![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 8 months ago
Closed 8 months ago
#16900 closed defect (can't reproduce)
Crash getting secondary structure ID
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 1200000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac15,5",
"coalitionID" : 2349,
"osVersion" : {
"train" : "macOS 15.2",
"build" : "24C101",
"releaseType" : "User"
},
"captureTime" : "2025-02-19 10:38:16.1098 +0800",
"codeSigningMonitor" : 1,
"incident" : "9B0FFED2-EB10-447B-801C-98A572553BE5",
"pid" : 6844,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-18 10:56:22.4910 +0800",
"procStartAbsTime" : 27072468147733,
"procExitAbsTime" : 29119994796771,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
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"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "7CB27297-6E58-F4F0-73C8-F244E4D24A94",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"bootSessionUUID" : "76040BF6-B93A-4D6C-BF07-1283DD0D461F",
"sip" : "enabled",
"vmRegionInfo" : "0x3a646d637a73 is not in any region. Bytes after previous region: 63721970039412 Bytes before following region: 41350109889933\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x65733a646d637a73","rawCodes":[1,7310250823158823539],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x65733a646d637a73 -> 0x00003a646d637a73 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":6844},
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"name" : "QtPdf"
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"name" : "libqicns.dylib"
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{
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"name" : "libqtga.dylib"
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{
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"name" : "libqmacjp2.dylib"
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{
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"name" : "libobjc-trampolines.dylib"
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{
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"name" : "_mac_util.cpython-311-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/numpy_formathandler.cpython-311-darwin.so",
"name" : "numpy_formathandler.cpython-311-darwin.so"
},
{
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"uuid" : "12c53516-421d-3f7a-a81e-95bcfdb8a3ff",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/OpenGL_accelerate\/nones_formathandler.cpython-311-darwin.so",
"name" : "nones_formathandler.cpython-311-darwin.so"
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{
"source" : "P",
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"uuid" : "2c043e84-38d8-33d9-a9a4-ff18ae1f885f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_osx.abi3.so",
"name" : "_psutil_osx.abi3.so"
},
{
"source" : "P",
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"base" : 13101826048,
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"uuid" : "802f0c32-e7ad-3a81-ac8d-ae72c0022ae6",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/psutil\/_psutil_posix.abi3.so",
"name" : "_psutil_posix.abi3.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5878824960,
"size" : 458752,
"uuid" : "6b6db01c-1280-3773-b08f-d693798baba7",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/mmcif.cpython-311-darwin.so",
"name" : "mmcif.cpython-311-darwin.so"
},
{
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"uuid" : "f03f0cb6-82d1-33ee-a10b-cc8d92c14417",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/mmcif\/_mmcif.cpython-311-darwin.so",
"name" : "_mmcif.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5847187456,
"size" : 81920,
"uuid" : "2f167b0b-b0ab-3b3f-a99e-27fc153b427d",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/atomic\/_ribbons.cpython-311-darwin.so",
"name" : "_ribbons.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5847023616,
"size" : 16384,
"uuid" : "c802abe8-4352-3827-8717-7d4c0f0892ff",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/graphics\/_graphics.cpython-311-darwin.so",
"name" : "_graphics.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5848006656,
"size" : 147456,
"uuid" : "96691a20-aa26-3905-98c4-0939edf5bdd4",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/chimerax\/pdb\/_pdbio.cpython-311-darwin.so",
"name" : "_pdbio.cpython-311-darwin.so"
},
{
"source" : "P",
"arch" : "arm64",
"base" : 5849759744,
"size" : 32768,
"uuid" : "f6112c45-e8b3-3787-a9ab-c7209e77530f",
"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PIL\/_imagingmath.cpython-311-darwin.so",
"name" : "_imagingmath.cpython-311-darwin.so"
},
{
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"uuid" : "dfc9530c-e75b-3d1c-a9a6-85c8a709d6a7",
"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
{
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"arch" : "arm64e",
"base" : 6610325504,
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"uuid" : "f1661613-b1c8-320d-b69d-97f174130e29",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
{
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"uuid" : "67989e50-e562-3062-9ff9-44bd90648e66",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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{
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"uuid" : "d215e3b2-fa4f-328a-a080-7650c0991858",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
"base" : 6909923328,
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"uuid" : "ffe67683-09de-31c4-9600-7b8def8cd6d7",
"path" : "\/usr\/lib\/libffi.dylib",
"name" : "libffi.dylib"
},
{
"source" : "P",
"arch" : "arm64e",
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"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5197824,
"uuid" : "41fdd393-3acc-328d-8108-e59a3a947ec5",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
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{
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"size" : 3178496,
"uuid" : "83159ee1-0ca4-3a91-887a-db80b7029337",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
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"arch" : "arm64e",
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"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21204992,
"uuid" : "4251ee1c-062c-3b9a-b6e2-751f77ef9f4a",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2575.30.19"
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{
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"uuid" : "4ce86d18-f3fa-3d2a-a1b8-e7cd8a52fb0d",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
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{
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"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
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"size" : 581628,
"uuid" : "fe5f2fbb-d3b5-30bc-bad8-3571ac2a72a0",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
}
],
"sharedCache" : {
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"size" : 4861722624,
"uuid" : "e36100c7-89e7-3970-8938-8483ccd7019a"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=32.2G written=16.8M(0%) resident=16.8M(0%) swapped_out=0K(0%) unallocated=32.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 272K 12 \nColorSync 688K 33 \nCoreAnimation 1552K 94 \nCoreGraphics 128K 8 \nCoreUI image data 5056K 36 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 31.5G 232 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 688K 43 \nStack 180.5M 44 \nStack Guard 56.0M 1 \nVM_ALLOCATE 261.3M 307 \nVM_ALLOCATE (reserved) 160.0M 3 reserved VM address space (unallocated)\n__AUTH 5280K 671 \n__AUTH_CONST 70.8M 919 \n__CTF 824 1 \n__DATA 33.1M 1058 \n__DATA_CONST 33.9M 1073 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 636.3M 148 \n__OBJC_RW 2373K 1 \n__TEXT 1.2G 1093 \n__TPRO_CONST 272K 2 \ndyld private memory 256K 1 \nmapped file 595.7M 98 \nowned unmapped memory 79.8M 1 \npage table in kernel 16.8M 1 \nshared memory 3184K 26 \n=========== ======= ======= \nTOTAL 34.9G 6280 \nTOTAL, minus reserved VM space 34.7G 6280 \n",
"legacyInfo" : {
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "bfb37be78d711f5ffc77fe96a887fc3d32e4f8cf",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "639124e81d92412bfb4880b3",
"factorPackIds" : {
},
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},
{
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"factorPackIds" : {
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}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/geqijun/Documents/Projects/model_building/Foldseek/P14_J90_006/P14—J90—coot-0.pdb
Chain information for P14—J90—coot-0.pdb #1
---
Chain | Description
0 | No description available
1 | No description available
2 e | No description available
3 | No description available
4 | No description available
5 9 c o q w | No description available
6 | No description available
7 | No description available
8 X Y z | No description available
A | No description available
B F x | No description available
C | No description available
D | No description available
E V y | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L Q | No description available
M | No description available
N | No description available
O | No description available
P | No description available
R | No description available
S n | No description available
T | No description available
U | No description available
W s | No description available
Z | No description available
a | No description available
b | No description available
d | No description available
f | No description available
g | No description available
h | No description available
i | No description available
j v | No description available
k | No description available
l | No description available
m | No description available
p | No description available
r | No description available
t | No description available
u | No description available
> select clear
Drag select of 732 atoms, 2 pseudobonds, 333 bonds
> delete sel
Drag select of 2295 atoms, 10 pseudobonds, 1364 bonds
> delete sel
Drag select of 1228 atoms, 9 pseudobonds, 722 bonds
> delete sel
Drag select of 322 atoms, 4 pseudobonds, 127 bonds
> delete sel
Drag select of 2 atoms, 1 bonds
> delete sel
Drag select of 1291 atoms, 13 pseudobonds, 520 bonds
> delete sel
Drag select of 1924 atoms, 15 pseudobonds, 1218 bonds
> delete sel
Drag select of 125 atoms, 2 pseudobonds, 62 bonds
> delete sel
Drag select of 656 atoms, 16 pseudobonds, 429 bonds
> delete sel
Drag select of 610 atoms, 7 pseudobonds, 383 bonds
> delete sel
Drag select of 406 atoms, 3 pseudobonds, 280 bonds
> delete sel
Drag select of 18 atoms, 9 bonds
> delete sel
Drag select of 55 atoms, 1 pseudobonds, 27 bonds
> delete sel
Drag select of 10 atoms, 5 bonds
> delete sel
Drag select of 11 atoms, 5 bonds
> delete sel
Drag select of 7 atoms
> delete sel
Drag select of 4 atoms, 1 pseudobonds
> delete sel
Drag select of 34 atoms, 19 bonds
> delete sel
Drag select of 3 atoms
> delete sel
Drag select of 2 atoms
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 1 atoms
> delete sel
> select /A:3@ND2
1 atom, 1 residue, 1 model selected
> delete sel
> select /A:3@CA
1 atom, 1 residue, 1 model selected
> delete sel
> select /A:3@CG
1 atom, 1 residue, 1 model selected
> delete sel
> select /A:3@CB
1 atom, 1 residue, 1 model selected
> delete sel
> select /A:3@OD1
1 atom, 1 residue, 1 model selected
> delete sel
> select /A:3@C
1 atom, 1 residue, 1 model selected
> delete sel
> select /A:3@O
1 atom, 1 residue, 1 model selected
> delete sel
Drag select of 4 atoms, 3 bonds
> delete sel
Drag select of 4 atoms, 3 bonds
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 3 atoms, 2 bonds
> delete sel
Drag select of 2 atoms
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 3 atoms
> delete sel
Drag select of 2 atoms
> delete sel
Drag select of 11 atoms, 9 bonds
> delete sel
Drag select of 5 atoms, 4 bonds
> delete sel
Drag select of 2 atoms, 1 bonds
> delete sel
> select clear
Drag select of 17 atoms, 14 bonds
> delete sel
Drag select of 5 atoms, 4 bonds
> delete sel
Drag select of 17 atoms, 10 bonds
> delete sel
Drag select of 19 atoms, 11 bonds
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 14 atoms, 14 bonds
> delete sel
Drag select of 5 atoms, 5 bonds
> delete sel
> select @@serial_number=9574
1 atom, 1 residue, 1 model selected
> delete sel
Drag select of 13 atoms, 10 bonds
> delete sel
Drag select of 2 atoms
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 4 atoms, 2 bonds
> delete sel
Drag select of 5 atoms, 3 bonds
> delete sel
Drag select of 5 atoms, 5 bonds
> delete sel
Drag select of 5 atoms, 5 bonds
> delete sel
Drag select of 8 atoms, 4 bonds
> delete sel
Drag select of 3 atoms, 2 bonds
> delete sel
Drag select of 5 atoms, 4 bonds
> delete sel
Drag select of 2 atoms, 1 bonds
> delete sel
Drag select of 1 atoms, 2 bonds
> delete sel
Drag select of 4 atoms, 2 bonds
> delete sel
Drag select of 5 atoms, 3 bonds
> delete sel
Drag select of 5 atoms, 3 bonds
> delete sel
> select /V:1@CA
1 atom, 1 residue, 1 model selected
> delete sel
Drag select of 3 atoms, 1 bonds
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 2 atoms
> delete sel
Drag select of 2 atoms, 1 bonds
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 2 atoms, 1 bonds
> delete sel
> select /g:1@O3'
1 atom, 1 residue, 1 model selected
> delete sel
Drag select of 20 atoms, 18 bonds
> delete sel
Drag select of 23 atoms, 23 bonds
> delete sel
Drag select of 3 atoms, 1 bonds
> delete sel
Drag select of 4 atoms, 5 bonds
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 2 atoms
> delete sel
Drag select of 1 atoms
> delete sel
Drag select of 9 atoms, 8 bonds
> delete sel
> save
> /Users/geqijun/Documents/Projects/model_building/Foldseek/P14_J90_006/P14_J90_1.pdb
> relModel #1
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/geqijun/Documents/Projects/model_building/Foldseek/P14_J90_006/P14_J90_1.pdb
Chain information for P14_J90_1.pdb #1
---
Chain | Description
GG | No description available
Ii | No description available
OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M3
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: Mac15,5
Model Number: Z19K0006YCH/A
Chip: Apple M3
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 24 GB
System Firmware Version: 11881.61.3
OS Loader Version: 11881.61.3
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 14天1小时21分钟
Graphics/Displays:
Apple M3:
Chipset Model: Apple M3
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 4.5K (4480 x 2520)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Studio Display:
Display Type: Retina LCD
Resolution: 5120 x 2880 Retina
Display Serial Number: GWPL2G1C92
Display Firmware Version: Version 16.4 (Build 20E246)
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash getting secondary structure ID |
comment:2 by , 8 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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