![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 years ago
Closed 3 years ago
#8761 closed defect (fixed)
Crash in readcif::CIFFile::parse
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | Zach Pearson | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6rc202303292224 (2023-03-29 22:24:14 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007000158ce000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000148cb000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00007ff856e46680 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/__init__.py", line 43 in open
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 465 in collated_open
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 194 in provider_open
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/manager.py", line 198 in open_data
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/mmcif/__init__.py", line 97 in fetch
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 435 in remember_data_format
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 464 in collated_open
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 154 in provider_open
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py", line 119 in cmd_open
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 2897 in run
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 284 in event_loop
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX.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":"2023-04-02 00:05:57.00 -0700","app_version":"1.6.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.2.1 (22D68)","roots_installed":0,"name":"ChimeraX","incident_id":"8B43D60A-9D1B-4B63-8D32-C6E760AFDCB8"}
{
"uptime" : 84000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 2124760682,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 7549,
"osVersion" : {
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"build" : "22D68",
"releaseType" : "User"
},
"captureTime" : "2023-04-02 00:05:49.3184 -0700",
"incident" : "8B43D60A-9D1B-4B63-8D32-C6E760AFDCB8",
"pid" : 34367,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-04-01 22:56:13.7824 -0700",
"procStartAbsTime" : 80064483866458,
"procExitAbsTime" : 84240482107035,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.0","CFBundleVersion":"1.6.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"246055EA-B1CD-5AB2-A1B5-067181129162","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "098641B6-E50D-E7BC-F7D0-3278B91F433F",
"throttleTimeout" : 2147483647,
"wakeTime" : 4450,
"bridgeVersion" : {"build":"20P3045","train":"7.2"},
"sleepWakeUUID" : "91A4EA12-0A7B-49CA-B9F4-4D1E872DD363",
"sip" : "enabled",
"vmRegionInfo" : "0x50 is not in any region. Bytes before following region: 140737487019952\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffeba000-7fffffebb000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000050","rawCodes":[1,80],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000050"},
"vmregioninfo" : "0x50 is not in any region. Bytes before following region: 140737487019952\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffeba000-7fffffebb000 [ 4K] r-x\/r-x SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
UCSF ChimeraX version: 1.6rc202303292224 (2023-03-29)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> devel build /Users/meji656/Sources/cysptm_chimerax
running build
running build_py
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/do_ptm.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/cmd.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/settings.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/contextmenu.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
running install_egg_info
running egg_info
writing ChimeraX_DoPTM.egg-info/PKG-INFO
writing dependency_links to ChimeraX_DoPTM.egg-info/dependency_links.txt
writing requirements to ChimeraX_DoPTM.egg-info/requires.txt
writing top-level names to ChimeraX_DoPTM.egg-info/top_level.txt
writing manifest file 'ChimeraX_DoPTM.egg-info/SOURCES.txt'
Copying ChimeraX_DoPTM.egg-info to
build/bdist.macosx-10.9-universal2/wheel/ChimeraX_DoPTM-0.1-py3.9.egg-info
running install_scripts
creating build/bdist.macosx-10.9-universal2/wheel/ChimeraX_DoPTM-0.1.dist-
info/WHEEL
creating 'dist/ChimeraX_DoPTM-0.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding 'chimerax/do_ptm/__init__.py'
adding 'chimerax/do_ptm/cmd.py'
adding 'chimerax/do_ptm/contextmenu.py'
adding 'chimerax/do_ptm/do_ptm.py'
adding 'chimerax/do_ptm/settings.py'
adding 'chimerax/do_ptm/tool.py'
adding 'ChimeraX_DoPTM-0.1.dist-info/METADATA'
adding 'ChimeraX_DoPTM-0.1.dist-info/WHEEL'
adding 'ChimeraX_DoPTM-0.1.dist-info/top_level.txt'
adding 'ChimeraX_DoPTM-0.1.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in
/Users/meji656/Sources/cysptm_chimerax/dist/ChimeraX_DoPTM-0.1-py3-none-
any.whl
> devel build /Users/meji656/Sources/cysptm_chimerax
running build
running build_py
running bdist_wheel
installing to build/bdist.macosx-10.9-universal2/wheel
running install
running install_lib
creating build/bdist.macosx-10.9-universal2/wheel
creating build/bdist.macosx-10.9-universal2/wheel/chimerax
creating build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/do_ptm.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/cmd.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/__init__.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/settings.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/tool.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
copying build/lib/chimerax/do_ptm/contextmenu.py ->
build/bdist.macosx-10.9-universal2/wheel/chimerax/do_ptm
running install_egg_info
running egg_info
writing ChimeraX_DoPTM.egg-info/PKG-INFO
writing dependency_links to ChimeraX_DoPTM.egg-info/dependency_links.txt
writing requirements to ChimeraX_DoPTM.egg-info/requires.txt
writing top-level names to ChimeraX_DoPTM.egg-info/top_level.txt
writing manifest file 'ChimeraX_DoPTM.egg-info/SOURCES.txt'
Copying ChimeraX_DoPTM.egg-info to
build/bdist.macosx-10.9-universal2/wheel/ChimeraX_DoPTM-0.1-py3.9.egg-info
running install_scripts
creating build/bdist.macosx-10.9-universal2/wheel/ChimeraX_DoPTM-0.1.dist-
info/WHEEL
creating 'dist/ChimeraX_DoPTM-0.1-py3-none-any.whl' and adding
'build/bdist.macosx-10.9-universal2/wheel' to it
adding 'chimerax/do_ptm/__init__.py'
adding 'chimerax/do_ptm/cmd.py'
adding 'chimerax/do_ptm/contextmenu.py'
adding 'chimerax/do_ptm/do_ptm.py'
adding 'chimerax/do_ptm/settings.py'
adding 'chimerax/do_ptm/tool.py'
adding 'ChimeraX_DoPTM-0.1.dist-info/METADATA'
adding 'ChimeraX_DoPTM-0.1.dist-info/WHEEL'
adding 'ChimeraX_DoPTM-0.1.dist-info/top_level.txt'
adding 'ChimeraX_DoPTM-0.1.dist-info/RECORD'
removing build/bdist.macosx-10.9-universal2/wheel
Distribution is in
/Users/meji656/Sources/cysptm_chimerax/dist/ChimeraX_DoPTM-0.1-py3-none-
any.whl
> toolshed install
> /Users/meji656/Downloads/ChimeraX_RotamerLibsCysPTM-0.1-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip is available: 23.0 -> 23.0.1
[notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m
pip install --upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /Users/meji656/Downloads/ChimeraX_RotamerLibsCysPTM-0.1-py3-none-
any.whl
Requirement already satisfied: ChimeraX-Core>=0.9 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-RotamerLibsCysPTM==0.1) (1.6rc202303292224)
Requirement already satisfied: ChimeraX-RotamerLibMgr~=3.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-RotamerLibsCysPTM==0.1) (3.0)
Installing collected packages: ChimeraX-RotamerLibsCysPTM
Successfully installed ChimeraX-RotamerLibsCysPTM-0.1
\---
Successfully installed ChimeraX-RotamerLibsCysPTM-0.1
Installed ChimeraX-RotamerLibsCysPTM (0.1)
> toolshed install /Users/meji656/Downloads/ChimeraX_DoPTM-0.1-py3-none-
> any.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip is available: 23.0 -> 23.0.1
[notice] To update, run: /Applications/ChimeraX.app/Contents/MacOS/ChimeraX -m
pip install --upgrade pip
\---
pip standard output:
\---
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/
Processing /Users/meji656/Downloads/ChimeraX_DoPTM-0.1-py3-none-any.whl
Requirement already satisfied: ChimeraX-RotamerLibMgr~=3.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-DoPTM==0.1) (3.0)
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-DoPTM==0.1) (1.28.4)
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-DoPTM==0.1) (1.3)
Requirement already satisfied: ChimeraX-Hbonds~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-DoPTM==0.1) (2.4)
Requirement already satisfied: ChimeraX-Core~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-DoPTM==0.1) (1.6rc202303292224)
Requirement already satisfied: ChimeraX-Atomic~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-DoPTM==0.1) (1.43.10)
Requirement already satisfied: ChimeraX-Clashes~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-DoPTM==0.1) (2.2.4)
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0.1)
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.12)
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.1.1)
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0.3)
Requirement already satisfied: ChimeraX-AtomicLibrary~=10.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (10.0.6)
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.7)
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.0.2)
Requirement already satisfied: ChimeraX-Arrays~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.1)
Requirement already satisfied: ChimeraX-AtomSearch~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Clashes~=2.0->ChimeraX-DoPTM==0.1) (2.0.1)
Requirement already satisfied: ChimeraX-ChemGroup~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Hbonds~=2.0->ChimeraX-DoPTM==0.1) (2.0.1)
Requirement already satisfied: ChimeraX-SelInspector~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-DoPTM==0.1) (1.0)
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-UI~=1.0->ChimeraX-DoPTM==0.1) (1.2)
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1)
(1.2.3)
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1)
(1.5.1)
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1)
(1.10.1)
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-
DoPTM==0.1) (1.0.1)
Requirement already satisfied: ChimeraX-IO~=1.0.1 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PDB~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1)
(1.0.1)
Requirement already satisfied: ChimeraX-ItemsInspection~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-SelInspector~=1.0->ChimeraX-UI~=1.0->ChimeraX-
DoPTM==0.1) (1.0.1)
Requirement already satisfied: ChimeraX-Map~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.1.4)
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.10.2)
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0)
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0.1)
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.1.1)
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0)
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (2.0)
Requirement already satisfied: ChimeraX-DistMonitor~=1.2 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.0->ChimeraX-DoPTM==0.1) (1.4)
Installing collected packages: ChimeraX-DoPTM
Successfully installed ChimeraX-DoPTM-0.1
\---
Successfully installed ChimeraX-DoPTM-0.1
Installed ChimeraX-DoPTM (0.1)
> fetch 2d2i
Unknown command: fetch 2d2i
> clear
Unknown command: clear
> log clear
> open 2d2i
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6rc202303292224 (2023-03-29)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
OS Loader Version: 564.40.4~66
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 2 days, 14 hours, 19 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
DELL U2720Q:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 57WKX13
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.4
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6rc202303292224
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-DoPTM: 0.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsCysPTM: 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: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.6
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.1.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.2.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Attachments (1)
Change History (16)
comment:1 by , 3 years ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash in readcif::CIFFile::parse |
comment:2 by , 3 years ago
Hello, can you share the mmCIF/CIF file that caused the problem? If you need to keep it private, send it to me directly at gregc@…. With that file, I should be able to fix it later today or tomorrow. -- Greg
follow-up: 3 comment:3 by , 3 years ago
Hi Greg, I was just fetching 2D2I from the Protein Data Bank using open 2d2i . Changing to open 2d2i format pdb works, so the issue might be localized to readcif. Daniel
comment:4 by , 3 years ago
I can not reproduce this with "open 2d2i" on Windows nor Linux. And I didn't find any memory errors with valgrind. So maybe this a macOS bug. Or maybe your copy of 2d2i.cif is corrupt. Or maybe one of the residue template files is corrupt.
What is the output from the following two commands:
sum ~/Downloads/ChimeraX/PDB/2d2i.cif
and:
sum ~/Downloads/ChimeraX/CCD/{NAP,SO4}.cif
Those are the checksums for the 2d2i.cif and the non-standard residue templates it needs.
And please don't delete any files until after we've figured this out.
follow-up: 6 comment:6 by , 3 years ago
sum ~/Downloads/ChimeraX/PDB/2d2i.cif
22527 1653 /Users/meji656/Downloads/ChimeraX/PDB/2d2i.cif
sum ~/Downloads/ChimeraX/CCD/{NAP,SO4}.cif
sum: /Users/meji656/Downloads/ChimeraX/CCD/NAP.cif: No such file or directory
sum: /Users/meji656/Downloads/ChimeraX/CCD/SO4.cif: No such file or directory
follow-up: 7 comment:7 by , 3 years ago
Ok, I figured out what is happening.
If I turn off PNNL’s VPN then ChimeraX can fetch NAP and SO4 and everything works. With the VPN ChimeraX crashes
Daniel
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Tuesday, April 4, 2023 at 11:42 AM
To:
Cc: Mejia Rodriguez, Daniel <daniel.mejia@pnnl.gov>, gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8761: Crash in readcif::CIFFile::parse
Check twice before you click! This email originated from outside PNNL.
#8761: Crash in readcif::CIFFile::parse
-------------------------------------+------------------------
Reporter: daniel.mejia@… | Owner: Greg Couch
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+------------------------
Comment (by Greg Couch):
Couldn't reproduce on a Mac either.
--
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ChimeraX Issue Tracker
comment:8 by , 3 years ago
When using the PPNL VPN, what happens when you try to download:
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
using your web browser?
follow-up: 9 comment:9 by , 3 years ago
Downloading from the browser works just fine. However, wget complains:
wget https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
--2023-04-04 12:19:50-- https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
Resolving files.wwpdb.org (files.wwpdb.org)... 132.249.210.222
Connecting to files.wwpdb.org (files.wwpdb.org)|132.249.210.222|:443... connected.
OpenSSL: error:0A000152:SSL routines::unsafe legacy renegotiation disabled
Unable to establish SSL connection.
But curl works:
curl -L https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif -o NAP.cif
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 14848 100 14848 0 0 35449 0 --:--:-- --:--:-- --:--:-- 36571
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Tuesday, April 4, 2023 at 12:07 PM
To:
Cc: Mejia Rodriguez, Daniel <daniel.mejia@pnnl.gov>, gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8761: Crash in readcif::CIFFile::parse
Check twice before you click! This email originated from outside PNNL.
#8761: Crash in readcif::CIFFile::parse
-------------------------------------+------------------------
Reporter: daniel.mejia@… | Owner: Greg Couch
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+------------------------
Comment (by Greg Couch):
When using the PPNL VPN, what happens when you try to download:
https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffiles.wwpdb.org%2Fpub%2Fpdb%2Frefdata%2Fchem_comp%2FP%2FNAP%2FNAP.cif&data=05%7C01%7Cdaniel.mejia%40pnnl.gov%7C08a0c25e83de4c5a6e5a08db353fe4e4%7Cd6faa5f90ae240338c0130048a38deeb%7C0%7C0%7C638162320782595436%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=%2FBw29JMCYnUrsmO83ZGx5%2B7LgrP14KCbIY1Yugqwkkg%3D&reserved=0
using your web browser?
--
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ChimeraX Issue Tracker
Version 0, edited 3 years ago by (next)
comment:10 by , 3 years ago
| Cc: | added |
|---|
Put in a fix that prevents the crash when the residue template can not be fetched.
Not sure how to debug why/how the VPN interferes with that. Will keep thinking about it.
comment:11 by , 3 years ago
Hi Daniel, I've attached a Python test script, fetchtest.py, to this ticket. Please run in a Terminal window:
/Applications/ChimeraX.app/Contents/bin/python3.9 fetchtest.py
when you are on the VPN, and send us the output. That should give us more information about what is failing.
comment:12 by , 3 years ago
Sorry for the late response. Please find the output of fetchtest.py below.
/Applications/ChimeraX.app/Contents/bin/python3.9 fetchtest.py
Try without checking certificates
Fetching https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
Fetched https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif
Try with checking certificates
Traceback (most recent call last):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 1346, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1285, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1331, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1280, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1040, in _send_output
self.send(msg)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 980, in send
self.connect()
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/http/client.py", line 1454, in connect
self.sock = self._context.wrap_socket(self.sock,
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py", line 500, in wrap_socket
return self.sslsocket_class._create(
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py", line 1040, in _create
self.do_handshake()
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/ssl.py", line 1309, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:1129)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/meji656/fetchtest.py", line 37, in <module>
retrieve_url(url)
File "/Users/meji656/fetchtest.py", line 17, in retrieve_url
with urlopen(request, timeout=timeout, context=ssl_context) as response:
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 214, in urlopen
return opener.open(url, data, timeout)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 517, in open
response = self._open(req, data)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 534, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 494, in _call_chain
result = func(*args)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 1389, in https_open
return self.do_open(http.client.HTTPSConnection, req,
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/urllib/request.py", line 1349, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: self signed certificate in certificate chain (_ssl.c:1129)>
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Saturday, April 8, 2023 at 10:27 AM
To:
Cc: Mejia Rodriguez, Daniel <daniel.mejia@pnnl.gov>, gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>, zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8761: Crash in readcif::CIFFile::parse
Check twice before you click! This email originated from outside PNNL.
#8761: Crash in readcif::CIFFile::parse
-------------------------------------+------------------------
Reporter: daniel.mejia@… | Owner: Greg Couch
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+------------------------
Comment (by Greg Couch):
Hi Daniel, I've attached a Python test script, fetchtest.py, to this
ticket. Please run in a Terminal window:
/Applications/ChimeraX.app/Contents/bin/python3.9 fetchtest.py
when you are on the VPN, and send us the output. That should give us more
information about what is failing.
--
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follow-up: 12 comment:13 by , 3 years ago
Thank you. My guess it that your VPN is doing a man-in-the-middle attack on your encrypted traffic so it can scan for incoming malware. And to do that, you (or your IT folks) had to install a root certificate that allows the VPN to impersonate other hostnames. On the Mac, ChimeraX has it's own list of root certificates. So it fails.
There are several possible soutions: (1) use a different VPN product, (2) turn off the scanning of encrypted web traffic, or (3) add files.wwpdb.org to an allowlist/safelist/whitelist.
What VPN product are you using?
comment:14 by , 3 years ago
Your guess seems about right.
We are using Cisco AnyConnect.
I will contact our IT department for a permanent fix.
For now, I have been setting https_proxy to connect to a proxy with http protocol.
Thanks!
Daniel
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Date: Tuesday, April 11, 2023 at 4:38 PM
To:
Cc: Mejia Rodriguez, Daniel <daniel.mejia@pnnl.gov>, gregc@cgl.ucsf.edu <gregc@cgl.ucsf.edu>, zjp@cgl.ucsf.edu <zjp@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #8761: Crash in readcif::CIFFile::parse
Check twice before you click! This email originated from outside PNNL.
#8761: Crash in readcif::CIFFile::parse
-------------------------------------+------------------------
Reporter: daniel.mejia@… | Owner: Greg Couch
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Input/Output | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
-------------------------------------+------------------------
Comment (by Greg Couch):
Thank you. My guess it that your VPN is doing a man-in-the-middle attack
on your encrypted traffic so it can scan for incoming malware. And to do
that, you (or your IT folks) had to install a root certificate that allows
the VPN to impersonate other hostnames. On the Mac, ChimeraX has it's own
list of root certificates. So it fails.
There are several possible soutions: (1) use a different VPN product, (2)
turn off the scanning of encrypted web traffic, or (3) add files.wwpdb.org
to an allowlist/safelist/whitelist.
What VPN product are you using?
--
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ChimeraX Issue Tracker
follow-up: 14 comment:15 by , 3 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Thank you for following up on this. One more possible fix.
Option (4) add the VPN's root certificate to ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/certifi/cacert.pem
Note:
See TracTickets
for help on using tickets.
Reported by Danial Mejia Rodriguez
Daniel, our "mmCIF guy" (Greg) is on vacation this week, so you may not hear back about this until next week.