![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 22 months ago
Closed 22 months ago
#10418 closed defect (can't reproduce)
Crash destroying MatchMaker tool
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | UI | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000002b5013000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001da941000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2301 in destroy
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 2165 in _destroy
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 772 in remove_tool
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 335 in remove_tool
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/tools.py", line 154 in delete
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/match_maker/tool.py", line 290 in run_matchmaker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2024-01-02 13:35:19.00 +0100","app_version":"1.5.0","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.2.1 (23C71)","roots_installed":0,"name":"ChimeraX","incident_id":"69AF9990-78AF-4398-A1D0-3606852ACB6C"}
{
"uptime" : 75000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 2128,
"osVersion" : {
"train" : "macOS 14.2.1",
"build" : "23C71",
"releaseType" : "User"
},
"captureTime" : "2024-01-02 13:35:10.8870 +0100",
"codeSigningMonitor" : 1,
"incident" : "69AF9990-78AF-4398-A1D0-3606852ACB6C",
"pid" : 77186,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-01-02 12:56:46.4599 +0100",
"procStartAbsTime" : 1749228209300,
"procExitAbsTime" : 1804532264902,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F5CF2187-F084-5AEB-837A-865CE26F5F69","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "4867AB37-3462-B712-10CF-B05185E4905D",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 16077,
"sleepWakeUUID" : "0B8FC89A-B9A5-4DB3-907D-4B68D3840381",
"sip" : "enabled",
"vmRegionInfo" : "0x1e6d0a02ef68 is not in any region. Bytes after previous region: 32972631895913 Bytes before following region: 72099448033432\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00009e6d0a02ef68","rawCodes":[1,174191156588392],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00009e6d0a02ef68 -> 0x00001e6d0a02ef68 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":77186},
"vmregioninfo" : "0x1e6d0a02ef68 is not in any region. Bytes after previous region: 32972631895913 Bytes before following region: 72099448033432\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL ...(unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
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"name" : "_heapq.cpython-39-darwin.so"
},
{
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"arch" : "arm64",
"base" : 4354244608,
"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2555904,
"uuid" : "5ee765c2-b52f-3980-9781-73db1abd2bde",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.11"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 4342120448,
"CFBundleShortVersionString" : "1.5.0",
"CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
"size" : 16384,
"uuid" : "a5992708-d5b4-36ec-ac0a-e525f6105b56",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"name" : "ChimeraX",
"CFBundleVersion" : "1.5.0.0"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6510739456,
"size" : 241664,
"uuid" : "ca94fc21-bc40-3b43-b65d-b87ece9e1d48",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6510981120,
"size" : 53236,
"uuid" : "a7d94c96-7b1f-3229-9bea-048d037c3292",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6509522944,
"size" : 520188,
"uuid" : "ab8a0a0b-9a1e-3284-9243-5a0334468ae5",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6511190016,
"size" : 28668,
"uuid" : "e1840daa-9c10-393d-a3a3-94dde6fe0011",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6511403008,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5079040,
"uuid" : "47e4ec09-8f6e-30a8-99d0-34024d4f8122",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2202"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6685442048,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2883584,
"uuid" : "e2187dfe-1fb4-3b47-874e-a0a6291e51b2",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6570250240,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 20033536,
"uuid" : "f3527312-e426-3f7c-b77b-2bf49d1b7c04",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.30.108"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6507311104,
"size" : 607048,
"uuid" : "324e4ad9-e01f-3183-b09f-3e20b326643a",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
}
],
"sharedCache" : {
"base" : 6506561536,
"size" : 4061216768,
"uuid" : "f9ddd844-7f3f-34bd-be29-f0c72d5e5449"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=8.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=8.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG image 1008K 47 \nColorSync 608K 30 \nCoreAnimation 4624K 256 \nCoreGraphics 80K 5 \nCoreUI image data 5408K 38 \nFoundation 32K 2 \nKernel Alloc Once 32K 1 \nMALLOC 7.3G 130 \nMALLOC guard page 384K 24 \nMach message 64K 2 \nOpenGL GLSL 256K 3 \nSTACK GUARD 56.5M 34 \nStack 168.2M 34 \nVM_ALLOCATE 612.9M 1421 \nVM_ALLOCATE (reserved) 160.0M 3 reserved VM address space (unallocated)\n__AUTH 3030K 432 \n__AUTH_CONST 34.3M 662 \n__CTF 824 1 \n__DATA 24.9M 815 \n__DATA_CONST 43.8M 826 \n__DATA_DIRTY 2027K 238 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 923.4M 159 \n__OBJC_RO 71.1M 1 \n__OBJC_RW 2168K 1 \n__TEXT 977.9M 843 \ndyld private memory 432K 4 \nmapped file 605.1M 91 \nshared memory 3136K 24 \n=========== ======= ======= \nTOTAL 10.9G 6136 \nTOTAL, minus reserved VM space 10.8G 6136 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "55288b1e4228c9f55a4353282e8677e37bddb745",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
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"SIRI_UNDERSTANDING_ASR_ASSISTANT" : "654b1d0e1c6fd434e20893b7",
"SIRI_UNDERSTANDING_NL" : "6570e25de4d5b2524442a0c1",
"SIRI_UNDERSTANDING_MORPHUN" : "64e5135c4e666d798a8ffc38"
},
"deploymentId" : 240000531
},
{
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"factorPackIds" : {
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},
"deploymentId" : 240000001
}
],
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"
Log from Mon Jan 1 16:54:24 2024UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"
Log from Mon Jan 1 11:44:25 2024UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"
Log from Mon Jan 1 11:35:17 2024UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 6msj
6msj title:
Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome
[more info...]
Chain information for 6msj #1
---
Chain | Description | UniProt
A | 26S proteasome regulatory subunit 7 | PRS7_HUMAN
B | Rpt2, NP_002793.2 (26SHA chain B) | PRS4_HUMAN
C | 26S proteasome regulatory subunit 8 | PRS8_HUMAN
D | 26S proteasome regulatory subunit 6B | PRS6B_HUMAN
E | 26S proteasome regulatory subunit 10B | A0A087X2I1_HUMAN
F | 26S proteasome regulatory subunit 6A | PRS6A_HUMAN
G | Proteasome subunit alpha type-6 | PSA6_HUMAN
H h | Proteasome subunit alpha type-2 | PSA2_HUMAN
I i | Proteasome subunit alpha type-4 | PSA4_HUMAN
J j | Proteasome subunit alpha type-7 | PSA7_HUMAN
K k | Proteasome subunit alpha type-5 | PSA5_HUMAN
L l | Proteasome subunit alpha type-1 | PSA1_HUMAN
M m | Proteasome subunit alpha type-3 | PSA3_HUMAN
N n | Proteasome subunit beta type-6 | PSB6_HUMAN
O o | Proteasome subunit beta type-7 | PSB7_HUMAN
P p | Proteasome subunit beta type-3 | PSB3_HUMAN
Q q | Proteasome subunit beta type-2 | PSB2_HUMAN
R r | Proteasome subunit beta type-5 | PSB5_HUMAN
S s | Proteasome subunit beta type-1 | PSB1_HUMAN
T t | Proteasome subunit beta type-4 | PSB4_HUMAN
U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN
V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN
W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN
X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN
Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN
Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN
a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN
b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN
c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN
d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN
e | 26S proteasome complex subunit SEM1 | SEM1_HUMAN
f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN
g | Proteasome subunit alpha type-6 | PSA6_HUMAN
v | substrate |
Non-standard residues in 6msj #1
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> hide atoms
> show cartoons
> set bgColor white
> lighting soft
> 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
> split #1
Split 6msj (#1) into 47 models
Chain information for 6msj A #1.1
---
Chain | Description
A | No description available
Chain information for 6msj B #1.2
---
Chain | Description
B | No description available
Chain information for 6msj C #1.3
---
Chain | Description
C | No description available
Chain information for 6msj D #1.4
---
Chain | Description
D | No description available
Chain information for 6msj E #1.5
---
Chain | Description
E | No description available
Chain information for 6msj F #1.6
---
Chain | Description
F | No description available
Chain information for 6msj G #1.7
---
Chain | Description
G | No description available
Chain information for 6msj H #1.8
---
Chain | Description
H | No description available
Chain information for 6msj I #1.9
---
Chain | Description
I | No description available
Chain information for 6msj J #1.10
---
Chain | Description
J | No description available
Chain information for 6msj K #1.11
---
Chain | Description
K | No description available
Chain information for 6msj L #1.12
---
Chain | Description
L | No description available
Chain information for 6msj M #1.13
---
Chain | Description
M | No description available
Chain information for 6msj N #1.14
---
Chain | Description
N | No description available
Chain information for 6msj O #1.15
---
Chain | Description
O | No description available
Chain information for 6msj P #1.16
---
Chain | Description
P | No description available
Chain information for 6msj Q #1.17
---
Chain | Description
Q | No description available
Chain information for 6msj R #1.18
---
Chain | Description
R | No description available
Chain information for 6msj S #1.19
---
Chain | Description
S | No description available
Chain information for 6msj T #1.20
---
Chain | Description
T | No description available
Chain information for 6msj U #1.21
---
Chain | Description
U | No description available
Chain information for 6msj V #1.22
---
Chain | Description
V | No description available
Chain information for 6msj W #1.23
---
Chain | Description
W | No description available
Chain information for 6msj X #1.24
---
Chain | Description
X | No description available
Chain information for 6msj Y #1.25
---
Chain | Description
Y | No description available
Chain information for 6msj Z #1.26
---
Chain | Description
Z | No description available
Chain information for 6msj a #1.27
---
Chain | Description
a | No description available
Chain information for 6msj b #1.28
---
Chain | Description
b | No description available
Chain information for 6msj c #1.29
---
Chain | Description
c | No description available
Chain information for 6msj d #1.30
---
Chain | Description
d | No description available
Chain information for 6msj e #1.31
---
Chain | Description
e | No description available
Chain information for 6msj f #1.32
---
Chain | Description
f | No description available
Chain information for 6msj g #1.33
---
Chain | Description
g | No description available
Chain information for 6msj h #1.34
---
Chain | Description
h | No description available
Chain information for 6msj i #1.35
---
Chain | Description
i | No description available
Chain information for 6msj j #1.36
---
Chain | Description
j | No description available
Chain information for 6msj k #1.37
---
Chain | Description
k | No description available
Chain information for 6msj l #1.38
---
Chain | Description
l | No description available
Chain information for 6msj m #1.39
---
Chain | Description
m | No description available
Chain information for 6msj n #1.40
---
Chain | Description
n | No description available
Chain information for 6msj o #1.41
---
Chain | Description
o | No description available
Chain information for 6msj p #1.42
---
Chain | Description
p | No description available
Chain information for 6msj q #1.43
---
Chain | Description
q | No description available
Chain information for 6msj r #1.44
---
Chain | Description
r | No description available
Chain information for 6msj s #1.45
---
Chain | Description
s | No description available
Chain information for 6msj t #1.46
---
Chain | Description
t | No description available
Chain information for 6msj v #1.47
---
Chain | Description
v | No description available
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #1.5 models
> hide #!1.6 models
> hide #1.7 models
> hide #1.8 models
> hide #1.9 models
> show #1.8 models
> show #1.9 models
> show #1.7 models
> hide #1.32 models
> hide #1.33 models
> show #1.33 models
> hide #1.23 models
> hide #1.24 models
> hide #1.25 models
> ui mousemode right "translate selected models"
Drag select of 2193 residues
> hide #!1.21 models
> hide #1.22 models
> hide #1.26 models
> hide #1.27 models
> hide #1.28 models
> hide #!1.29 models
> hide #1.30 models
> hide #!1.31 models
> select add #1.15
19040 atoms, 1670 bonds, 2413 residues, 10 models selected
> select subtract #1.15
17397 atoms, 2193 residues, 9 models selected
> select add #1
105316 atoms, 107125 bonds, 18 pseudobonds, 13534 residues, 58 models selected
> select subtract #1
Nothing selected
> show #!1.1 models
> show #!1.2 models
> hide #1.47 models
> show #1.47 models
> hide #1.47 models
> show #1.47 models
> hide #1.47 models
> hide #!1.1 models
> hide #!1.2 models
> show #1.47 models
> hide #1.47 models
> show #1.47 models
> hide #1.47 models
> show #!1.1 models
> select add #1.1
3261 atoms, 3317 bonds, 3 pseudobonds, 415 residues, 2 models selected
Alignment identifier is 1.1/A
> select #1.1/A:431
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1.1/A:431-433
27 atoms, 27 bonds, 3 residues, 1 model selected
> select add #1.1
3261 atoms, 3317 bonds, 3 pseudobonds, 415 residues, 2 models selected
> select subtract #1.1
Nothing selected
> hide #!1.1 models
> show #!1.2 models
Destroying pre-existing alignment with identifier 1.1/A
Alignment identifier is 1.1/A
Alignment identifier is 1.2/B
Alignment identifier is 1.3/C
Alignment identifier is 1.4/D
Alignment identifier is 1.5/E
Alignment identifier is 1.6/F
Alignment identifier is 1.7/G
Alignment identifier is 1.8/H
Alignment identifier is 1.9/I
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Alignment identifier is 11
Alignment identifier is 1.21/U
Alignment identifier is 1.22/V
Alignment identifier is 1.23/W
Alignment identifier is 1.24/X
Alignment identifier is 1.25/Y
Alignment identifier is 1.26/Z
Alignment identifier is 1.27/a
Alignment identifier is 1.28/b
Alignment identifier is 1.29/c
Alignment identifier is 1.30/d
Alignment identifier is 1.31/e
Alignment identifier is 1.32/f
Alignment identifier is 1.33/g
Alignment identifier is 1.34/h
Alignment identifier is 1.35/i
Alignment identifier is 1.47/v
> select add #1.2
3239 atoms, 3287 bonds, 2 pseudobonds, 413 residues, 2 models selected
Alignment identifier is 1.2/B
> select #1.2/B:438
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/B:438-440
28 atoms, 28 bonds, 3 residues, 1 model selected
> select #1.2/B:438
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/B:438-440
28 atoms, 28 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 28 atom styles
> color sel byhetero
> select #1.2/B:306-351
368 atoms, 370 bonds, 46 residues, 1 model selected
> select #1.2/B:307-351
359 atoms, 361 bonds, 45 residues, 1 model selected
> select add #1.2
3239 atoms, 3287 bonds, 2 pseudobonds, 413 residues, 2 models selected
> select subtract #1.2
Nothing selected
> show #!1.3 models
> select add #1.3
3137 atoms, 3179 bonds, 2 pseudobonds, 398 residues, 2 models selected
Alignment identifier is 1.3/C
> select subtract #1.3
Nothing selected
> hide #!1.3 models
> show #!1.4 models
> select add #1.4
3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected
Alignment identifier is 1.4/D
> select subtract #1.4
Nothing selected
> hide #!1.4 models
> show #!1.3 models
> select add #1.3
3137 atoms, 3179 bonds, 2 pseudobonds, 398 residues, 2 models selected
Alignment identifier is 1.3/C
> select subtract #1.3
Nothing selected
> hide #!1.3 models
> show #!1.4 models
> select add #1.4
3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected
Alignment identifier is 1.4/D
> select #1.4/D:416
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.4/D:416-418
33 atoms, 34 bonds, 3 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 33 atom styles
> color sel byhetero
> select add #1.4
3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected
> select subtract #1.4
Nothing selected
> hide #!1.4 models
> show #!1.1 models
> select add #1.1
3261 atoms, 3317 bonds, 3 pseudobonds, 415 residues, 2 models selected
Alignment identifier is 1.1/A
> select subtract #1.1
Nothing selected
> show #!1.4 models
> show #1.5 models
> select add #1.5
3124 atoms, 3174 bonds, 390 residues, 1 model selected
Alignment identifier is 1.5/E
> select subtract #1.5
Nothing selected
> hide #1.5 models
> show #!1.6 models
Alignment identifier is 1.1/A
Alignment identifier is 1.2/B
Alignment identifier is 1.3/C
Alignment identifier is 1.4/D
Alignment identifier is 1.5/E
Alignment identifier is 1.6/F
Alignment identifier is 1.7/G
Alignment identifier is 1.8/H
Alignment identifier is 1.9/I
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Alignment identifier is 11
Alignment identifier is 1.21/U
Alignment identifier is 1.22/V
Alignment identifier is 1.23/W
Alignment identifier is 1.24/X
Alignment identifier is 1.25/Y
Alignment identifier is 1.26/Z
Alignment identifier is 1.27/a
Alignment identifier is 1.28/b
Alignment identifier is 1.29/c
Alignment identifier is 1.30/d
Alignment identifier is 1.31/e
Alignment identifier is 1.32/f
Alignment identifier is 1.33/g
Alignment identifier is 1.34/h
Alignment identifier is 1.35/i
Alignment identifier is 1.47/v
> select add #1.4
3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected
Alignment identifier is 1.4/D
> select #1.4/D:416
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #1.4/D:416-418
33 atoms, 34 bonds, 3 residues, 1 model selected
> select add #1.4
3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected
> select subtract #1.4
Nothing selected
> hide #!1.4 models
> show #!1.4 models
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1.2 models
> show #!1.2 models
> show #1.5 models
> select add #1.5
3124 atoms, 3174 bonds, 390 residues, 1 model selected
Alignment identifier is 1.5/E
> select subtract #1.5
Nothing selected
> hide #1.5 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.6 models
> show #!1.6 models
> select add #1.6
3098 atoms, 3137 bonds, 1 pseudobond, 395 residues, 2 models selected
Alignment identifier is 1.6/F
> select subtract #1.6
Nothing selected
> hide #!1.6 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.6 models
> hide #!1.6 models
> show #!1.21 models
> hide #!1.21 models
> show #1.22 models
> hide #1.22 models
> show #1.23 models
> hide #1.23 models
> show #1.23 models
> hide #1.23 models
> show #1.24 models
> hide #1.24 models
> show #1.25 models
> hide #1.25 models
> show #1.26 models
> hide #1.26 models
> show #1.26 models
> hide #1.26 models
> show #1.27 models
> hide #1.27 models
> show #1.28 models
> hide #1.28 models
> show #!1.29 models
> hide #!1.29 models
> show #1.30 models
> hide #1.30 models
> show #!1.31 models
> hide #!1.31 models
> show #1.32 models
> hide #1.32 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.4 models
> hide #!1.4 models
> hide #1.10 models
> show #1.10 models
> hide #1.7 models
> show #1.7 models
> hide #1.8 models
> hide #1.9 models
> show #1.9 models
> select add #1.9
1908 atoms, 1938 bonds, 248 residues, 1 model selected
Alignment identifier is 1.9/I
> select #1.9/I:4
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1.9/I
1908 atoms, 1938 bonds, 248 residues, 1 model selected
> select subtract #1.9
Nothing selected
> select add #1.10
1739 atoms, 1763 bonds, 239 residues, 1 model selected
Alignment identifier is 1.10/J
> select #1.10/J:2-3
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #1.10/J
1739 atoms, 1763 bonds, 239 residues, 1 model selected
> select #1.10/J:240
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1.10/J
1739 atoms, 1763 bonds, 239 residues, 1 model selected
> select subtract #1.10
Nothing selected
> color #1.9 white
> color #1.9 #1f92eaff
> color #1.9 #66ffffff
> color #1.9 #8fc9f5ff
> color #1.9 #66ffffff
> color #1.9 #8fc9f5ff
> hide #1.10 models
> show #1.10 models
> color #1.10 #66ffffff
> select add #1.2
3239 atoms, 3287 bonds, 2 pseudobonds, 413 residues, 2 models selected
Alignment identifier is 1.2/B
> select #1.2/B:30
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.2/B:30-440
3207 atoms, 3254 bonds, 411 residues, 1 model selected
> select add #1.2
3239 atoms, 3287 bonds, 2 pseudobonds, 413 residues, 2 models selected
> select subtract #1.2
Nothing selected
> save /Users/jiale/Desktop/image1.png supersample 3
> hide #!1.2 models
> show #!1.4 models
> show #1.8 models
> select add #1.9
1908 atoms, 1938 bonds, 248 residues, 1 model selected
> select subtract #1.9
Nothing selected
> select add #1.9
1908 atoms, 1938 bonds, 248 residues, 1 model selected
> select subtract #1.9
Nothing selected
> select add #1.8
1723 atoms, 1759 bonds, 230 residues, 1 model selected
Alignment identifier is 1.8/H
> select #1.8/H:5-6
16 atoms, 16 bonds, 2 residues, 1 model selected
> select #1.8/H
1723 atoms, 1759 bonds, 230 residues, 1 model selected
> color #1.8 #33ccffff
> color #1.7 #c7e4faff
> color #1.13 #306db1ff
> select subtract #1.8
Nothing selected
> hide #1.15 models
> hide #1.13 models
> hide #1.19 models
> show #1.19 models
> hide #1.12 models
> select add #1.4
3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected
Alignment identifier is 1.4/D
> select #1.4/D:39-40
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #1.4/D:39-418
3040 atoms, 3090 bonds, 380 residues, 1 model selected
> select add #1.4
3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected
> select subtract #1.4
Nothing selected
> save /Users/jiale/Desktop/image2.png supersample 3
> save "/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"
——— End of log from Mon Jan 1 11:35:17 2024 ———
opened ChimeraX session
> color #1.7 #ccffccff
> color #1.8 #99ff99ff
> color #1.8 #33ff33ff
> save /Users/jiale/Desktop/image1.png supersample 3
> color #1.9 #99ff99ff
> color #1.10 #66cc66ff
> hide #!1.4 models
> show #!1.2 models
> hide #1.14 models
> show #1.14 models
> hide #1.17 models
> hide #1.8 models
> color #1.10 #00cc00ff
> save /Users/jiale/Desktop/image2.png supersample 3
> save /Users/jiale/Desktop/image3.png supersample 3
> save "/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"
——— End of log from Mon Jan 1 11:44:25 2024 ———
opened ChimeraX session
> show #1.8 models
> show #1.12 models
> show #1.13 models
> show #!1.3 models
> show #!1.4 models
> show #1.5 models
> show #!1.6 models
> show #!1.1 models
> show #1.15 models
> show #1.17 models
> show #!1.21 models
> show #1.22 models
> hide #1.22 models
> show #1.22 models
> show #1.23 models
> show #1.24 models
> show #1.25 models
> show #1.26 models
> show #1.27 models
> show #!1.29 models
> show #1.28 models
> show #1.30 models
> show #!1.31 models
> show #1.32 models
> color #1.11 #006600ff
> color #1.12 #66ffffff
> select #1.6/F:436
9 atoms, 8 bonds, 1 residue, 1 model selected
> view orient
> view sel
> select clear
> select #1.6/F:436
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.6/F:437
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
92 atoms, 93 bonds, 11 residues, 1 model selected
> select down
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
92 atoms, 93 bonds, 11 residues, 1 model selected
> select down
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
92 atoms, 93 bonds, 11 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 92 atom styles
> color sel byhetero
> select clear
> ui tool show "Side View"
> select #1.12/L:10
7 atoms, 6 bonds, 1 residue, 1 model selected
> view sel
> select clear
> ui tool show "Side View"
> select #1.5/E:389
7 atoms, 6 bonds, 1 residue, 1 model selected
> view sel
> select clear
> hide #!1 models
> open 6msh
Summary of feedback from opening 6msh fetched from pdb
---
note | Fetching compressed mmCIF 6msh from
http://files.rcsb.org/download/6msh.cif
6msh title:
Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome
[more info...]
Chain information for 6msh #2
---
Chain | Description | UniProt
A | 26S proteasome regulatory subunit 7 | PRS7_HUMAN
B | 26S proteasome regulatory subunit 4 | PRS4_HUMAN
C | 26S proteasome regulatory subunit 8 | PRS8_HUMAN
D | 26S proteasome regulatory subunit 6B | PRS6B_HUMAN
E | 26S proteasome regulatory subunit 10B | A0A087X2I1_HUMAN
F | 26S proteasome regulatory subunit 6A | PRS6A_HUMAN
G g | Proteasome subunit alpha type-6 | PSA6_HUMAN
H h | Proteasome subunit alpha type-2 | PSA2_HUMAN
I i | Proteasome subunit alpha type-4 | PSA4_HUMAN
J j | Proteasome subunit alpha type-7 | PSA7_HUMAN
K k | Proteasome subunit alpha type-5 | PSA5_HUMAN
L l | Proteasome subunit alpha type-1 | PSA1_HUMAN
M m | Proteasome subunit alpha type-3 | PSA3_HUMAN
N n | Proteasome subunit beta type-6 | PSB6_HUMAN
O o | Proteasome subunit beta type-7 | PSB7_HUMAN
P p | Proteasome subunit beta type-3 | PSB3_HUMAN
Q q | Proteasome subunit beta type-2 | PSB2_HUMAN
R r | Proteasome subunit beta type-5 | PSB5_HUMAN
S s | Proteasome subunit beta type-1 | PSB1_HUMAN
T t | Proteasome subunit beta type-4 | PSB4_HUMAN
U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN
V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN
W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN
X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN
Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN
Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN
a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN
b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN
c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN
d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN
e | 26S proteasome complex subunit SEM1 | SEM1_HUMAN
f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN
v | substrate |
Non-standard residues in 6msh #2
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
ZN — zinc ion
> hide #!2 atoms
> show #!2 cartoons
> split #2
Split 6msh (#2) into 47 models
Chain information for 6msh A #2.1
---
Chain | Description
A | No description available
Chain information for 6msh B #2.2
---
Chain | Description
B | No description available
Chain information for 6msh C #2.3
---
Chain | Description
C | No description available
Chain information for 6msh D #2.4
---
Chain | Description
D | No description available
Chain information for 6msh E #2.5
---
Chain | Description
E | No description available
Chain information for 6msh F #2.6
---
Chain | Description
F | No description available
Chain information for 6msh G #2.7
---
Chain | Description
G | No description available
Chain information for 6msh H #2.8
---
Chain | Description
H | No description available
Chain information for 6msh I #2.9
---
Chain | Description
I | No description available
Chain information for 6msh J #2.10
---
Chain | Description
J | No description available
Chain information for 6msh K #2.11
---
Chain | Description
K | No description available
Chain information for 6msh L #2.12
---
Chain | Description
L | No description available
Chain information for 6msh M #2.13
---
Chain | Description
M | No description available
Chain information for 6msh N #2.14
---
Chain | Description
N | No description available
Chain information for 6msh O #2.15
---
Chain | Description
O | No description available
Chain information for 6msh P #2.16
---
Chain | Description
P | No description available
Chain information for 6msh Q #2.17
---
Chain | Description
Q | No description available
Chain information for 6msh R #2.18
---
Chain | Description
R | No description available
Chain information for 6msh S #2.19
---
Chain | Description
S | No description available
Chain information for 6msh T #2.20
---
Chain | Description
T | No description available
Chain information for 6msh U #2.21
---
Chain | Description
U | No description available
Chain information for 6msh V #2.22
---
Chain | Description
V | No description available
Chain information for 6msh W #2.23
---
Chain | Description
W | No description available
Chain information for 6msh X #2.24
---
Chain | Description
X | No description available
Chain information for 6msh Y #2.25
---
Chain | Description
Y | No description available
Chain information for 6msh Z #2.26
---
Chain | Description
Z | No description available
Chain information for 6msh a #2.27
---
Chain | Description
a | No description available
Chain information for 6msh b #2.28
---
Chain | Description
b | No description available
Chain information for 6msh c #2.29
---
Chain | Description
c | No description available
Chain information for 6msh d #2.30
---
Chain | Description
d | No description available
Chain information for 6msh e #2.31
---
Chain | Description
e | No description available
Chain information for 6msh f #2.32
---
Chain | Description
f | No description available
Chain information for 6msh g #2.33
---
Chain | Description
g | No description available
Chain information for 6msh h #2.34
---
Chain | Description
h | No description available
Chain information for 6msh i #2.35
---
Chain | Description
i | No description available
Chain information for 6msh j #2.36
---
Chain | Description
j | No description available
Chain information for 6msh k #2.37
---
Chain | Description
k | No description available
Chain information for 6msh l #2.38
---
Chain | Description
l | No description available
Chain information for 6msh m #2.39
---
Chain | Description
m | No description available
Chain information for 6msh n #2.40
---
Chain | Description
n | No description available
Chain information for 6msh o #2.41
---
Chain | Description
o | No description available
Chain information for 6msh p #2.42
---
Chain | Description
p | No description available
Chain information for 6msh q #2.43
---
Chain | Description
q | No description available
Chain information for 6msh r #2.44
---
Chain | Description
r | No description available
Chain information for 6msh s #2.45
---
Chain | Description
s | No description available
Chain information for 6msh t #2.46
---
Chain | Description
t | No description available
Chain information for 6msh v #2.47
---
Chain | Description
v | No description available
> hide #!2.6 models
> show #!2.6 models
> hide #2.13 models
> show #2.13 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> show #!1 models
> open 5gjr
Summary of feedback from opening 5gjr fetched from pdb
---
note | Fetching compressed mmCIF 5gjr from
http://files.rcsb.org/download/5gjr.cif
5gjr title:
An atomic structure of the human 26S proteasome [more info...]
Chain information for 5gjr #3
---
Chain | Description | UniProt
0 M | 26S protease regulatory subunit 6A | PRS6A_HUMAN
1 N | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN
2 O | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN
3 P | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN
4 Q | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN
5 R | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN
6 S | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN
7 T | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN
8 U | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN
9 V | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN
AA W | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN
AB Y | 26S proteasome complex subunit DSS1 | DSS1_HUMAN
AC Z | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN
B h | Proteasome subunit alpha type-6 | PSA6_HUMAN
C i | Proteasome subunit alpha type-2 | PSA2_HUMAN
D j | Proteasome subunit alpha type-4 | PSA4_HUMAN
E k | Proteasome subunit alpha type-7 | PSA7_HUMAN
F l | Proteasome subunit alpha type-5 | PSA5_HUMAN
G m | Proteasome subunit alpha type-1 | PSA1_HUMAN
H v | 26S protease regulatory subunit 7 | PRS7_HUMAN
I w | 26S protease regulatory subunit 4 | PRS4_HUMAN
J x | 26S protease regulatory subunit 8 | PRS8_HUMAN
K y | 26S protease regulatory subunit 6B | PRS6B_HUMAN
L z | 26S protease regulatory subunit 10B | PRS10_HUMAN
X n | Proteasome subunit alpha type-3 | PSA3_HUMAN
a o | Proteasome subunit beta type-6 | PSB6_HUMAN
b p | Proteasome subunit beta type-7 | PSB7_HUMAN
c q | Proteasome subunit beta type-3 | PSB3_HUMAN
d r | Proteasome subunit beta type-2 | PSB2_HUMAN
e s | Proteasome subunit beta type-5 | PSB5_HUMAN
f t | Proteasome subunit beta type-1 | PSB1_HUMAN
g u | Proteasome subunit beta type-4 | PSB4_HUMAN
Non-standard residues in 5gjr #3
---
ADP — adenosine-5'-diphosphate
> hide #!2 models
> hide #!1 models
> hide #!3 atoms
> show #!3 cartoons
> hide #!3 models
> show #!1 models
> color #1.11 #339933ff
> color #1.12 #006600ff
> color #1.13 #006600ff
> color #1.12 #00cc00ff
> color #1.11 #66cc00ff
> color #1.12 #339933ff
> select #1.1/A:415
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
137 atoms, 138 bonds, 17 residues, 1 model selected
> select up
3229 atoms, 3284 bonds, 413 residues, 1 model selected
> color sel bynucleotide
Alignment identifier is 1.1/A
> select #1.1/A:21
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #1.1/A:21-433
3229 atoms, 3284 bonds, 413 residues, 1 model selected
> select #1.13/M:198
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #1.5 models
> hide #!1.6 models
> hide #1.7 models
> show #1.7 models
> select add #1.13
1856 atoms, 1892 bonds, 240 residues, 1 model selected
> select subtract #1.13
Nothing selected
> hide #1.14 models
> hide #1.15 models
> hide #1.16 models
> hide #1.17 models
> hide #1.18 models
> hide #1.19 models
> hide #1.20 models
> hide #!1.21 models
> hide #1.22 models
> hide #1.23 models
> hide #1.24 models
> hide #1.25 models
> hide #1.26 models
> hide #1.27 models
> hide #1.28 models
> hide #!1.29 models
> hide #1.30 models
> hide #!1.31 models
> hide #1.32 models
> hide #1.33 models
> hide #1.34 models
> hide #1.35 models
> hide #1.36 models
> hide #!1.37 models
> hide #1.38 models
> hide #1.39 models
> hide #1.40 models
> show #1.40 models
> hide #1.46 models
> hide #1.45 models
> hide #1.44 models
> hide #1.43 models
> hide #1.42 models
> hide #1.41 models
> hide #1.40 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.4 models
> hide #!1.4 models
> show #!1.6 models
> select add #1.6
3098 atoms, 3137 bonds, 1 pseudobond, 395 residues, 2 models selected
> hide sel atoms
Alignment identifier is 1.6/F
> select #1.6/F:436
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #1.6/F:436-438
33 atoms, 34 bonds, 3 residues, 1 model selected
> select #1.6/F:437-438
24 atoms, 25 bonds, 2 residues, 1 model selected
> select #1.6/F:437-439
30 atoms, 31 bonds, 3 residues, 1 model selected
> style sel stick
Changed 30 atom styles
> show sel atoms
> select add #1.6
3098 atoms, 3137 bonds, 1 pseudobond, 395 residues, 2 models selected
> select subtract #1.6
Nothing selected
> select #1.6/F:25-27
26 atoms, 25 bonds, 3 residues, 1 model selected
> select #1.6/F
3098 atoms, 3137 bonds, 1 pseudobond, 395 residues, 2 models selected
> hide #1.7 models
> hide #1.8 models
> hide #1.9 models
> hide #1.10 models
> hide #!1.11 models
> show #!1.11 models
> hide #1.13 models
> select subtract #1.6
Nothing selected
> hide #!1.11 models
> show #!1.11 models
> hide #1.12 models
> show #1.12 models
> save /Users/jiale/Desktop/image1.png supersample 3
> hide #!1.6 models
> hide #!1.11 models
> hide #1.12 models
> show #1.12 models
> show #1.13 models
> color #1.13 #8efa00ff
> show #!1.11 models
> show #1.10 models
> hide #1.10 models
> show #1.7 models
> show #!1.1 models
> show #!1.2 models
> show #!1.3 models
> show #!1.4 models
> show #1.5 models
> show #!1.6 models
> hide #!1.1 models
> hide #!1.2 models
> hide #!1.3 models
> hide #!1.4 models
> hide #1.5 models
> hide #!1.6 models
> save /Users/jiale/Desktop/image2.png supersample 3
> save "/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"
——— End of log from Mon Jan 1 16:54:24 2024 ———
opened ChimeraX session
> close #2
> close #3
> select add #1.13
1856 atoms, 1892 bonds, 240 residues, 1 model selected
Alignment identifier is 1.13/M
> style sel stick
Changed 1856 atom styles
> show sel atoms
> color sel byhetero
> select clear
> select #1.12/L:20
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
99 atoms, 100 bonds, 12 residues, 1 model selected
> select up
1850 atoms, 1885 bonds, 238 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 1850 atom styles
> color sel byhetero
> select clear
> open
> "/Users/jiale/Desktop/Ptsm_paper_pdb_deposition/Adolf_Du_Proteasome_Assembly_Submission/Maps_Models/Adolf_Du_Model1_
> PDB-8QYJ.pdb"
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb #2
---
Chain | Description
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
> select add #2
19402 atoms, 19748 bonds, 8 pseudobonds, 2501 residues, 2 models selected
> style sel stick
Changed 19402 atom styles
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel cartoons
> select add #1
124718 atoms, 126873 bonds, 26 pseudobonds, 16035 residues, 60 models selected
> select subtract #2
105316 atoms, 107125 bonds, 18 pseudobonds, 13534 residues, 58 models selected
> combine sel
> select subtract #1
Nothing selected
> hide #!1 models
> rename #3 26S
> select add #2
19402 atoms, 19748 bonds, 8 pseudobonds, 2501 residues, 2 models selected
> select add #3
124718 atoms, 126873 bonds, 26 pseudobonds, 16035 residues, 5 models selected
> select subtract #3
19402 atoms, 19748 bonds, 8 pseudobonds, 2501 residues, 2 models selected
> select subtract #2
Nothing selected
> ui tool show Matchmaker
> matchmaker #!3 to #2
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 Adolf_Du_Model1_ PDB-8QYJ.pdb, chain F (#2) with 26S, chain M (#3),
sequence alignment score = 1132
RMSD between 226 pruned atom pairs is 0.743 angstroms; (across all 239 pairs:
1.111)
> matchmaker #!3 to #2
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 Adolf_Du_Model1_ PDB-8QYJ.pdb, chain F (#2) with 26S, chain M (#3),
sequence alignment score = 1132
RMSD between 226 pruned atom pairs is 0.743 angstroms; (across all 239 pairs:
1.111)
> hide #!3 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #2.1 models
> hide #!2 models
> show #!2 models
> ui tool show Matchmaker
> matchmaker #!2 to #3
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 26S, chain M (#3) with Adolf_Du_Model1_ PDB-8QYJ.pdb, chain F (#2),
sequence alignment score = 1132
RMSD between 226 pruned atom pairs is 0.743 angstroms; (across all 239 pairs:
1.111)
> matchmaker #!2 to #3
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 26S, chain M (#3) with Adolf_Du_Model1_ PDB-8QYJ.pdb, chain F (#2),
sequence alignment score = 1132
RMSD between 226 pruned atom pairs is 0.743 angstroms; (across all 239 pairs:
1.111)
> show #!3 models
> hide #!1 models
> hide #!3 models
> split #2
Split Adolf_Du_Model1_ PDB-8QYJ.pdb (#2) into 13 models
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb A #2.1
---
Chain | Description
A | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb B #2.2
---
Chain | Description
B | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb C #2.3
---
Chain | Description
C | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb D #2.4
---
Chain | Description
D | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb E #2.5
---
Chain | Description
E | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb F #2.6
---
Chain | Description
F | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb G #2.7
---
Chain | Description
G | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb H #2.8
---
Chain | Description
H | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb I #2.9
---
Chain | Description
I | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb J #2.10
---
Chain | Description
J | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb K #2.11
---
Chain | Description
K | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb L #2.12
---
Chain | Description
L | No description available
Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb M #2.13
---
Chain | Description
M | No description available
> hide #2.1 models
> hide #!2.2 models
> hide #2.3 models
> show #2.3 models
> show #!2.2 models
> show #2.1 models
> hide #2.8 models
> hide #!2.9 models
> hide #!2.10 models
> show #!2.10 models
> show #!2.9 models
> hide #!2.9 models
> hide #!2.11 models
> hide #2.12 models
> hide #2.13 models
> hide #!2.7 models
> show #!2.7 models
> select add #2.7
1787 atoms, 1819 bonds, 1 pseudobond, 235 residues, 2 models selected
> view sel
> select subtract #2.7
Nothing selected
> select add #2.10
1909 atoms, 1951 bonds, 2 pseudobonds, 248 residues, 2 models selected
> view sel
> select clear
> select #2.10/J:262
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
224 atoms, 232 bonds, 28 residues, 1 model selected
> select down
5 atoms, 4 bonds, 1 residue, 1 model selected
> view sel
> ui tool show "Side View"
> view sel
> select clear
> show #!3 models
> hide #!3 models
> show #!3 models
> close #1
> rename #2 "Structure 1"
> hide #!3 models
> color #2.2 #8fc9f5ff
> color #2.3 #57adefff
> color #2.4 #1f92eaff
> color #2.5 #1171bbff
> color #2.6 #306db1ff
> color #2.7 #c7e4faff
> color #2.8 #ff8f00ff
> color #2.9 #ffccccff
> color #2.9 #ff6666ff
> color #2.10 #ffccccff
> color #2.11 #f4d6ffff
> color #2.12 #ffe784ff
> color #2.13 #e0b403ff
> ui mousemode right "translate selected models"
> ui mousemode right zoom
> show #!2.9 models
> color #2.2 #33ccffff
> color #2.2 #8fc9f5ff
> color #2.1 #33ccffff
> color #2.3 #66ffffff
> color #2.5 #666fffff
> select add #2.9
1933 atoms, 1974 bonds, 1 pseudobond, 243 residues, 2 models selected
> select subtract #2.9
Nothing selected
> show #!3 models
> close #3.1
> close #3.2
> hide #!2 models
> split #3
Split 26S (#3) into 47 models
Chain information for 26S A #3.1
---
Chain | Description
A | No description available
Chain information for 26S B #3.2
---
Chain | Description
B | No description available
Chain information for 26S C #3.3
---
Chain | Description
C | No description available
Chain information for 26S D #3.4
---
Chain | Description
D | No description available
Chain information for 26S E #3.5
---
Chain | Description
E | No description available
Chain information for 26S F #3.6
---
Chain | Description
F | No description available
Chain information for 26S G #3.7
---
Chain | Description
G | No description available
Chain information for 26S H #3.8
---
Chain | Description
H | No description available
Chain information for 26S I #3.9
---
Chain | Description
I | No description available
Chain information for 26S J #3.10
---
Chain | Description
J | No description available
Chain information for 26S K #3.11
---
Chain | Description
K | No description available
Chain information for 26S L #3.12
---
Chain | Description
L | No description available
Chain information for 26S M #3.13
---
Chain | Description
M | No description available
Chain information for 26S N #3.14
---
Chain | Description
N | No description available
Chain information for 26S O #3.15
---
Chain | Description
O | No description available
Chain information for 26S P #3.16
---
Chain | Description
P | No description available
Chain information for 26S Q #3.17
---
Chain | Description
Q | No description available
Chain information for 26S R #3.18
---
Chain | Description
R | No description available
Chain information for 26S S #3.19
---
Chain | Description
S | No description available
Chain information for 26S T #3.20
---
Chain | Description
T | No description available
Chain information for 26S U #3.21
---
Chain | Description
U | No description available
Chain information for 26S V #3.22
---
Chain | Description
V | No description available
Chain information for 26S W #3.23
---
Chain | Description
W | No description available
Chain information for 26S X #3.24
---
Chain | Description
X | No description available
Chain information for 26S Y #3.25
---
Chain | Description
Y | No description available
Chain information for 26S Z #3.26
---
Chain | Description
Z | No description available
Chain information for 26S a #3.27
---
Chain | Description
a | No description available
Chain information for 26S b #3.28
---
Chain | Description
b | No description available
Chain information for 26S c #3.29
---
Chain | Description
c | No description available
Chain information for 26S d #3.30
---
Chain | Description
d | No description available
Chain information for 26S e #3.31
---
Chain | Description
e | No description available
Chain information for 26S f #3.32
---
Chain | Description
f | No description available
Chain information for 26S g #3.33
---
Chain | Description
g | No description available
Chain information for 26S h #3.34
---
Chain | Description
h | No description available
Chain information for 26S i #3.35
---
Chain | Description
i | No description available
Chain information for 26S j #3.36
---
Chain | Description
j | No description available
Chain information for 26S k #3.37
---
Chain | Description
k | No description available
Chain information for 26S l #3.38
---
Chain | Description
l | No description available
Chain information for 26S m #3.39
---
Chain | Description
m | No description available
Chain information for 26S n #3.40
---
Chain | Description
n | No description available
Chain information for 26S o #3.41
---
Chain | Description
o | No description available
Chain information for 26S p #3.42
---
Chain | Description
p | No description available
Chain information for 26S q #3.43
---
Chain | Description
q | No description available
Chain information for 26S r #3.44
---
Chain | Description
r | No description available
Chain information for 26S s #3.45
---
Chain | Description
s | No description available
Chain information for 26S t #3.46
---
Chain | Description
t | No description available
Chain information for 26S v #3.47
---
Chain | Description
v | No description available
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> hide #3.6 models
> hide #3.7 models
> show #3.7 models
> hide #3.14 models
> show #3.14 models
> hide #3.15 models
> show #3.15 models
> hide #3.32 models
> hide #3.31 models
> ui mousemode right "translate selected models"
Drag select of 2166 residues
> select add #3.21
17495 atoms, 6946 bonds, 2211 residues, 11 models selected
> select subtract #3.21
10667 atoms, 1339 residues, 10 models selected
> select add #3.22
11584 atoms, 3929 bonds, 1454 residues, 10 models selected
> select add #3.23
14977 atoms, 7680 bonds, 1872 residues, 10 models selected
> select add #3.24
17978 atoms, 10733 bonds, 2251 residues, 10 models selected
> hide #3.22 models
> hide #3.23 models
> hide #3.24 models
> hide #3.25 models
> hide #3.26 models
> hide #3.27 models
> hide #3.28 models
> hide #3.29 models
> hide #3.30 models
> hide #3.47 models
> select clear
Drag select of 263 residues
> hide #3.21 models
> select add #3.21
6828 atoms, 6946 bonds, 872 residues, 1 model selected
> select subtract #3.21
Nothing selected
> color #3.7 #c7e4faff
> color #3.8 #33ccffff
> color #3.9 #8fc9f5ff
> color #3.10 #66ffffff
> color #3.11 #1f92eaff
> color #3.11 #666fffff
> color #3.11 #1f92eaff
> color #3.12 #666fffff
> color #3.13 #306db1ff
> color #3.14 #f4d6ffff
> select add #3.14
1430 atoms, 1454 bonds, 191 residues, 1 model selected
> select subtract #3.14
Nothing selected
> ui tool show "Side View"
> hide #3.15 models
> show #3.15 models
> color #3.14 #9600ccff
> color #3.15 #f4d6ffff
> color #3.16 #efc2ffff
> color #3.17 #e499ffff
> color #3.18 #d35cffff
> color #3.19 #c31fffff
> color #3.20 #a500e0ff
> color #3.33 #c7e4faff
> color #3.34 #a2d2f6ff
> color #3.35 #8fc9f5ff
> color #3.36 #57adefff
> color #3.37 #1f92eaff
> color #3.38 #1171bbff
> color #3.39 #306db1ff
> color #3.40 #9600ccff
> color #3.41 #f4d6ffff
> color #3.42 #efc2ffff
> color #3.43 #e499ffff
> color #3.44 #d35cffff
> color #3.45 #c31fffff
> color #3.46 #a500e0ff
> ui mousemode right zoom
> show #!2 models
> select add #2.9
1933 atoms, 1974 bonds, 1 pseudobond, 243 residues, 2 models selected
> select subtract #2.9
Nothing selected
> select add #2.9
1933 atoms, 1974 bonds, 1 pseudobond, 243 residues, 2 models selected
> select add #2.4
3781 atoms, 3851 bonds, 1 pseudobond, 485 residues, 3 models selected
> select add #2.5
5667 atoms, 5772 bonds, 1 pseudobond, 725 residues, 4 models selected
> combine sel
> rename #1 id #4
> rename #2 id #1
> rename #3 id #2
> rename #4 id #3
> rename #3 S1_5_6_pac1
> select add #1
19402 atoms, 19748 bonds, 8 pseudobonds, 2501 residues, 19 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> hide #!2 models
> show #!2 models
> select add #2.11
1729 atoms, 1755 bonds, 228 residues, 1 model selected
> select add #2.12
3579 atoms, 3640 bonds, 466 residues, 2 models selected
> show #2.4 models
> hide #2.4 models
> show #2.5 models
> hide #2.5 models
> show #2.6 models
> select add #2.6
6677 atoms, 6777 bonds, 861 residues, 3 models selected
> combine sel
> rename #4 26S_5_6_rpt5
> select add #2
105316 atoms, 107125 bonds, 13534 residues, 48 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> color #4 #00fdffff
> color #4 white
> hide #4#!3 atoms
> select #4/K
1729 atoms, 1755 bonds, 228 residues, 1 model selected
> color sel #1f92eaff
> select #4/L
1850 atoms, 1885 bonds, 238 residues, 1 model selected
> color sel #666fffff
> select #4/F
3098 atoms, 3137 bonds, 395 residues, 1 model selected
> color sel #ccffccff
> color sel #33ff33ff
> color sel #ffff00ff
> color sel #ffe784ff
> color sel #ffeb99ff
> select clear
> ui tool show Matchmaker
> matchmaker #4 to #3
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 S1_5_6_pac1, chain E (#3) with 26S_5_6_rpt5, chain L (#4), sequence
alignment score = 1130.7
RMSD between 226 pruned atom pairs is 0.654 angstroms; (across all 236 pairs:
1.014)
> matchmaker #4 to #3
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 S1_5_6_pac1, chain E (#3) with 26S_5_6_rpt5, chain L (#4), sequence
alignment score = 1130.7
RMSD between 226 pruned atom pairs is 0.654 angstroms; (across all 236 pairs:
1.014)
> matchmaker #4 to #3
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 S1_5_6_pac1, chain E (#3) with 26S_5_6_rpt5, chain L (#4), sequence
alignment score = 1130.7
RMSD between 226 pruned atom pairs is 0.654 angstroms; (across all 236 pairs:
1.014)
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MYDC2LL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 4 days, 4 hours, 49 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2415Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 30.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.5
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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
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: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 22 months ago
| Component: | Unassigned → UI |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash destroying MatchMaker tool |
comment:2 by , 22 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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