseudobonds, 176 residues, 2 models selected
> show sel cartoons
> select #1/u
976 atoms, 996 bonds, 116 residues, 1 model selected
> show sel cartoons
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Feb 23 15:56:32 2024 ———
opened ChimeraX session
> select #1/1
52595 atoms, 58864 bonds, 2177 pseudobonds, 2457 residues, 3 models selected
> select 1:970-1110
Expected an objects specifier or a keyword
> select 1/1:970-1110
Expected an objects specifier or a keyword
> select 2/1:970-1110
Expected an objects specifier or a keyword
> select 1/1:970-1110
Expected an objects specifier or a keyword
> select 1/1: 970-1110
Expected an objects specifier or a keyword
> select clear
> select 1/1:970-1110
Expected an objects specifier or a keyword
> select #1/1
52595 atoms, 58864 bonds, 2177 pseudobonds, 2457 residues, 3 models selected
Alignment identifier is 1/1
> select #1/1:990
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/1:977-990
292 atoms, 324 bonds, 14 residues, 1 model selected
> select clear
> select #1/1
52595 atoms, 58864 bonds, 2177 pseudobonds, 2457 residues, 3 models selected
> select #1/1:2826
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/1:2826
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/1:2823-2824
46 atoms, 51 bonds, 2 residues, 1 model selected
> select #1/1:2824-2880
850 atoms, 947 bonds, 19 pseudobonds, 40 residues, 3 models selected
> select #1/1:2611
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/1:2611-2925
2295 atoms, 2562 bonds, 43 pseudobonds, 108 residues, 3 models selected
> select clear
> select #1/1:2820
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel red
> select #1/1:2922
23 atoms, 25 bonds, 1 residue, 1 model selected
> select #1/1:2922
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel red
> select #1/q:510
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/q:510-511
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> color (#!1 & sel) #b5ffcdff
> color (#!1 & sel) #a7ffe4ff
> color (#!1 & sel) #76ffb2ff
> color (#!1 & sel) #56ff7dff
> color (#!1 & sel) #6dffa9ff
> color (#!1 & sel) #4dccffff
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
> color (#!1 & sel) #6fffb0ff
> color (#!1 & sel) #3aff92ff
> select clear
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/q:550
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/q:550
4 atoms, 3 bonds, 1 residue, 1 model selected
> color (#!1 & sel) white
> undo
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/q:550
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/q:550
4 atoms, 3 bonds, 1 residue, 1 model selected
> color (#!1 & sel) white
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/q:227-228
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #1/q:227
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!1 & sel) white
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
Alignment identifier is 1/J
> select #1/J:196-197
16 atoms, 15 bonds, 2 residues, 1 model selected
> color (#!1 & sel) white
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
> select #1/J:340
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/J:340
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) white
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/q:550
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/q:550
4 atoms, 3 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select clear
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/q:227
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/q:227
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
> select #1/J:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/J:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
> select #1/J:340
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/J:340
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/n
3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected
> color (#!1 & sel) #62ffb0ff
> color (#!1 & sel) #acff7eff
> color (#!1 & sel) #c3ffadff
> select clear
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> color (#!1 & sel) dark gray
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
> color (#!1 & sel) dark gray
> select #1/D
1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected
> color (#!1 & sel) dark gray
> select #1/w
3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected
> color (#!1 & sel) dim gray
> color (#!1 & sel) gray
> select #1/o
1107 atoms, 1129 bonds, 133 residues, 1 model selected
> color (#!1 & sel) dark gray
> select #1/n
3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected
> color (#!1 & sel) gray
> select #1/W
1870 atoms, 1902 bonds, 232 residues, 1 model selected
> show sel surfaces
> color sel gray
> select #1/l
1377 atoms, 1408 bonds, 174 residues, 1 model selected
> show sel surfaces
> select clear
> select #1/r
1438 atoms, 1462 bonds, 2 pseudobonds, 176 residues, 2 models selected
> select #1/t
2328 atoms, 2355 bonds, 1 pseudobond, 290 residues, 2 models selected
> select #1/u
976 atoms, 996 bonds, 116 residues, 1 model selected
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
> select #1/J:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/J:196-197
16 atoms, 15 bonds, 2 residues, 1 model selected
> color (#!1 & sel) red
> select #1/1:2858
20 atoms, 21 bonds, 1 residue, 1 model selected
> select #1/1:2855-2858
83 atoms, 91 bonds, 4 residues, 1 model selected
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs-grey.cxs"
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> preset "overall look" interactive
Using preset: Overall Look / Interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
lighting depthCue t
> set bgColor gray
> set bgColor white
> set bgColor black
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: 1.6rc202304252053 (2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Feb 23 15:56:32 2024UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Tue Jan 30 16:17:55 2024UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Nov 3 09:32:22 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Oct 20 15:54:08 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Oct 20 15:24:47 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Oct 20 15:08:11 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/state E IDRs.cxs"
Log from Fri Oct 20 14:52:35 2023UCSF ChimeraX version: 1.6rc202304252053
(2023-04-25)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/stefhed/Library/Mobile
> Documents/com~apple~CloudDocs/Downloads/6elz 2.cif"
6elz 2.cif title:
State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar
pre-60S ribosomes [more info...]
Chain information for 6elz 2.cif #1
---
Chain | Description | UniProt
1 | 25S ribosomal RNA |
2 | 5.8S ribosomal RNA |
6 | Internal transcribed spacer 2 |
A | Ribosome biogenesis protein BRX1 | BRX1_YEAST 1-291
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | ATP-dependent RNA helicase HAS1 | HAS1_YEAST 1-505
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
I | Nucleolar complex-associated protein 3 | NOC3_YEAST 1-663
J | rRNA-processing protein EBP2 | EBP2_YEAST 1-427
K | Proteasome-interacting protein CIC1 | CIC1_YEAST 1-376
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosome subunit biogenesis protein NIP7 | NIP7_YEAST 1-181
m | Ribosome biogenesis protein ERB1 | ERB1_YEAST 1-807
n | Pescadillo homolog | PESC_YEAS7 1-605
o | Ribosome biogenesis protein 15 | NOP15_YEAST 1-220
p | Ribosome biogenesis protein YTM1 | YTM1_YEAS7 1-460
q | 25S rRNA (cytosine(2870)-C(5))-methyltransferase | NOP2_YEAST 1-618
r | Ribosome biogenesis protein NSA2 | NSA2_YEAS7 1-261
s | Nuclear GTP-binding protein NUG1 | NUG1_YEAST 1-520
t | Ribosome biogenesis protein RLP7 | RLP7_YEAST 1-322
u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v | Nucleolar protein 16 | NOP16_YEAST 1-231
w | 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase | SPB1_YEAST 1-841
y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
z | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 6elz 2.cif #1
---
ZN — zinc ion
> select all
134887 atoms, 143091 bonds, 2452 pseudobonds, 12372 residues, 4 models
selected
> hide sel
> show nucleic
> hide sel surfaces
> show sel cartoons
> hide sel surfaces
> hide surfaces
> select all
134887 atoms, 143091 bonds, 2452 pseudobonds, 12372 residues, 4 models
selected
> hide all
> select clear
> select #1:I, y, s, K, W, A, r, u, t, p, z
29269 atoms, 32087 bonds, 715 pseudobonds, 1392 residues, 3 models selected
> hide sel
> hide sel cartoons
> hide sel surfaces
> select #1:K
Nothing selected
> select #1/K
2073 atoms, 2107 bonds, 1 pseudobond, 257 residues, 2 models selected
> hide sel
> hide sel cartoons
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> hide sel cartoons
> select #1/y, s, K, W, A, r, u, t, p, z
15075 atoms, 15315 bonds, 10 pseudobonds, 1883 residues, 2 models selected
> hide sel cartoons
> select nucleic
57318 atoms, 64137 bonds, 2412 pseudobonds, 2680 residues, 3 models selected
> show sel cartoons
> ladder nucleotides
Unknown command: ladder nucleotides
> show nucleotides ladder
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> nucleotides sel ladder
[Repeated 2 time(s)]
> select #1/A-Z
38689 atoms, 39375 bonds, 15 pseudobonds, 4848 residues, 2 models selected
> hide sel
> hide sel cartoons
> select #1/a, c-k
7802 atoms, 7921 bonds, 4 pseudobonds, 981 residues, 2 models selected
> hide sel cartoons
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
> show sel surfaces
> hide sel cartoons
> color sel yellow
> select #1/D
1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected
> select #1/D
1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> color sel red
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
> hide sel cartoons
> show sel surfaces
> select #1/o
1107 atoms, 1129 bonds, 133 residues, 1 model selected
> hide sel cartoons
> show sel surfaces
> color sel blue
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> hide sel surfaces
> hide sel cartoons
> show sel surfaces
> color sel light green
> select #1/w
3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> color sel orange
> select clear
> select #1/b
3410 atoms, 3474 bonds, 3 pseudobonds, 421 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> color sel light blue
> select clear
> select #1/n
3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected
> hide sel cartoons
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
> hide sel cartoons
> show sel surfaces
> select clear
> select #1/:42-635
Expected an objects specifier or a keyword
> select #1/1:42-635
11543 atoms, 12934 bonds, 447 pseudobonds, 537 residues, 3 models selected
> color sel lightblue red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel red
> color sel lightred
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel lightblue red
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> select #1/1:662-1435
14182 atoms, 15879 bonds, 569 pseudobonds, 661 residues, 3 models selected
> color sel orange
> select #1/1:1452-1878
8891 atoms, 9946 bonds, 390 pseudobonds, 416 residues, 3 models selected
> color sel yellow
> select up
52595 atoms, 58864 bonds, 390 pseudobonds, 2457 residues, 3 models selected
> select up
134887 atoms, 143091 bonds, 2448 pseudobonds, 12372 residues, 3 models
selected
> select #1/1:1911-2332
902 atoms, 1007 bonds, 48 pseudobonds, 42 residues, 3 models selected
> color sel light green
> color sel forest green
> select #1/1:2400-2980
4471 atoms, 4995 bonds, 172 pseudobonds, 210 residues, 3 models selected
> color sel medium blue
> select #1/1:2995-3396
8560 atoms, 9569 bonds, 344 pseudobonds, 402 residues, 2 models selected
> color sel lightblue purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel purple
> color medium purple
> color sel medium purple
> select #1/2
3353 atoms, 3746 bonds, 83 pseudobonds, 158 residues, 2 models selected
> color sel pink
> color sel hot pink
> select clear
> sequence chain #1/D
Alignment identifier is 1/D
> select #1/D
1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select /I:132-601
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select /I:132-601
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> sequence chain #1/I
Alignment identifier is 1/I
> select /I:132-133
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /I:132-133
18 atoms, 17 bonds, 2 residues, 1 model selected
> color sel white
> select clear
Alignment identifier is 1/1
Alignment identifier is 1/2
Alignment identifier is 1/6
Alignment identifier is 1/L
Alignment identifier is 1/N
Alignment identifier is 1/Q
Alignment identifier is 1/R
Alignment identifier is 1/S
Alignment identifier is 1/T
Alignment identifier is 1/U
Alignment identifier is 1/Z
Alignment identifier is 1/c
Alignment identifier is 1/d
Alignment identifier is 1/e
Alignment identifier is 1/f
Alignment identifier is 1/g
Alignment identifier is 1/i
Alignment identifier is 1/j
Alignment identifier is 1/k
Alignment identifier is 1/O
Alignment identifier is 1/V
Alignment identifier is 1/a
Alignment identifier is 1/P
Alignment identifier is 1/X
Alignment identifier is 1/Y
Alignment identifier is 1/h
Alignment identifier is 1/F
Alignment identifier is 1/B
Alignment identifier is 1/C
Alignment identifier is 1/H
Alignment identifier is 1/A
Alignment identifier is 1/K
Alignment identifier is 1/m
Alignment identifier is 1/D
Alignment identifier is 1/W
Alignment identifier is 1/l
Alignment identifier is 1/b
Alignment identifier is 1/o
Alignment identifier is 1/n
Alignment identifier is 1/r
Alignment identifier is 1/s
Alignment identifier is 1/t
Alignment identifier is 1/y
Alignment identifier is 1/z
Alignment identifier is 1/p
Alignment identifier is 1/q
Alignment identifier is 1/u
Alignment identifier is 1/v
Alignment identifier is 1/w
Destroying pre-existing alignment with identifier 1/I
Alignment identifier is 1/I
Alignment identifier is 1/J
Alignment identifier is 1/E
Alignment identifier is 1/G
Alignment identifier is 1/M
Window position QRect(2176,1854 100x30) outside any known screen, using
primary screen
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
Alignment identifier is 1/J
> select /J:196
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /J:196-197
16 atoms, 15 bonds, 2 residues, 1 model selected
> color sel white
> select #1/J
1215 atoms, 1232 bonds, 145 residues, 1 model selected
> select /J:339
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /J:339-340
14 atoms, 13 bonds, 2 residues, 1 model selected
> color sel white
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
Alignment identifier is 1/m
> select /m:125
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /m:125-126
18 atoms, 18 bonds, 2 residues, 1 model selected
> color sel white
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
> select #1/o
1107 atoms, 1129 bonds, 133 residues, 1 model selected
Alignment identifier is 1/o
> select /o:88-89
21 atoms, 21 bonds, 2 residues, 1 model selected
> select /o:88-89
21 atoms, 21 bonds, 2 residues, 1 model selected
> color sel white
> select #1/o
1107 atoms, 1129 bonds, 133 residues, 1 model selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
Alignment identifier is 1/q
> select /q:227
12 atoms, 12 bonds, 1 residue, 1 model selected
> select /q:227-229
27 atoms, 27 bonds, 3 residues, 1 model selected
> color sel white
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select /q:549
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /q:549-550
12 atoms, 11 bonds, 2 residues, 1 model selected
> color sel white
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
Alignment identifier is 1/v
> select /v:65
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /v:65-66
13 atoms, 12 bonds, 2 residues, 1 model selected
> color sel white
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
> select /v:155
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /v:155-156
16 atoms, 15 bonds, 2 residues, 1 model selected
> color sel white
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
> select #1/w
3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected
Alignment identifier is 1/w
> select /w:328
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /w:328-329
16 atoms, 15 bonds, 2 residues, 1 model selected
> color sel white
> select #1/w
3511 atoms, 3571 bonds, 4 pseudobonds, 436 residues, 2 models selected
> select /w:639-640
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /w:639-640
15 atoms, 14 bonds, 2 residues, 1 model selected
> color sel white
> select clear
> ui mousemode right "move markers"
[Repeated 1 time(s)]
> lighting soft
> lighting simple
[Repeated 1 time(s)]
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> set bgColor gray
> set bgColor black
> set bgColor white
> set bgColor black
> select clear
> ui tool show "Side View"
> view orient
> ui mousemode right "mark maximum"
> ui mousemode right "mark plane"
> ui mousemode right "mark surface"
> ui mousemode right "mark center"
> ui mousemode right "mark point"
> ui mousemode right "link markers"
> ui mousemode right "move markers"
> ui mousemode right "resize markers"
> select /D:267-481
1590 atoms, 1626 bonds, 2 pseudobonds, 194 residues, 2 models selected
Alignment identifier is 1/D
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> lighting soft
> select clear
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
Alignment identifier is 1/I
> select #1/v
1087 atoms, 1100 bonds, 2 pseudobonds, 130 residues, 2 models selected
Alignment identifier is 1/v
> select /v:3
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /v:3-45
352 atoms, 355 bonds, 43 residues, 1 model selected
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Oct 20 14:52:35 2023 ———
opened ChimeraX session
> lighting simple
> lighting soft
> lighting full
> lighting soft
> select /L
998 atoms, 1017 bonds, 122 residues, 1 model selected
> open "/Users/stefhed/Library/CloudStorage/OneDrive-Personal/Woolford
> Lab/Structures-chimera stuff/3jct-nog2state1.cif"
3jct-nog2state1.cif title:
Cryo-em structure of eukaryotic pre-60S ribosomal subunits [more info...]
Chain information for 3jct-nog2state1.cif #2
---
Chain | Description | UniProt
1 | RDN25-1 rRNA |
2 | RDN58-1 rRNA |
3 | RDN5-2 rRNA |
4 | Probable metalloprotease ARX1 | Q03862 1-593
5 | rRNA-processing protein CGR1 | P53188 1-120
6 | ITS2-1 miscRNA |
A | 60S ribosomal protein L2-A | RL2A_YEAST 1-254
B | 60S ribosomal protein L3 | RL3_YEAST 1-387
C | 60S ribosomal protein L4-A | RL4A_YEAST 1-362
D | 60S ribosomal protein L5 | RL5_YEAST 1-297
E | 60S ribosomal protein L6-A | RL6A_YEAST 1-176
F | 60S ribosomal protein L7-A | RL7A_YEAST 1-244
G | 60S ribosomal protein L8-A | RL8A_YEAST 1-256
H | 60S ribosomal protein L9-A | RL9A_YEAST 1-191
I | Bud site selection protein 20 | BUD20_YEAST 1-166
J | 60S ribosomal protein L11-A | RL11A_YEAST 1-174
K | Proteasome-interacting protein CIC1 | CIC1_YEAST 1-376
L | 60S ribosomal protein L13-A | RL13A_YEAST 1-199
M | 60S ribosomal protein L14-A | RL14A_YEAST 1-138
N | 60S ribosomal protein L15-A | RL15A_YEAST 1-204
O | 60S ribosomal protein L16-A | RL16A_YEAST 1-199
P | 60S ribosomal protein L17-A | RL17A_YEAST 1-184
Q | 60S ribosomal protein L18-A | RL18A_YEAST 1-186
R | 60S ribosomal protein L19-A | RL19A_YEAST 1-189
S | 60S ribosomal protein L20-A | RL20A_YEAST 1-172
T | 60S ribosomal protein L21-A | RL21A_YEAST 1-160
U | 60S ribosomal protein L22-A | RL22A_YEAST 1-121
V | 60S ribosomal protein L23-A | RL23A_YEAST 1-137
W | Ribosome assembly factor MRT4 | MRT4_YEAST 1-236
X | 60S ribosomal protein L25 | RL25_YEAST 1-142
Y | 60S ribosomal protein L26-A | RL26A_YEAST 1-127
Z | 60S ribosomal protein L27-A | RL27A_YEAST 1-136
a | 60S ribosomal protein L28 | RL28_YEAST 1-149
b | Nucleolar GTP-binding protein 1 | NOG1_YEAST 1-647
c | 60S ribosomal protein L30 | RL30_YEAST 1-105
d | 60S ribosomal protein L31-A | RL31A_YEAST 1-113
e | 60S ribosomal protein L32 | RL32_YEAST 1-130
f | 60S ribosomal protein L33-A | RL33A_YEAST 1-107
g | 60S ribosomal protein L34-A | RL34A_YEAST 1-121
h | 60S ribosomal protein L35-A | RL35A_YEAST 1-120
i | 60S ribosomal protein L36-A | RL36A_YEAST 1-100
j | 60S ribosomal protein L37-A | RL37A_YEAST 1-88
k | 60S ribosomal protein L38 | RL38_YEAST 1-78
l | 60S ribosomal protein L39 | RL39_YEAST 1-51
m | Nucleolar GTP-binding protein 2 | NOG2_YEAST 1-486
n | Pescadillo homolog | PESC_YEAST 1-605
o | Ribosome biogenesis protein 15 | NOP15_YEAST 1-220
p | 60S ribosomal protein L43-A | RL43A_YEAST 1-92
q | Ribosome biogenesis protein NOP53 | NOP53_YEAST 1-455
r | Ribosome biogenesis protein NSA2 | NSA2_YEAST 1-261
s | Nuclear GTP-binding protein NUG1 | NUG1_YEAST 1-520
t | Ribosome biogenesis protein RLP7 | RLP7_YEAST 1-322
u | Ribosome biogenesis protein RLP24 | RLP24_YEAST 1-199
v | Ribosome biogenesis protein RPF2 | RPF2_YEAST 1-344
w | Regulator of ribosome biosynthesis | RRS1_YEAST 1-203
x | Ribosome assembly protein 4 | NLE1_YEAST 1-515
y | Eukaryotic translation initiation factor 6 | IF6_YEAST 1-245
z | UPF0642 protein YBL028C | YBC8_YEAST 1-106
Non-standard residues in 3jct-nog2state1.cif #2
---
GTP — guanosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> hide all
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Oct 20 15:08:11 2023 ———
opened ChimeraX session
> select #1/A
1623 atoms, 1663 bonds, 2 pseudobonds, 198 residues, 2 models selected
> show sel surfaces
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
Alignment identifier is 1/m
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Oct 20 15:24:47 2023 ———
opened ChimeraX session
> select #1/m:156
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/m:156-169
105 atoms, 107 bonds, 14 residues, 1 model selected
> select #1/m:125
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/m:125-155
246 atoms, 250 bonds, 31 residues, 1 model selected
> color sel lightblue orange
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color (#!1 & sel) #fff125ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffd00bff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffb80cff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffdc10ff
[Repeated 1 time(s)]
> color (#!1 & sel) #fff612ff
> color (#!1 & sel) #fff613ff
> color (#!1 & sel) #ffdd16ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffd617ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffcf13ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffbc13ff
[Repeated 1 time(s)]
> color (#!1 & sel) #ffa50aff
> select clear
> select #1/m:125
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/m:125-155
246 atoms, 250 bonds, 31 residues, 1 model selected
> color (#!1 & sel) #ffb51dff
> color (#!1 & sel) #ffbf40ff
> color (#!1 & sel) #ffd8aeff
> color (#!1 & sel) #ffdbb2ff
> color (#!1 & sel) #ffe0b5ff
> color (#!1 & sel) #ffe5bbff
> color (#!1 & sel) #fff2c7ff
> color (#!1 & sel) #ffe2b1ff
> select clear
> select #1/m
5223 atoms, 5356 bonds, 1 pseudobond, 645 residues, 2 models selected
> select #1/m:125
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/m:125-126
18 atoms, 18 bonds, 2 residues, 1 model selected
> color sel white
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Oct 20 15:54:08 2023 ———
opened ChimeraX session
> select #1/n
3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected
> show sel surfaces
Alignment identifier is 1/n
> select clear
> color sel red
[Repeated 1 time(s)]
> select #1/n
3369 atoms, 3441 bonds, 3 pseudobonds, 411 residues, 2 models selected
> select #1/n:594
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1/n:591-594
31 atoms, 30 bonds, 4 residues, 1 model selected
> color sel red
> select clear
> select #1/u
976 atoms, 996 bonds, 116 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select #1/l
1377 atoms, 1408 bonds, 174 residues, 1 model selected
> hide sel
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
Alignment identifier is 1/I
> select clear
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Nov 3 09:32:22 2023 ———
opened ChimeraX session
> hide #!2 models
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
Alignment identifier is 1/q
> color (#!1 & sel) red
> undo
> color (#!1 & sel) red
> undo
> select #1/I:562,564,599,605
27 atoms, 25 bonds, 3 residues, 1 model selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/w:562,564,599,605
Nothing selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select clear
> select #1/q:562,564,599,605
Nothing selected
> color #1 red
> undo
> select clear
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select clear
> select #1/q:562,564,599,605
Nothing selected
> select #1/q :562,564,599,605
Nothing selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select clear
> select #1/q: 562, 564, 599, 605
Nothing selected
> select #1/ q:562, 564, 599, 605
Nothing selected
> select #1/ q: 562, 564, 599, 605
Nothing selected
> select #1/q: 562, 564, 599, 605
Nothing selected
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select clear
> color #1 red
> undo
> select #1/q
2485 atoms, 2536 bonds, 1 pseudobond, 317 residues, 2 models selected
> select #1/q: 388, 392, 449, 482, 510
39 atoms, 35 bonds, 5 residues, 1 model selected
> color (#!1 & sel) red
> select clear
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Tue Jan 30 16:17:55 2024 ———
opened ChimeraX session
> select #1/I
3470 atoms, 3516 bonds, 5 pseudobonds, 433 residues, 2 models selected
> select #1/l
1377 atoms, 1408 bonds, 174 residues, 1 model selected
Alignment identifier is 1/l
> select #1/G
1438 atoms, 1463 bonds, 1 pseudobond, 184 residues, 2 models selected
> show sel cartoons
> select #1/P
1442 atoms, 1465 bonds, 183 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/s
301 atoms, 301 bonds, 36 residues, 1 model selected
> show sel cartoons
> select #1/W
1870 atoms, 1902 bonds, 232 residues, 1 model selected
> show sel cartoons
> select clear
> select #1/z
444 atoms, 445 bonds, 55 residues, 1 model selected
> show sel cartoons
> select #1/r
1438 atoms, 1462 bonds, 2 pseudobonds, 176 residues, 2 models selected
> show sel cartoons
> select #1/u
976 atoms, 996 bonds, 116 residues, 1 model selected
> show sel cartoons
> save "/Users/stefhed/OneDrive/Woolford Lab/Structures-chimera stuff/state E
> IDRs.cxs"
——— End of log from Fri Feb 23 15:56:32 2024 ———
opened ChimeraX session
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple
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 Air
Model Identifier: Mac14,2
Model Number: FLY33LL/A
Chip: Apple M2
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 8422.121.1
OS Loader Version: 8422.121.1
Software:
System Software Overview:
System Version: macOS 13.4 (22F66)
Kernel Version: Darwin 22.5.0
Time since boot: 28 days, 15 hours, 25 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL SE2422HX:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
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: 2.2.4
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-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: 1.6rc202304252053
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-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: 3.3.0
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 , 18 months 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 , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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