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Opened 23 months ago
Closed 23 months ago
#10300 closed defect (can't reproduce)
Crash adding Volume menu
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x000070001d0f6000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x000070001c0f3000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x000070001b0f0000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x000070001a0ed000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x00007000190ea000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x00007000180e7000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x00007000170e4000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x00007000160e1000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x00007000150de000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x00007000140db000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x00007000130d8000 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 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 0x000000010ddf3600 (most recent call first):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1859 in _get_target_menu
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1726 in add_menu_entry
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/volume_menu/volmenu.py", line 56 in show
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/volume_menu/volmenu.py", line 37 in display
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/toolshed/info.py", line 562 in start_tool
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/cmd.py", line 219 in ui_tool_show
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/core/commands/run.py", line 38 in run
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 1656 in
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX.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":"2023-12-07 14:51:02.00 +0100","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.7.1 (21G920)","incident_id":"F5D420C4-BB3A-4BED-BB9E-D865FF6E7D90","name":"ChimeraX"}
{
"uptime" : 710000,
"procLaunch" : "2023-11-10 09:18:49.6533 +0100",
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro11,4",
"procStartAbsTime" : 164793435005800,
"coalitionID" : 25402,
"osVersion" : {
"train" : "macOS 12.7.1",
"build" : "21G920",
"releaseType" : "User"
},
"captureTime" : "2023-12-07 14:50:27.5768 +0100",
"incident" : "F5D420C4-BB3A-4BED-BB9E-D865FF6E7D90",
"bug_type" : "309",
"pid" : 56857,
"procExitAbsTime" : 718247840412479,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"4E3785CA-6BA2-5259-8CE3-6494719DA4AD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "FB274B70-81F7-B8A4-C642-35FCB98D9BFC",
"wakeTime" : 16483,
"sleepWakeUUID" : "3F16D008-4DAC-4323-BAB1-7C0CA87F8A41",
"sip" : "enabled",
"vmRegionInfo" : "0x40 is not in any region. Bytes before following region: 140737487425472\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff1d000-7ffffff1e000 [ 4K] r-x\/r-x SM=ALI ",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000001, 0x0000000000000040","rawCodes":[1,64],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000040"},
"ktriageinfo" : "VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\n",
"vmregioninfo" : "0x40 is not in any region. Bytes before following region: 140737487425472\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff1d000-7ffffff1e000 [ 4K] r-x\/r-x SM=ALI ",
"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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UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show AlphaFold
> alphafold search
> GSATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVGSLIKRMKQIEDKIEEILSKIYHIENEIARIKKLIGEENLYFQGSSFLVQSGDGRHHHHHHHH
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Webservices job id: 8KBVQ80443G5LWH2
> alphafold match
> GSATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVGSLIKRMKQIEDKIEEILSKIYHIENEIARIKKLIGEENLYFQGSSFLVQSGDGRHHHHHHHH
Fetching compressed AlphaFold A0A2V5LC98 from
https://alphafold.ebi.ac.uk/files/AF-A0A2V5LC98-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: A0A2V5LC98 (1
sequences)
Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
A0A2V5LC98_9MICC | GSATL...HHHHH | 41.2 | 89.3
Opened 1 AlphaFold model
> alphafold match
> GSATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVGSLIKRMKQIEDKIEEILSKIYHIENEIARIKKLIGEENLYFQGSSFLVQSGDGRHHHHHHHH
1 AlphaFold model found using sequence similarity searches: A0A2V5LC98 (1
sequences)
| Sequence Similarity
---
AlphaFold Model| Query Sequence| Identity %| Coverage %
A0A2V5LC98_9MICC | GSATL...HHHHH | 41.2 | 89.3
Opened 1 AlphaFold model
> close #2
> alphafold predict
> GSATLCLGHHAVPNGTIVKTITNDQIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSNNSFFSRLNWLTHLNFKYPALNVTMPNNEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRNIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVGSLIKRMKQIEDKIEEILSKIYHIENEIARIKKLIGEENLYFQGSSFLVQSGDGRHHHHHHHH
Please cite ColabFold: Making protein folding accessible to all. Nature
Methods (2022) if you use these predictions.
Running AlphaFold prediction
> volume flip #6
Running AlphaFold prediction
AlphaFold prediction finished
Results in /Users/tilpap/Downloads/ChimeraX/AlphaFold/prediction_1
> open /Users/tilpap/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
| Chain information for best_model.pdb #2
---
Chain | Description
A | No description available
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> toolshed show
Downloading bundle ChimeraX_PDBImages-1.2-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip is available: 23.0 -> 23.3.1
[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/tilpap/Downloads/ChimeraX_PDBImages-1.2-py3-none-any.whl
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-PDBImages==1.2) (2.12)
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-PDBImages==1.2) (1.10.3)
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-PDBImages==1.2) (1.6.1)
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-PDBImages==1.2) (1.5.1)
Requirement already satisfied: ChimeraX-Atomic~=1.34 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.43.10)
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-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (2.7.2)
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-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.0.2)
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-PDBImages==1.2) (1.10.1)
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-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.1)
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-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (10.0.6)
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-PDBImages==1.2) (1.2.3)
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-PDBImages==1.2) (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-PDBImages==1.2) (2.0)
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-StdCommands~=1.0->ChimeraX-PDBImages==1.2) (1.1.1)
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-PDBImages==1.2) (1.4)
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-StdCommands~=1.0->ChimeraX-PDBImages==1.2) (1.3)
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~=1.34->ChimeraX-mmCIF~=2.0->ChimeraX-
PDBImages==1.2) (2.0.3)
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~=1.34->ChimeraX-mmCIF~=2.0->ChimeraX-
PDBImages==1.2) (2.0.1)
Requirement already satisfied: ChimeraX-IO~=1.0 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-
PDBImages==1.2) (1.0.1)
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-MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-
PDBImages==1.2) (2.0)
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-MapFit~=2.0->ChimeraX-StdCommands~=1.0->ChimeraX-
PDBImages==1.2) (1.1.4)
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-OpenCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-
PDBImages==1.2) (1.28.4)
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-MapFit~=2.0->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.2) (2.1.1)
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-Map~=1.0->ChimeraX-MapFit~=2.0->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.2) (1.2)
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-MapFit~=2.0->ChimeraX-
StdCommands~=1.0->ChimeraX-PDBImages==1.2) (2.0.1)
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~=1.34->ChimeraX-
mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.0.1)
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-OpenCommand~=1.0->ChimeraX-
mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.0)
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-
OpenCommand~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-PDBImages==1.2) (1.0.1)
Installing collected packages: ChimeraX-PDBImages
Successfully installed ChimeraX-PDBImages-1.2
\---
Successfully installed ChimeraX-PDBImages-1.2
Installed ChimeraX-PDBImages (1.2)
Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl
> select add #2
4453 atoms, 4547 bonds, 560 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.96421,-0.20983,0.16206,-1.5295,0.21546,0.97635,-0.017767,-8.0458,-0.1545,0.052048,0.98662,6.24
> view matrix models
> #2,0.41111,0.90962,0.059811,43.614,-0.3259,0.20793,-0.92225,-24.097,-0.85134,0.35965,0.38193,27.481
> view matrix models
> #2,0.57481,0.80996,-0.11645,32.81,-0.4968,0.23234,-0.83619,-16.414,-0.65022,0.5385,0.53594,27.811
> view matrix models
> #2,0.57481,0.80996,-0.11645,4.8277,-0.4968,0.23234,-0.83619,-21.72,-0.65022,0.5385,0.53594,33.395
> view matrix models
> #2,0.57481,0.80996,-0.11645,-13.13,-0.4968,0.23234,-0.83619,-1.6484,-0.65022,0.5385,0.53594,22.914
> view matrix models
> #2,0.57481,0.80996,-0.11645,-2.6914,-0.4968,0.23234,-0.83619,2.6437,-0.65022,0.5385,0.53594,7.874
> ui tool show "Fit in Map"
> ui tool show "Volume Viewer"
> ui tool show Updates
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip is available: 23.0 -> 23.3.1
[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/
Collecting ChimeraX-ISOLDE==1.6.0
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxisolde/releases/1.6.0/ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl
(87.7 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.7/87.7 MB 3.5 MB/s eta 0:00:00
Collecting ChimeraX-PhenixUI==1.2.0
Downloading
https://cxtoolshed.rbvi.ucsf.edu/media/chimeraxphenixui/releases/1.2.0/ChimeraX_PhenixUI-1.2.0-py3-none-
any.whl (236 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 236.8/236.8 kB 1.2 MB/s eta 0:00:00
Installing collected packages: ChimeraX-PhenixUI, ChimeraX-ISOLDE
Successfully installed ChimeraX-ISOLDE-1.6.0 ChimeraX-PhenixUI-1.2.0
\---
Successfully installed ChimeraX-ISOLDE-1.6.0 ChimeraX-PhenixUI-1.2.0
Installed ChimeraX-ISOLDE (1.6.0)
Installed ChimeraX-PhenixUI (1.2.0)
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module
m = importlib.import_module(self.package_name)
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py",
line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import
File "", line 1007, in _find_and_load
File "", line 986, in _find_and_load_unlocked
File "", line 680, in _load_unlocked
File "", line 850, in exec_module
File "", line 228, in _call_with_frames_removed
File "/Users/tilpap/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 51, in
__version__ = _version()
File "/Users/tilpap/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 49, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 956, in require
needed = self.resolve(parse_requirements(requirements))
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 815, in resolve
dist = self._resolve_dist(
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 856, in _resolve_dist
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.21.0'
distribution was not found and is required by ChimeraX-ISOLDE
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize
api = self._get_api(session.logger)
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api
m = self.get_module()
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is
required by ChimeraX-ISOLDE
ChimeraX-ISOLDE (installed) [version: 1.6.0] [api package: chimerax.isolde]
[category: General] [tool: ISOLDE [categories: General] [synopsis: Interactive
Molecular Dynamics Flexible Fitting (iMDFF)]] [tool: Ramachandran Plot
[categories: Validation] [synopsis: Interactive Ramachandran plot]] [command:
isolde [categories: General] [synopsis: Command-line control of ISOLDE
simulations]] [command: rama [categories: General] [synopsis: Live
Ramachandran validation of models]] [command: rota [categories: General]
[synopsis: Live rotamer validation of models]] [command: ~rama [categories:
General] [synopsis: Turn off live Ramachandran validation of models]]
[command: ~rota [categories: General] [synopsis: Turn off live rotamer
validation of models]]: custom initialization failed
> view matrix models
> #2,0.32066,0.81227,-0.48723,-0.14818,-0.454,-0.31964,-0.83169,-12.713,-0.8313,0.4879,0.26628,8.2717
> view matrix models
> #2,0.25702,0.79691,-0.5467,0.62083,-0.56071,-0.33778,-0.75598,-8.4099,-0.78711,0.50084,0.36002,8.6391
> view matrix models
> #2,0.27809,0.75768,-0.59042,-1.7777,-0.64201,-0.3106,-0.70097,-4.1337,-0.71449,0.57398,0.40006,8.7255
> ui mousemode right "rotate selected models"
> view orient
> view matrix models
> #2,0.29051,0.78738,-0.54373,-0.68629,-0.62096,-0.2772,-0.73319,-4.5038,-0.72802,0.55063,0.4084,8.7167
> view
Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl
> toolshed show
Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl
> toolshed show
Downloading bundle ChimeraX_PhenixUI-1.2.1-py3-none-any.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip is available: 23.0 -> 23.3.1
[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/tilpap/Downloads/ChimeraX_PhenixUI-1.2.1-py3-none-any.whl
Requirement already satisfied: ChimeraX-Geometry~=1.3 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PhenixUI==1.2.1) (1.3)
Requirement already satisfied: ChimeraX-CheckWaters~=1.3 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PhenixUI==1.2.1) (1.3.1)
Requirement already satisfied: ChimeraX-Core~=1.5dev1 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PhenixUI==1.2.1) (1.6.1)
Requirement already satisfied: ChimeraX-Atomic~=1.32 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PhenixUI==1.2.1) (1.43.10)
Requirement already satisfied: ChimeraX-PDB~=2.6 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PhenixUI==1.2.1) (2.7.2)
Requirement already satisfied: ChimeraX-MapFilter~=2.0.1 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PhenixUI==1.2.1) (2.0.1)
Requirement already satisfied: ChimeraX-UI~=1.21 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PhenixUI==1.2.1) (1.28.4)
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-PhenixUI==1.2.1) (2.0)
Requirement already satisfied: ChimeraX-Map~=1.1.3 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-PhenixUI==1.2.1) (1.1.4)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (2.0.3)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (1.1.1)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (2.12)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (10.0.6)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (1.1)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (2.0.1)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (1.0.2)
Requirement already satisfied: ChimeraX-HBonds~=2.3 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-CheckWaters~=1.3->ChimeraX-PhenixUI==1.2.1) (2.4)
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-Map~=1.1.3->ChimeraX-PhenixUI==1.2.1) (1.5.1)
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-Map~=1.1.3->ChimeraX-PhenixUI==1.2.1) (1.2)
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~=1.1.3->ChimeraX-PhenixUI==1.2.1) (2.1.1)
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-Map~=1.1.3->ChimeraX-PhenixUI==1.2.1) (1.10.1)
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-MapData~=2.0->ChimeraX-PhenixUI==1.2.1) (1.2.3)
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~=2.6->ChimeraX-PhenixUI==1.2.1) (1.0.1)
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~=1.21->ChimeraX-PhenixUI==1.2.1) (1.0)
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~=2.3->ChimeraX-CheckWaters~=1.3->ChimeraX-
PhenixUI==1.2.1) (2.0.1)
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-HBonds~=2.3->ChimeraX-CheckWaters~=1.3->ChimeraX-
PhenixUI==1.2.1) (2.0.1)
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-MapSeries~=2.0->ChimeraX-Map~=1.1.3->ChimeraX-
PhenixUI==1.2.1) (2.0)
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~=1.32->ChimeraX-
PhenixUI==1.2.1) (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~=1.21->ChimeraX-
PhenixUI==1.2.1) (1.0.1)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (1.10.3)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (1.4)
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~=1.32->ChimeraX-PhenixUI==1.2.1) (2.0)
Installing collected packages: ChimeraX-PhenixUI
Attempting uninstall: ChimeraX-PhenixUI
Found existing installation: ChimeraX-PhenixUI 1.2.0
Uninstalling ChimeraX-PhenixUI-1.2.0:
Successfully uninstalled ChimeraX-PhenixUI-1.2.0
Successfully installed ChimeraX-PhenixUI-1.2.1
\---
Successfully installed ChimeraX-PhenixUI-1.2.1
Installed ChimeraX-PhenixUI (1.2.1)
Downloading bundle ChimeraX_QScore-1.0-cp39-cp39-macosx_10_13_universal2.whl
Errors may have occurred when running pip:
pip standard error:
\---
[notice] A new release of pip is available: 23.0 -> 23.3.1
[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/tilpap/Downloads/ChimeraX_QScore-1.0-cp39-cp39-macosx_10_13_universal2.whl
Requirement already satisfied: ChimeraX-Core>=1.5 in
/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages (from ChimeraX-QScore==1.0) (1.6.1)
Installing collected packages: ChimeraX-QScore
Successfully installed ChimeraX-QScore-1.0
\---
Successfully installed ChimeraX-QScore-1.0
Installed ChimeraX-QScore (1.0)
> select subtract #2
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Alignment identifier is 2/A
> ui tool show "Show Volume Menu"
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> select
> #1/A:8-10,27-28,86-89,92-97,123-131,178-182,194,207-214,291,324-325,339,341,352-354,391-410,428-479,499-506,512-526,534-564
1388 atoms, 1395 bonds, 172 residues, 1 model selected
> hide #1 models
> show #1 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/A
Destroying pre-existing alignment with identifier 2/A
Alignment identifier is 2/A
> hide #1 models
> show #2 models
> select
> #2/A:58-63,66-71,97-107,180-187,324-342,359-391,395-450,467-475,480-491,498-543
1674 atoms, 1690 bonds, 206 residues, 1 model selected
> select add #2
4453 atoms, 4547 bonds, 560 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
4453 atoms, 4547 bonds, 560 residues, 1 model selected
> select subtract #2
Nothing selected
> select
> #2/A:4-6,16-18,26-28,31-33,50-52,78-81,112-114,128-133,136-138,143-145,156-161,167-176,194-197,202-205,221-229,234-239,244-246,248-252,258-261,273-275,278-280,307-309,451-453,458-461
802 atoms, 795 bonds, 101 residues, 1 model selected
> open /Users/tilpap/Downloads/cryosparc_P144_J39_009_volume_map_sharp(1).mrc
Opened cryosparc_P144_J39_009_volume_map_sharp(1).mrc as #3, grid size
512,512,512, pixel 0.867, shown at level 0.142, step 2, values float32
> hide #2 models
> view
> surface dust #3 size 8.67
> volume #3 step 1
> view
> surface dust #3 size 8.67
> ui tool show "Hide Dust"
> help help:user/tools/hidedust.html
> surface dust #3 size 8.75
> surface dust #3 size 14.55
> surface dust #3 size 8.86
> surface dust #3 size 16.15
> surface dust #3 size 8.86
> surface dust #3 size 16.37
> ui tool show "Map Coordinates"
> ui tool show "Map Eraser"
> ui tool show "Hide Dust"
> view
> volume #3 level 0.4856
> save /Users/tilpap/Desktop/Template_model.mrc models #3
> open /Users/tilpap/Desktop/Template_model.mrc
Opened Template_model.mrc as #4, grid size 512,512,512, pixel 0.827, shown at
level 0.142, step 2, values float32
> view
> surface dust #3 size 8.27
> surface dust #4 size 8.27
> close #4
> ui tool show "Map Eraser"
> view
> volume erase #3 center 210.32,208.32,215.54 radius 74 outside true
Opened cryosparc_P144_J39_009_volume_map_sharp(1).mrc copy as #5, grid size
512,512,512, pixel 0.827, shown at step 1, values float32
> close #3
> close #4
> volume #5 level 0.362
> ui tool show "Map Statistics"
> measure mapstats
Map cryosparc_P144_J39_009_volume_map_sharp(1).mrc copy #5, minimum -3.526,
maximum 5.634, mean 0.0005955, SD 0.05409, RMS 0.0541
> ui tool show "Map Coordinates"
> save /Users/tilpap/Desktop/Template_model.mrc models #5
> open /Users/tilpap/Desktop/Template_model.mrc
Opened Template_model.mrc as #3, grid size 512,512,512, pixel 0.827, shown at
level 0.0145, step 2, values float32
> close #5
> volume #3 step 1
> surface dust #3 size 8.27
> volume #3 level 0.193
> ui tool show "Hide Dust"
> surface dust #3 size 8.41
> surface dust #3 size 11.81
> transparency 50
> transparency 0
> lighting full
> close #3
> open /Users/tilpap/Downloads/cryosparc_P144_J39_009_volume_map_sharp(1).mrc
Opened cryosparc_P144_J39_009_volume_map_sharp(1).mrc as #3, grid size
512,512,512, pixel 0.867, shown at level 0.142, step 2, values float32
> ui tool show "Map Eraser"
> ui tool show "Map Coordinates"
> surface dust #3 size 8.67
> view
> select add #3
802 atoms, 795 bonds, 101 residues, 3 models selected
> select add #2
4453 atoms, 4547 bonds, 560 residues, 3 models selected
> select subtract #2
2 models selected
> save /Users/tilpap/Desktop/Template_pixel.mrc models #3
> select subtract #3
Nothing selected
> open /Users/tilpap/Downloads/cryosparc_P144_J94_011_volume_map_sharp.mrc
Opened cryosparc_P144_J94_011_volume_map_sharp.mrc as #4, grid size
512,512,512, pixel 0.827, shown at level 0.327, step 2, values float32
> volume #4 color #78b3ff
> volume #4 step 1
> volume #4 level 1.091
> view
> volume #3 step 1
> volume flip #4
Opened cryosparc_P144_J94_011_volume_map_sharp.mrc z flip as #5, grid size
512,512,512, pixel 0.827, shown at step 1, values float32
> volume #3 level 0.3674
> select add #5
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models #5,1,0,0,11.25,0,1,0,3.4608,0,0,1,15.259
> view matrix models #5,1,0,0,12.123,0,1,0,3.7138,0,0,1,21.82
> view
> lighting full
> view matrix models
> #5,0.98958,0.14396,-0.00055933,-16.081,-0.14395,0.98957,0.0049578,34.775,0.0012672,-0.0048257,0.99999,22.581
> view matrix models
> #5,0.93332,0.35876,-0.014195,-47.05,-0.35876,0.93343,0.0025647,91.752,0.01417,0.002699,0.9999,18.329
> view matrix models
> #5,0.84479,0.53444,-0.026452,-63.324,-0.53456,0.84512,0.0030066,146.85,0.023962,0.0116,0.99965,14.463
> view matrix models
> #5,0.75034,0.66007,-0.036024,-68.328,-0.66036,0.75093,0.0050803,192.48,0.030405,0.019977,0.99934,11.416
> view matrix models
> #5,0.75034,0.66007,-0.036024,-69.344,-0.66036,0.75093,0.0050803,199.07,0.030405,0.019977,0.99934,11.114
> view matrix models
> #5,0.75034,0.66007,-0.036024,-69.937,-0.66036,0.75093,0.0050803,202.85,0.030405,0.019977,0.99934,10.94
> select subtract #5
Nothing selected
> ui tool show "Fit in Map"
> fitmap #5 inMap #3
Fit map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip in map
cryosparc_P144_J39_009_volume_map_sharp(1).mrc using 120819 points
correlation = 0.3466, correlation about mean = 0.1197, overlap = 1.184e+05
steps = 68, shift = 1.58, angle = 3.63 degrees
Position of cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) relative
to cryosparc_P144_J39_009_volume_map_sharp(1).mrc (#3) coordinates:
Matrix rotation and translation
0.70736438 0.70598306 -0.03497933 -70.33781613
-0.70596274 0.70808925 0.01504069 221.11143351
0.03538696 0.01405485 0.99927485 11.58309161
Axis -0.00069734 -0.04977461 -0.99876023
Axis point 230.84538258 195.34053078 0.00000000
Rotation angle (degrees) 44.97913456
Shift along axis -22.52541635
> fitmap #5 inMap #3
Fit map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip in map
cryosparc_P144_J39_009_volume_map_sharp(1).mrc using 120819 points
correlation = 0.3466, correlation about mean = 0.1198, overlap = 1.184e+05
steps = 40, shift = 0.00995, angle = 0.009 degrees
Position of cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) relative
to cryosparc_P144_J39_009_volume_map_sharp(1).mrc (#3) coordinates:
Matrix rotation and translation
0.70740058 0.70594243 -0.03506723 -70.31923972
-0.70591919 0.70813020 0.01515684 221.07979672
0.03553202 0.01403267 0.99927001 11.56279291
Axis -0.00079524 -0.04994195 -0.99875181
Axis point 230.83229388 195.31133072 0.00000000
Rotation angle (degrees) 44.97620409
Shift along axis -22.53359617
> view
> select add #5
2 models selected
> view matrix models
> #5,0.67894,0.73322,-0.037663,-69.649,-0.73317,0.67981,0.017956,232.15,0.038769,0.015422,0.99913,10.626
> view matrix models
> #5,0.64618,0.76212,-0.040407,-68.395,-0.76202,0.64721,0.021174,244.37,0.042289,0.017109,0.99896,9.5735
> view matrix models
> #5,0.64618,0.76212,-0.040407,-69.278,-0.76202,0.64721,0.021174,243.59,0.042289,0.017109,0.99896,9.6687
> fitmap #5 inMap #3
Fit map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip in map
cryosparc_P144_J39_009_volume_map_sharp(1).mrc using 120819 points
correlation = 0.6153, correlation about mean = 0.3637, overlap = 2.52e+05
steps = 64, shift = 1.93, angle = 2.73 degrees
Position of cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) relative
to cryosparc_P144_J39_009_volume_map_sharp(1).mrc (#3) coordinates:
Matrix rotation and translation
0.63748007 0.77046681 0.00025641 -76.16794974
-0.77046680 0.63748011 -0.00014962 250.13809629
-0.00027873 -0.00010217 0.99999996 21.18116524
Axis 0.00003079 0.00034728 -0.99999994
Axis point 227.73451656 206.01225219 0.00000000
Rotation angle (degrees) 50.39583000
Shift along axis -21.09664013
> fitmap #5 inMap #3
Fit map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip in map
cryosparc_P144_J39_009_volume_map_sharp(1).mrc using 120819 points
correlation = 0.6153, correlation about mean = 0.3639, overlap = 2.52e+05
steps = 28, shift = 0.014, angle = 0.0205 degrees
Position of cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) relative
to cryosparc_P144_J39_009_volume_map_sharp(1).mrc (#3) coordinates:
Matrix rotation and translation
0.63749232 0.77045671 0.00005837 -76.13875137
-0.77045671 0.63749231 0.00014751 250.08110464
0.00007644 -0.00013901 0.99999999 21.10400615
Axis -0.00018594 -0.00001173 -0.99999998
Axis point 227.68368502 205.95544995 0.00000000
Rotation angle (degrees) 50.39491972
Shift along axis -21.09278192
> select subtract #5
Nothing selected
> transparency #3.1#5.1 50
> show #2 models
> view
> hide #2 models
> view
> surface dust #5 size 8.27
> transparency #5.1 0
> view
> volume #4 level 1.481
> volume #4 level 4.289
> view
> transparency #5.1 50
> transparency #5.1 0
> open /Users/tilpap/Desktop/IEVA_FINAL/RealSpaceRefine_1/6wxb_Ieva-
> coot_manualfit-coot-11_real_space_refined_001.pdb
Chain information for 6wxb_Ieva-coot_manualfit-
coot-11_real_space_refined_001.pdb #6
---
Chain | Description
A B C | No description available
> select add #6
12433 atoms, 12740 bonds, 2 pseudobonds, 1534 residues, 2 models selected
> view matrix models #6,1,0,0,66.057,0,1,0,82.334,0,0,1,32.561
> view matrix models #6,1,0,0,91.134,0,1,0,116.14,0,0,1,56.843
> view
> view matrix models #6,1,0,0,78.294,0,1,0,102.87,0,0,1,62.176
> view matrix models #6,1,0,0,73.415,0,1,0,72.028,0,0,1,67.004
> view matrix models
> #6,0.93478,-0.35083,0.055714,128.28,0.35235,0.93566,-0.019885,32.587,-0.045153,0.038218,0.99825,68.129
> view matrix models
> #6,0.59674,-0.78886,0.14697,231.66,0.79831,0.60217,-0.0092049,15.916,-0.08124,0.12282,0.9891,61.908
> fitmap #6 inMap #5
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433
atoms
average map value = 0.3386, steps = 88
shifted from previous position = 3.8
rotated from previous position = 4.21 degrees
atoms outside contour = 10000, contour level = 1.0908
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5)
coordinates:
Matrix rotation and translation
-0.30404502 -0.94826858 0.09134185 385.88090492
0.94809837 -0.29182648 0.12628061 95.64462646
-0.09309196 0.12499605 0.98778028 45.11093558
Axis -0.00067420 0.09679965 0.99530366
Axis point 159.76946495 187.25777936 0.00000000
Rotation angle (degrees) 107.70075457
Shift along axis 53.89728586
> view matrix models
> #6,0.5369,-0.83498,0.12062,249.72,0.83243,0.54756,0.085143,2.7693,-0.13714,0.054696,0.98904,83.326
> fitmap #6 inMap #5
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433
atoms
average map value = 0.3286, steps = 120
shifted from previous position = 1.95
rotated from previous position = 3.47 degrees
atoms outside contour = 10007, contour level = 1.0908
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5)
coordinates:
Matrix rotation and translation
-0.34607559 -0.93713009 0.04493208 398.55940282
0.92906755 -0.33564292 0.15549056 99.61443454
-0.13063375 0.09555643 0.98681498 53.95082594
Axis -0.03195813 0.09361535 0.99509539
Axis point 166.95982175 187.19443851 0.00000000
Rotation angle (degrees) 110.33153281
Shift along axis 50.27444654
> view matrix models
> #6,0.49518,-0.85601,0.1485,254.68,0.85889,0.50806,0.064651,5.9688,-0.13079,0.095531,0.9868,82.398
> view matrix models
> #6,0.46514,-0.88265,0.067636,275.59,0.88515,0.46267,-0.049512,26.498,0.012409,0.082899,0.99648,61.614
> fitmap #6 inMap #5
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433
atoms
average map value = 0.4337, steps = 92
shifted from previous position = 3.35
rotated from previous position = 4.53 degrees
atoms outside contour = 9457, contour level = 1.0908
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5)
coordinates:
Matrix rotation and translation
-0.45421105 -0.88813785 0.07002486 401.24159261
0.89047660 -0.45499970 0.00516759 147.91925122
0.02727176 0.06470267 0.99753186 39.94887948
Axis 0.03344434 0.02401692 0.99915197
Axis point 155.11484390 195.65580904 0.00000000
Rotation angle (degrees) 117.11895860
Shift along axis 56.88682875
> fitmap #6 inMap #5
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433
atoms
average map value = 0.4331, steps = 44
shifted from previous position = 0.0315
rotated from previous position = 0.113 degrees
atoms outside contour = 9461, contour level = 1.0908
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5)
coordinates:
Matrix rotation and translation
-0.45594649 -0.88727920 0.06963061 401.45758588
0.88959247 -0.45672525 0.00522397 148.29000161
0.02716694 0.06432472 0.99755917 40.02658725
Axis 0.03323326 0.02387798 0.99916235
Axis point 155.20772266 195.64674027 0.00000000
Rotation angle (degrees) 117.22953117
Shift along axis 56.87566996
> view matrix models
> #6,0.39473,-0.91752,0.048472,292.63,0.9184,0.39246,-0.05017,34.035,0.027008,0.06432,0.99756,61.022
> view matrix models
> #6,0.39473,-0.91752,0.048472,296.22,0.9184,0.39246,-0.05017,30.891,0.027008,0.06432,0.99756,60.772
> view matrix models
> #6,0.39473,-0.91752,0.048472,294.39,0.9184,0.39246,-0.05017,29.362,0.027008,0.06432,0.99756,60.129
> view matrix models
> #6,0.29445,-0.95372,0.060973,312.97,0.95517,0.29163,-0.051051,39.48,0.030907,0.073271,0.99683,58.287
> view matrix models
> #6,0.19886,-0.97734,0.072534,329.05,0.97939,0.19552,-0.050668,50.554,0.035338,0.081116,0.99608,56.54
> fitmap #6 inMap #5
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433
atoms
average map value = 2.872, steps = 88
shifted from previous position = 3.02
rotated from previous position = 5.93 degrees
atoms outside contour = 2354, contour level = 1.0908
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5)
coordinates:
Matrix rotation and translation
-0.66966311 -0.74266496 -0.00029198 423.24879435
0.74266500 -0.66966312 -0.00005650 200.78773879
-0.00015357 -0.00025468 0.99999996 52.80702091
Axis -0.00013343 -0.00009319 0.99999999
Axis point 166.97170419 194.52827874 0.00000000
Rotation angle (degrees) 132.04107081
Shift along axis 52.73183766
> fitmap #6 inMap #5
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) using 12433
atoms
average map value = 2.872, steps = 28
shifted from previous position = 0.0131
rotated from previous position = 0.00384 degrees
atoms outside contour = 2358, contour level = 1.0908
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5)
coordinates:
Matrix rotation and translation
-0.66964668 -0.74267975 -0.00033751 423.25389191
0.74267981 -0.66964669 -0.00010054 200.78927035
-0.00015135 -0.00031798 0.99999994 52.82920489
Axis -0.00014639 -0.00012533 0.99999998
Axis point 166.97254962 194.53398331 0.00000000
Rotation angle (degrees) 132.03980421
Shift along axis 52.74207646
> select subtract #6
Nothing selected
> view
> volume #5 level 0.873
> volume #5 level 0.752
> show #!6 cartoons
> rainbow #!6
> transparency #5.1 50
> show #!6 atoms
> view
> ui tool show "Volume Viewer"
> volume #5 level 2.142
> transparency #5.1 0
> volume #5 level 0.4934
> transparency #5.1 50
> color #!6 bychain
> view
> open /Users/tilpap/Downloads/cryosparc_P144_J100_010_volume_map_sharp.mrc
Opened cryosparc_P144_J100_010_volume_map_sharp.mrc as #7, grid size
512,512,512, pixel 0.827, shown at level 0.0327, step 2, values float32
> volume flip #7
Opened cryosparc_P144_J100_010_volume_map_sharp.mrc z flip as #8, grid size
512,512,512, pixel 0.827, shown at step 1, values float32
> close #7
> close #4
> volume #8 level 0.07744
> surface dust #5 size 8.27
> surface dust #8 size 8.27
> view
> ui tool show "Model Panel"
> select add #8
2 models selected
> view matrix models #8,1,0,0,17.275,0,1,0,9.3595,0,0,1,-4.1556
> view matrix models #8,1,0,0,10.418,0,1,0,11.296,0,0,1,21.823
> view matrix models #8,1,0,0,-2.6968,0,1,0,15.88,0,0,1,47.692
> view matrix models #8,1,0,0,-4.8533,0,1,0,19.108,0,0,1,43.561
> view matrix models #8,1,0,0,2.1203,0,1,0,5.882,0,0,1,43.468
> view matrix models #8,1,0,0,4.0235,0,1,0,3.3618,0,0,1,43.477
> view matrix models #8,1,0,0,7.7544,0,1,0,9.278,0,0,1,26.775
> view matrix models #8,1,0,0,7.7567,0,1,0,9.1237,0,0,1,22.031
> view matrix models
> #8,0.99098,0.13388,0.0053013,-20.229,-0.13395,0.99088,0.014729,36.434,-0.003281,-0.015306,0.99988,26.045
> view matrix models
> #8,0.98893,0.10903,0.10063,-34.063,-0.12631,0.9745,0.18546,3.211,-0.077845,-0.19612,0.97749,85.352
> view matrix models
> #8,0.97543,0.2196,-0.017463,-30.693,-0.21795,0.97355,0.068496,46.896,0.032043,-0.063007,0.9975,29.314
> view matrix models
> #8,0.93825,0.34533,-0.020574,-49.228,-0.34309,0.93648,0.072718,80.515,0.04438,-0.061169,0.99714,26.378
> view matrix models
> #8,0.91968,0.39207,-0.021616,-55.135,-0.3896,0.91797,0.074438,93.998,0.049028,-0.060038,0.99699,25.18
> ui tool show "Fit in Map"
> fitmap #8 inMap #5
Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map
cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points
correlation = 0.1876, correlation about mean = 0.03582, overlap = 1.081e+04
steps = 84, shift = 2.61, angle = 2.47 degrees
Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative
to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.88543959 -0.46040116 -0.06346264 134.45640129
0.46063513 0.88751158 -0.01176737 -73.46224731
0.06174154 -0.01881382 0.99791484 -8.79599391
Axis -0.00758063 -0.13469563 0.99085802
Axis point 217.53332221 237.91622919 0.00000000
Rotation angle (degrees) 27.69514593
Shift along axis 0.16019847
> fitmap #8 inMap #5
Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map
cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points
correlation = 0.1876, correlation about mean = 0.03584, overlap = 1.081e+04
steps = 44, shift = 0.00386, angle = 0.00241 degrees
Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative
to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.88545079 -0.46038471 -0.06342566 134.44121736
0.46061822 0.88752042 -0.01176281 -73.46322400
0.06170698 -0.01879962 0.99791724 -8.79478709
Axis -0.00757060 -0.13462486 0.99086772
Axis point 217.53483056 237.89662619 0.00000000
Rotation angle (degrees) 27.69376230
Shift along axis 0.15770505
> view matrix models
> #8,0.91936,0.3903,-0.049438,-43.061,-0.38855,0.92049,0.041515,101.02,0.061711,-0.018958,0.99791,12.543
> view matrix models
> #8,0.88044,0.47122,-0.052821,-51.527,-0.4694,0.88191,0.043504,126.04,0.067083,-0.013508,0.99766,10.285
> ui tool show "Fit in Map"
> fitmap #8 inMap #5
Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map
cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points
correlation = 0.2047, correlation about mean = 0.04911, overlap = 1.219e+04
steps = 80, shift = 0.699, angle = 2.7 degrees
Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative
to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.93653359 -0.34120415 -0.08052678 103.54324139
0.34308405 0.93924753 0.01036405 -60.05953890
0.07209832 -0.03733373 0.99669856 -6.26639293
Axis -0.06787563 -0.21719094 0.97376640
Axis point 221.54841481 262.23756222 0.00000000
Rotation angle (degrees) 20.57061795
Shift along axis -0.08567774
> fitmap #8 inMap #5
Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map
cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points
correlation = 0.2048, correlation about mean = 0.04919, overlap = 1.22e+04
steps = 44, shift = 0.0194, angle = 0.0135 degrees
Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative
to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.93647009 -0.34135654 -0.08061943 103.60616398
0.34324944 0.93918571 0.01048936 -60.09243656
0.07213600 -0.03749555 0.99668976 -6.22427286
Axis -0.06824953 -0.21726594 0.97372353
Axis point 221.58230641 262.25919035 0.00000000
Rotation angle (degrees) 20.58155097
Shift along axis -0.07575321
> fitmap #8 inMap #5
Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map
cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points
correlation = 0.2047, correlation about mean = 0.04912, overlap = 1.219e+04
steps = 44, shift = 0.0165, angle = 0.00569 degrees
Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative
to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.93649818 -0.34127935 -0.08061989 103.58467455
0.34316851 0.93921583 0.01044049 -60.08421321
0.07215635 -0.03744371 0.99669024 -6.25096488
Axis -0.06812144 -0.21734386 0.97371511
Axis point 221.59474536 262.26983057 0.00000000
Rotation angle (degrees) 20.57676805
Shift along axis -0.08406151
> view matrix models
> #8,0.80732,0.58971,-0.021792,-67.359,-0.58684,0.80618,0.075508,160.37,0.062097,-0.048171,0.99691,19.234
> view matrix models
> #8,0.66576,0.74593,0.019003,-79.371,-0.74457,0.66246,0.082233,223.33,0.048751,-0.068896,0.99643,26.618
> view matrix models
> #8,0.65446,0.75583,0.020208,-79.356,-0.75454,0.65116,0.081575,228,0.048497,-0.068635,0.99646,26.609
> ui tool show "Fit in Map"
> fitmap #8 inMap #5
Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map
cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points
correlation = 0.97, correlation about mean = 0.9154, overlap = 9.164e+04
steps = 112, shift = 1.25, angle = 4.9 degrees
Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative
to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.99998675 -0.00514666 0.00005815 1.08549866
0.00514666 0.99998675 0.00006222 -1.09282105
-0.00005847 -0.00006192 1.00000000 0.17330457
Axis -0.01205947 0.01132894 0.99986310
Axis point 213.20362866 210.71068577 0.00000000
Rotation angle (degrees) 0.29492370
Shift along axis 0.14780980
> fitmap #8 inMap #5
Fit map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip in map
cryosparc_P144_J94_011_volume_map_sharp.mrc z flip using 150683 points
correlation = 0.97, correlation about mean = 0.9155, overlap = 9.16e+04
steps = 24, shift = 0.0102, angle = 0.00529 degrees
Position of cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) relative
to cryosparc_P144_J94_011_volume_map_sharp.mrc z flip (#5) coordinates:
Matrix rotation and translation
0.99998679 -0.00514036 -0.00003301 1.09253131
0.00514036 0.99998679 0.00007480 -1.09231530
0.00003262 -0.00007497 1.00000000 0.16067979
Axis -0.01456665 -0.00638317 0.99987353
Axis point 212.85543994 212.42271076 0.00000000
Rotation angle (degrees) 0.29455951
Shift along axis 0.15171738
> ui tool show "Model Panel"
> select subtract #8
Nothing selected
> volume #8 level 0.06065
> volume #8 level 0.1166
> volume #8 level 0.1558
> volume #8 level 0.04385
> volume #8 level 0.04
> ui tool show "Fit in Map"
> fitmap #6 inMap #8
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) using 12433
atoms
average map value = 0.2414, steps = 28
shifted from previous position = 0.0285
rotated from previous position = 0.0348 degrees
atoms outside contour = 1035, contour level = 0.04
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8)
coordinates:
Matrix rotation and translation
-0.66626061 -0.74571889 -0.00037366 423.21428798
0.74571896 -0.66626064 -0.00005095 199.82839059
-0.00021096 -0.00031259 0.99999993 52.70876822
Axis -0.00017543 -0.00010909 0.99999998
Axis point 166.89484434 194.62188074 0.00000000
Rotation angle (degrees) 131.77911239
Shift along axis 52.61272510
> fitmap #6 inMap #8
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) using 12433
atoms
average map value = 0.2414, steps = 28
shifted from previous position = 0.0228
rotated from previous position = 0.00297 degrees
atoms outside contour = 1052, contour level = 0.04
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8)
coordinates:
Matrix rotation and translation
-0.66629689 -0.74568646 -0.00038035 423.20551252
0.74568653 -0.66629692 -0.00006771 199.83152932
-0.00020293 -0.00032873 0.99999993 52.69205639
Axis -0.00017502 -0.00011896 0.99999998
Axis point 166.89254447 194.61556026 0.00000000
Rotation angle (degrees) 131.78190059
Shift along axis 52.59421279
> transparency #8.1 50
> view
> surface dust #8 size 8.27
> ui tool show "Map Eraser"
> volume erase #8 center 224.99,229.05,357.13 radius 30.518
Opened cryosparc_P144_J100_010_volume_map_sharp.mrc z flip copy as #7, grid
size 512,512,512, pixel 0.827, shown at step 1, values float32
> surface dust #7 size 8.27
> volume erase #7 center 221.6,233.53,373.55 radius 30.487
> volume erase #7 center 215.01,211.18,385.14 radius 30.487
> volume erase #7 center 237.91,273.32,358.91 radius 30.487
> view
> open /Users/tilpap/Downloads/cryosparc_P144_J102_006_volume_map_sharp.mrc
Opened cryosparc_P144_J102_006_volume_map_sharp.mrc as #4, grid size
512,512,512, pixel 0.827, shown at level 0.0465, step 2, values float32
> volume flip #4
Opened cryosparc_P144_J102_006_volume_map_sharp.mrc z flip as #9, grid size
512,512,512, pixel 0.827, shown at step 1, values float32
> close #4
> surface dust #7 size 8.27
> surface dust #9 size 8.27
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
> volume #9 level 0.06903
> ui tool show "Model Panel"
> select add #9
2 models selected
> view
> ui mousemode right "rotate selected models"
> view matrix models #9,1,0,0,4.8209,0,1,0,-2.3742,0,0,1,14.405
> view matrix models #9,1,0,0,8.4096,0,1,0,-4.0268,0,0,1,24.425
> view matrix models #9,1,0,0,8.1749,0,1,0,-3.5191,0,0,1,21.325
> view matrix models #9,1,0,0,16.675,0,1,0,9.9479,0,0,1,21.765
> view matrix models
> #9,0.9814,0.19055,0.023426,-25.159,-0.19105,0.98134,0.021589,49.82,-0.018875,-0.025663,0.99949,31.365
> view matrix models
> #9,0.95896,0.2816,0.032992,-41.955,-0.28257,0.95879,0.029528,72.339,-0.023318,-0.037639,0.99902,34.973
> view matrix models
> #9,0.90839,0.41526,0.048908,-63.274,-0.4172,0.90794,0.039813,109.55,-0.027873,-0.05657,0.99801,40.209
> view matrix models
> #9,0.87873,0.47393,0.056686,-71.223,-0.47643,0.87812,0.043749,127.64,-0.029043,-0.065451,0.99743,42.482
> view matrix models
> #9,0.8334,0.54901,0.063541,-79.195,-0.55097,0.83434,0.017682,158.15,-0.043307,-0.049745,0.99782,42.038
> view matrix models
> #9,0.74194,0.66718,0.066267,-85.842,-0.66749,0.74433,-0.020504,209.95,-0.063005,-0.02902,0.99759,41.791
> view matrix models
> #9,0.75474,0.65586,0.014378,-75.414,-0.6556,0.7533,0.052158,190.53,0.023378,-0.048792,0.99854,27.614
> view matrix models
> #9,0.67262,0.73858,0.045656,-82.3,-0.73979,0.66974,0.064413,223.72,0.016996,-0.077101,0.99688,35.383
> view matrix models
> #9,0.67262,0.73858,0.045656,-84.852,-0.73979,0.66974,0.064413,223.62,0.016996,-0.077101,0.99688,35.705
> ui tool show "Fit in Map"
> fitmap #9 inMap #8
Fit map cryosparc_P144_J102_006_volume_map_sharp.mrc z flip in map
cryosparc_P144_J100_010_volume_map_sharp.mrc z flip using 198494 points
correlation = 0.9914, correlation about mean = 0.9794, overlap = 9487
steps = 132, shift = 1.6, angle = 5.14 degrees
Position of cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#9) relative
to cryosparc_P144_J100_010_volume_map_sharp.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.99999814 0.00193008 -0.00002018 -0.41174072
-0.00193008 0.99999814 -0.00000369 0.40752431
0.00002017 0.00000373 1.00000000 -0.02898894
Axis 0.00192263 -0.01045415 -0.99994351
Axis point 211.06782868 213.55641856 0.00000000
Rotation angle (degrees) 0.11059147
Shift along axis 0.02393536
> select subtract #9
Nothing selected
> transparency #7.1#9.1 0
> ui tool show "Model Panel"
> hide #!7 models
> hide #!6 models
> ui tool show "Model Panel"
> show #!6 models
> transparency #9.1 50
> open /Users/tilpap/Downloads/cryosparc_P144_J104_map_locres.mrc
Opened cryosparc_P144_J104_map_locres.mrc as #4, grid size 512,512,512, pixel
0.827, shown at level 6.6, step 2, values float32
> ui tool show "Volume Viewer"
> volume flip #4
Opened cryosparc_P144_J104_map_locres.mrc z flip as #10, grid size
512,512,512, pixel 0.827, shown at step 1, values float32
> close #4
> surface dust #9 size 8.27
> surface dust #10 size 8.27
> show #!6 surfaces
> hide #!6 surfaces
> volume #!9-10 style mesh
> volume #!9-10 style surface
> ui tool show "Color Zone"
QMainWidget::resizeDocks: all sizes need to be larger than 0
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> volume #!9-10 hide
> volume show
> close #10
> ui tool show "Volume Viewer"
> close #7
> ui tool show "Map Eraser"
Can only have one displayed volume when erasing
> ui windowfill toggle
> ui mousemode right "map eraser"
Can only have one displayed volume when erasing
> ui mousemode right "map eraser"
> ui tool show "Volume Viewer"
> ui tool show "Model Panel"
> select add #8
2 models selected
> ui tool show "Map Eraser"
> volume erase #8 center 232.47,236.73,378.2 radius 30.518
Opened cryosparc_P144_J100_010_volume_map_sharp.mrc z flip copy as #7, grid
size 512,512,512, pixel 0.827, shown at step 1, values float32
> volume erase #7 center 232.47,236.73,378.2 radius 30.487
> surface dust #7 size 8.27
> volume erase #7 center 265.87,242.31,370.42 radius 39.802
> volume erase #7 center 174.3,206.21,387.63 radius 39.802
> volume erase #7 center 215.32,222.14,381.43 radius 39.802
> view
> ui mousemode right zoom
> transparency #6.2-4#7.1 0
> ui tool show "Surface Color"
> open /Users/tilpap/Downloads/cryosparc_P144_J104_map_locres.mrc
Opened cryosparc_P144_J104_map_locres.mrc as #4, grid size 512,512,512, pixel
0.827, shown at level 6.6, step 2, values float32
> color sample #9.1 map #4 palette #ff0000:#ffffff:#0000ff
Map values for surface "surface": minimum 0, mean 2.427, maximum 43.23
> color sample #9.1 map #4 palette 2.5,#ff0000:3.5,#ffffff:4.5,#0000ff
Map values for surface "surface": minimum 0, mean 2.427, maximum 43.23
> color sample #9.1 map #4 palette 2.5,#ff0000:3.5,#ffffff:4.5,#0000ff
Map values for surface "surface": minimum 0, mean 2.427, maximum 43.23
> ui tool show "Model Panel"
> color sample #7.1 map #4 palette 2.5,#ff0000:3.5,#ffffff:4.5,#0000ff
Map values for surface "surface": minimum 0, mean 1.779, maximum 44.38
> color sample #7.1 map #4 palette #0000ff:#00ff00:#ff0000:#808080:#808080
Map values for surface "surface": minimum 0, mean 1.779, maximum 44.38
> color sample #7.1 map #4 palette #0000ff:#59e2f9:#31ff25:#eee34f:#e8181d
Map values for surface "surface": minimum 0, mean 1.779, maximum 44.38
> volume flip #4
Opened cryosparc_P144_J104_map_locres.mrc z flip as #10, grid size
512,512,512, pixel 0.827, shown at step 1, values float32
> color sample #7.1 map #4 palette
> 2.5,#0000ff:3,#59e2f9:3.5,#31ff25:4,#eee34f:4.5,#e8181d
Map values for surface "surface": minimum 0, mean 1.779, maximum 44.38
> ui tool show "Model Panel"
> hide #!10 models
> select subtract #8
Nothing selected
> open /Users/tilpap/Downloads/cryosparc_P144_J102_006_volume_map_sharp.mrc
Opened cryosparc_P144_J102_006_volume_map_sharp.mrc as #11, grid size
512,512,512, pixel 0.827, shown at level 0.0465, step 2, values float32
> surface dust #7 size 8.27
> surface dust #11 size 8.27
> volume flip #11
Opened cryosparc_P144_J102_006_volume_map_sharp.mrc z flip as #12, grid size
512,512,512, pixel 0.827, shown at step 1, values float32
> surface dust #12 size 8.27
> color sample #7.1 map #10 palette
> 2.5,#0000ff:3,#59e2f9:3.5,#31ff25:4,#eee34f:4.5,#e8181d
Map values for surface "surface": minimum 0, mean 1.713, maximum 40.53
> color sample #12.1 map #10 palette
> 2.5,#0000ff:3,#59e2f9:3.5,#31ff25:4,#eee34f:4.5,#e8181d
Map values for surface "surface": minimum 0, mean 0.7784, maximum 44.73
> color sample #12.1 map #10 palette
> 2.5,#0000ff:3,#59e2f9:3.5,#31ff25:4,#eee34f:4.5,#e8181d
Map values for surface "surface": minimum 0, mean 0.7784, maximum 44.73
> ui tool show "Model Panel"
> show #!12 models
> ui tool show "Fit in Map"
> fitmap #2 inMap #12
Fit molecule best_model.pdb (#2) to map
cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) using 4453 atoms
average map value = 3.114e-06, steps = 568
shifted from previous position = 3.28
rotated from previous position = 5.64 degrees
atoms outside contour = 4453, contour level = 0.04651
Position of best_model.pdb (#2) relative to
cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) coordinates:
Matrix rotation and translation
0.23275852 0.80649914 -0.54349113 -1.07359348
-0.68437071 -0.26122679 -0.68073291 -4.88240916
-0.69098495 0.53039579 0.49114163 11.23787951
Axis 0.62867824 0.07656177 -0.77388756
Axis point 1.99880654 -4.36415796 0.00000000
Rotation angle (degrees) 105.58474229
Shift along axis -9.74560596
> fitmap #2 inMap #12
Fit molecule best_model.pdb (#2) to map
cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) using 4453 atoms
average map value = 3.09e-06, steps = 76
shifted from previous position = 0.0526
rotated from previous position = 0.0967 degrees
atoms outside contour = 4453, contour level = 0.04651
Position of best_model.pdb (#2) relative to
cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) coordinates:
Matrix rotation and translation
0.23264762 0.80720495 -0.54248986 -1.05661673
-0.68338822 -0.26120075 -0.68172921 -4.87611477
-0.69199395 0.52933386 0.49086662 11.20398099
Axis 0.62867694 0.07760931 -0.77378427
Axis point 2.00106879 -4.35288911 0.00000000
Rotation angle (degrees) 105.59544533
Shift along axis -9.71216678
> view
> ui tool show "Volume Viewer"
> volume #12 level 0.07438
> select add #2
4453 atoms, 4547 bonds, 560 residues, 1 model selected
> select subtract #2
Nothing selected
> select add #2
4453 atoms, 4547 bonds, 560 residues, 1 model selected
> select add #1
8949 atoms, 9127 bonds, 1134 residues, 2 models selected
> select subtract #2
4496 atoms, 4580 bonds, 574 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #6
12433 atoms, 12740 bonds, 2 pseudobonds, 1534 residues, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.14468,-0.98948,-0.00020096,343.39,0.98948,0.14468,0.00046899,49.695,-0.00043498,-0.0002667,1,61.856
> view matrix models
> #6,0.14468,-0.98948,-0.00020096,332.78,0.98948,0.14468,0.00046899,46.697,-0.00043498,-0.0002667,1,57.408
> ui mousemode right rotate
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.14468,-0.98948,-0.00020096,335.48,0.98948,0.14468,0.00046899,47.2,-0.00043498,-0.0002667,1,57.226
> view matrix models
> #6,0.33541,-0.94205,-0.0069956,301.11,0.94202,0.33531,0.012944,23.148,-0.0098484,-0.010932,0.99989,60.263
> view matrix models
> #6,0.41757,-0.9086,-0.0087215,284.14,0.90856,0.41738,0.017878,14.783,-0.012604,-0.015389,0.9998,61.365
> view matrix models
> #6,0.54509,-0.83831,-0.010587,254.85,0.83822,0.5447,0.026251,4.4151,-0.01624,-0.023184,0.9996,63.125
> view matrix models
> #6,0.64481,-0.76426,-0.011203,228.9,0.76412,0.6442,0.033541,-0.97755,-0.018417,-0.030188,0.99937,64.552
> view matrix models
> #6,0.79021,-0.6128,-0.0067924,183.61,0.61265,0.78964,0.03369,-0.886,-0.015282,-0.030783,0.99941,64.175
> view matrix models
> #6,0.94148,-0.33707,-0.00035547,118.13,0.3369,0.94099,0.032187,16.895,-0.010515,-0.030423,0.99948,63.405
> view matrix models
> #6,0.91848,-0.34305,0.19675,92.369,0.32097,0.93729,0.13589,3.9922,-0.23103,-0.061661,0.97099,105.08
> view matrix models
> #6,0.93305,-0.34153,0.11304,102.76,0.32937,0.93737,0.11337,6.1754,-0.14467,-0.068547,0.9871,90.925
> view matrix models
> #6,0.93979,-0.33543,-0.065378,128.05,0.33894,0.93933,0.052737,13.713,0.043722,-0.071721,0.99647,62.176
> view matrix models
> #6,0.90501,-0.32963,-0.26891,163.34,0.34325,0.93923,0.0039019,20.54,0.25128,-0.095835,0.96316,40.311
> view matrix models
> #6,0.89205,-0.32775,-0.31116,171.41,0.34284,0.93937,-0.0065869,22.181,0.29445,-0.1008,0.95034,36.655
> view matrix models
> #6,0.92726,-0.33307,-0.17106,145.66,0.34245,0.93913,0.027717,17.043,0.15142,-0.084281,0.98487,49.97
> view matrix models
> #6,0.93471,-0.33437,-0.12044,137.03,0.3411,0.93918,0.039792,15.391,0.099806,-0.078274,0.99192,55.594
> view matrix models
> #6,0.93614,-0.33465,-0.10796,134.96,0.34067,0.93921,0.042742,15,0.087092,-0.076791,0.99324,57.043
> view
> ui tool show "Model Panel"
> select subtract #6
3 models selected
> ui tool show "Fit in Map"
> fitmap #6 inMap #12
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) using 12433
atoms
average map value = 0.04192, steps = 72
shifted from previous position = 1.12
rotated from previous position = 1.74 degrees
atoms outside contour = 8993, contour level = 0.074378
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12)
coordinates:
Matrix rotation and translation
0.92540790 -0.36081908 -0.11588708 142.73175856
0.36655256 0.92984830 0.03195887 13.86156265
0.09622603 -0.07205370 0.99274811 55.13564170
Axis -0.13600423 -0.27735378 0.95109291
Axis point 17.23278134 403.01433899 0.00000000
Rotation angle (degrees) 22.48163407
Shift along axis 29.18243870
> fitmap #6 inMap #12
Fit molecule 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
to map cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12) using 12433
atoms
average map value = 0.04192, steps = 48
shifted from previous position = 0.01
rotated from previous position = 0.00753 degrees
atoms outside contour = 8990, contour level = 0.074378
Position of 6wxb_Ieva-coot_manualfit-coot-11_real_space_refined_001.pdb (#6)
relative to cryosparc_P144_J102_006_volume_map_sharp.mrc z flip (#12)
coordinates:
Matrix rotation and translation
0.92540013 -0.36087074 -0.11578825 142.73543521
0.36660337 0.92982609 0.03202203 13.85087090
0.09610712 -0.07208156 0.99275761 55.15315033
Axis -0.13611443 -0.27705114 0.95116535
Axis point 17.29041027 402.96782995 0.00000000
Rotation angle (degrees) 22.48316845
Shift along axis 29.19401340
> volume #!12 hide
> hide #!6 atoms
> volume show
> ui tool show "Show Volume Menu"
> view
> ui tool show "Show Volume Menu"
===== Log before crash end =====
Log:
Startup Errors
---
error | Bundle 'ChimeraX-ISOLDE' custom initialization failed
warning | Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 490, in get_module
m = importlib.import_module(self.package_name)
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/importlib/__init__.py",
line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 850, in exec_module
File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
File "/Users/tilpap/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 51, in <module>
__version__ = _version()
File "/Users/tilpap/Library/Application Support/ChimeraX/1.6/site-
packages/chimerax/isolde/__init__.py", line 49, in _version
return pkg_resources.require('ChimeraX-ISOLDE')[0].version
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 956, in require
needed = self.resolve(parse_requirements(requirements))
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 815, in resolve
dist = self._resolve_dist(
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/pkg_resources/__init__.py", line 856, in _resolve_dist
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'ChimeraX-Clipper~=0.21.0'
distribution was not found and is required by ChimeraX-ISOLDE
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 364, in initialize
api = self._get_api(session.logger)
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 509, in _get_api
m = self.get_module()
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 492, in get_module
raise ToolshedError("Error importing bundle %s's module: %s" % (self.name,
str(e)))
chimerax.core.toolshed.ToolshedError: Error importing bundle ChimeraX-ISOLDE's
module: The 'ChimeraX-Clipper~=0.21.0' distribution was not found and is
required by ChimeraX-ISOLDE
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-18.8.6
OpenGL renderer: Intel Iris Pro 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: MacBookPro11,4
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2,8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 486.0.0.0.0
OS Loader Version: 540.120.3~37
SMC Version (system): 2.29f24
Software:
System Software Overview:
System Version: macOS 12.7.1 (21G920)
Kernel Version: Darwin 21.6.0
Time since boot: 41 days 19:11
Graphics/Displays:
Intel Iris Pro:
Chipset Model: Intel Iris Pro
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x0d26
Revision ID: 0x0008
Metal Family: Supported, Metal GPUFamily macOS 1
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.6.0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBImages: 1.2
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.1
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.0
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 23 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash adding Volume menu |
comment:2 by , 23 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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The exception info says "VM - Fault hit memory shortage" and memory usage was supposedly 22.3GB at the time.