![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#10055 closed defect (nonchimerax)
Graphics crash, macOS 12.6.2, Intel Iris Graphics 550
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| 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: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x0000700018655000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700017652000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001664f000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001564c000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700014649000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700013646000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700012643000 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x0000000113428600 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2702 in update_buffer_data
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1899 in update_buffers
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1911 in activate_bindings
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 798 in _draw_geometry
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 771 in draw_self
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 764 in draw
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1551 in _draw_multiple
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1538 in draw_opaque
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1563 in draw_depth
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 243 in _draw_scene
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 158 in update_graphics_now
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2233 in moved_marker_cb
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/histogram.py", line 416 in move_marker_cb
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2159 in _drag
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/map/volume_viewer.py", line 2162 in mouseReleaseEvent
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-10-24 11:38:02.00 -0400","app_version":"1.5.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.6.2 (21G320)","incident_id":"4EA8C30C-02D7-4A42-B079-484B1D93F8DA","name":"ChimeraX"}
{
"uptime" : 4600000,
"procLaunch" : "2023-10-24 11:15:25.2649 -0400",
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro13,2",
"procStartAbsTime" : 4636985072285397,
"coalitionID" : 65384,
"osVersion" : {
"train" : "macOS 12.6.2",
"build" : "21G320",
"releaseType" : "User"
},
"captureTime" : "2023-10-24 11:37:46.8525 -0400",
"incident" : "4EA8C30C-02D7-4A42-B079-484B1D93F8DA",
"bug_type" : "309",
"pid" : 87640,
"procExitAbsTime" : 4638326244314507,
"cpuType" : "X86-64",
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"A8A69B96-0C49-555B-A159-900CEEBCDDD0","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "411DB3CE-48C8-2414-D413-1120E067E339",
"bridgeVersion" : {"build":"14Y910","train":"3.0"},
"sip" : "enabled",
"isCorpse" : 1,
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"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",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
"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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},
{
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"arch" : "x86_64",
"base" : 140703359090688,
"size" : 40960,
"uuid" : "a8a33774-6d44-35e9-ad2a-bad9e4d5192a",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
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"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
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"base" : 140707927547904,
"size" : 45056,
"uuid" : "63875145-ff3b-3b7c-98ac-84f8ab9df5cc",
"path" : "\/System\/Library\/PrivateFrameworks\/GPUSupport.framework\/Versions\/A\/Libraries\/libGPUSupportMercury.dylib",
"name" : "libGPUSupportMercury.dylib"
},
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"source" : "P",
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"base" : 140712226729984,
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"size" : 15712256,
"uuid" : "43bba65d-1c31-3c39-aac4-c820f72f21cf",
"path" : "\/System\/Library\/Extensions\/AppleIntelSKLGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelSKLGraphicsGLDriver",
"name" : "AppleIntelSKLGraphicsGLDriver",
"CFBundleVersion" : "18.0.8"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712368459776,
"size" : 1613824,
"uuid" : "be1ea664-4c51-301b-8fb9-377e1241d10b",
"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine",
"name" : "GLEngine"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703599050752,
"size" : 24576,
"uuid" : "0b6dfb1a-110f-3f1f-810f-4ddc1425a9f1",
"path" : "\/usr\/lib\/libffi.dylib",
"name" : "libffi.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5104041984,
"size" : 165052416,
"uuid" : "4aa1de3e-464c-340c-ab61-bcd39bfc7658",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4536799232,
"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2527232,
"uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.11"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4617502720,
"size" : 8192,
"uuid" : "1eae6074-8612-3bc6-b16b-c173a995e90c",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/_queue.cpython-39-darwin.so",
"name" : "_queue.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4530806784,
"size" : 20480,
"uuid" : "2f042ce6-bef0-3ad9-97f5-2da7655122a4",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/lib-dynload\/select.cpython-39-darwin.so",
"name" : "select.cpython-39-darwin.so"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4707856384,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX-1.5.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703442685952,
"CFBundleShortVersionString" : "1.600.0",
"CFBundleIdentifier" : "com.apple.SkyLight",
"size" : 3796992,
"uuid" : "6563e632-526d-3c88-8035-049fcca8ca93",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703507152896,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 3096576,
"uuid" : "06fdecd6-9f69-397b-b1e2-a8226c0ba7ed",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703359307776,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 5255168,
"uuid" : "93c48919-68af-367e-9a67-db4159bc962c",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
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},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703403843584,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 15269888,
"uuid" : "af3d9501-0abf-3c79-955c-c42c29af6351",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2113.60.148"
}
],
"sharedCache" : {
"base" : 140703355736064,
"size" : 19331678208,
"uuid" : "3172f8f5-c412-3210-95e0-1cfd89e01f8a"
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"vmSummary" : "ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=6.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=6.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 640K 5 \nActivity Tracing 256K 1 \nCG backing stores 3600K 12 \nCG image 108K 20 \nColorSync 232K 28 \nCoreAnimation 68K 13 \nCoreGraphics 20K 4 \nCoreUI image data 1680K 25 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 4.9G 6290 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 128.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 108K 27 \nStack 257.7M 28 \nStack Guard 56.0M 1 \nVM_ALLOCATE 1.2G 145 \n__CTF 756 1 \n__DATA 45.1M 694 \n__DATA_CONST 32.5M 344 \n__DATA_DIRTY 1642K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 680.2M 166 \n__TEXT 815.5M 692 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 190.7M 49 \nshared memory 2976K 27 \n=========== ======= ======= \nTOTAL 8.3G 8811 \nTOTAL, minus reserved VM space 8.1G 8811 \n",
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/CPX/cpx.cxs"
Opened J178_003_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.16,
shown at level 0.344, step 1, values float32
Opened cryosparc_P33_J144_010_volume_map_sharp.mrc as #6, grid size
220,220,220, pixel 1.36, shown at level 0.294, step 1, values float32
Log from Tue Oct 24 11:12:09 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/jameslee/Downloads/cryosparc_P17_J126_002_volume_map.mrc
Opened cryosparc_P17_J126_002_volume_map.mrc as #1, grid size 96,96,96, pixel
3.04, shown at level 0.772, step 1, values float32
> open /Users/jameslee/Downloads/cryosparc_P17_J126_002_volume_map_sharp.mrc
Opened cryosparc_P17_J126_002_volume_map_sharp.mrc as #2, grid size 96,96,96,
pixel 3.04, shown at level 0.811, step 1, values float32
> hide #!2 models
> volume #1 level 0.5546
> ui tool show "Side View"
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/RealSpaceRefine_146/separated-
> coot-5_real_space_refined_146.pdb"
Chain information for separated-coot-5_real_space_refined_146.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/cryosparc_P19_J29_007_volume_map_sharp.mrc"
MRC file is truncated. Failed reading 1 values, type int32
> close #1
> close #2
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/cryosparc_P19_J29_007_volume_map_sharp.mrc"
Opened cryosparc_P19_J29_007_volume_map_sharp.mrc as #1, grid size
300,300,300, pixel 1.13, shown at level 0.158, step 2, values float32
> volume #1 step 1
> volume #1 level 0.4162
> volume #1 level 0.5073
> hide #!1 models
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/separated-coot-8.pdb"
Summary of feedback from opening /Users/jameslee/Dropbox (Dropbox
@RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/separated-coot-8.pdb
---
warning | Start residue of secondary structure not found: HELIX 20 20 VAL B
639 ALA B 644 1 6
Chain information for separated-coot-8.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #!2 models
> show #!2 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #3 models
> show #3 models
> hide #3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #3 models
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/separated-coot-7.pdb"
Chain information for separated-coot-7.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!2 models
> hide #3 models
> show #3 models
> hide #4 models
> show #4 models
> hide #3 models
> show #3 models
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/cryosparc_P19_J29_007_volume_map.mrc"
MRC file is truncated. Failed reading 1 values, type int32
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/cryosparc_P19_J29_007_volume_map.mrc"
Opened cryosparc_P19_J29_007_volume_map.mrc as #5, grid size 300,300,300,
pixel 1.13, shown at level 0.149, step 2, values float32
> volume #5 step 1
> volume #5 level 0.5871
> volume #5 level 0.583
> volume #5 level 0.4672
> close #2
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/separated-coot-8.pdb"
Chain information for separated-coot-8.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> close #4
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #2 models
> hide #3 models
> show #2 models
> show #!5 models
> show #!1 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!5 models
> hide #!5 models
> show #!5 models
> close #2-3#1,5
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_modeled/RealSpaceRefine_145/tap_b27_atp_tm-
> coot-12_real_space_refined_033_real_space_refined_145.pdb"
Chain information for tap_b27_atp_tm-
coot-12_real_space_refined_033_real_space_refined_145.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_modeled/cryosparc_P10_J42_006_volume_map.mrc"
Opened cryosparc_P10_J42_006_volume_map.mrc as #2, grid size 400,400,400,
pixel 0.86, shown at level 0.0461, step 2, values float32
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_modeled/cryosparc_P10_J42_006_volume_map_sharp.mrc"
Opened cryosparc_P10_J42_006_volume_map_sharp.mrc as #3, grid size
400,400,400, pixel 0.86, shown at level 0.0617, step 2, values float32
> volume #2 step 1
> hide #!3 models
> volume #2 level 0.1524
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> hide #!2 models
> volume #3 step 1
> volume #3 level 0.2372
> show #!2 models
> hide #!3 models
> volume #2 level 0.2014
> hide #!2 models
> show #!3 models
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_modeled/cryosparc_P10_J43_005_volume_map_sharp.mrc"
Opened cryosparc_P10_J43_005_volume_map_sharp.mrc as #4, grid size
400,400,400, pixel 0.86, shown at level 0.0635, step 2, values float32
> hide #!3 models
> hide #1 models
> volume #4 step 1
> volume #4 level 0.2803
> show #1 models
> volume #4 level 0.2401
> show #!3 models
> hide #!4 models
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_modeled/cryosparc_P10_J43_005_volume_map.mrc"
Opened cryosparc_P10_J43_005_volume_map.mrc as #5, grid size 400,400,400,
pixel 0.86, shown at level 0.0462, step 2, values float32
> volume #5 step 1
> volume #5 level 0.1723
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_wide_modeled/RealSpaceRefine_45/separated-
> coot-8_real_space_refined_045.pdb"
Chain information for separated-coot-8_real_space_refined_045.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!5 models
> show #!5 models
> hide #1 models
> show #1 models
> hide #1 models
> hide #!5 models
> delete #6/A
> delete #6/B:1-400
> delete #6/B:1-450
> delete #6/C
> show #1 models
> mmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker tap_b27_atp_tm-
coot-12_real_space_refined_033_real_space_refined_145.pdb, chain B (#1) with
separated-coot-8_real_space_refined_045.pdb, chain B (#6), sequence alignment
score = 2167.1
RMSD between 209 pruned atom pairs is 0.766 angstroms; (across all 231 pairs:
1.393)
> hide #1 models
> show #!5 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> volume #2 level 0.1404
> volume #2 level 0.2098
> volume #2 level 0.1762
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/cryosparc_P26_J56_006_volume_map_sharp.mrc"
Opened cryosparc_P26_J56_006_volume_map_sharp.mrc as #7, grid size
300,300,300, pixel 1.31, shown at level 0.176, step 2, values float32
> hide #!3 models
> hide #6 models
> volume #7 step 1
> volume #7 level 0.7964
> volume #7 level 0.7041
> volume #7 level 0.9283
> volume #7 level 0.7964
> show #1 models
> show #1 atoms
> hide #1 atoms
> select add #1
8810 atoms, 8974 bonds, 1125 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,2.4947,0,1,0,44.114,0,0,1,32.291
> view matrix models #1,1,0,0,21.105,0,1,0,49.815,0,0,1,33.064
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99672,0.054573,0.059802,1.948,-0.073073,0.92441,0.37433,4.7134,-0.034853,-0.37747,0.92537,112.45
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99672,0.054573,0.059802,-1.8352,-0.073073,0.92441,0.37433,-10.075,-0.034853,-0.37747,0.92537,109.46
> ui tool show "Fit in Map"
> fitmap #1 inMap #7
Fit molecule tap_b27_atp_tm-
coot-12_real_space_refined_033_real_space_refined_145.pdb (#1) to map
cryosparc_P26_J56_006_volume_map_sharp.mrc (#7) using 8810 atoms
average map value = 1.147, steps = 104
shifted from previous position = 8.95
rotated from previous position = 6.27 degrees
atoms outside contour = 3144, contour level = 0.79643
Position of tap_b27_atp_tm-
coot-12_real_space_refined_033_real_space_refined_145.pdb (#1) relative to
cryosparc_P26_J56_006_volume_map_sharp.mrc (#7) coordinates:
Matrix rotation and translation
0.99657727 -0.05028354 0.06561479 22.87352945
0.02405589 0.93578031 0.35176204 -26.46580861
-0.07908886 -0.34897963 0.93378700 110.22061867
Axis -0.97409413 0.20115113 0.10333852
Axis point 0.00000000 297.80668437 120.33500027
Rotation angle (degrees) 21.08109075
Shift along axis -16.21456282
> show #6 models
> select subtract #1
Nothing selected
> mmaker #6 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker tap_b27_atp_tm-
coot-12_real_space_refined_033_real_space_refined_145.pdb, chain B (#1) with
separated-coot-8_real_space_refined_045.pdb, chain B (#6), sequence alignment
score = 2167.1
RMSD between 209 pruned atom pairs is 0.766 angstroms; (across all 231 pairs:
1.393)
> hide #1 models
> hide #6 models
> show #1 models
> show #6 models
> hide #!7 models
> hide #6 models
> show #6 models
> show #!7 models
> volume #7 level 0.9315
> hide #6 models
> show #6 models
> hide #1 models
> hide #!7 models
> show #!7 models
> save "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/nbd2.pdb" relModel #7
> save "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/nbd2.pdb" models #6 relModel #7
> save "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/tap_b27.pdb" models #1 relModel
> #7
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/cryosparc_P26_J56_006_volume_map.mrc"
Opened cryosparc_P26_J56_006_volume_map.mrc as #8, grid size 300,300,300,
pixel 1.31, shown at level 0.0637, step 2, values float32
> hide #!7 models
> volume #8 step 1
> volume #8 level 0.6346
> volume #8 level 0.5043
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/tap_b27.pdb"
Chain information for tap_b27.pdb #9
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> delete #9/B:450-end
> save "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/tap_nonbd2.pdb" models #9
> relModel #9
> hide #9 models
> show #!8 models
> hide #!8 models
> show #!8 models
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/tap_b27-2.pdb"
Summary of feedback from opening /Users/jameslee/Dropbox (Dropbox
@RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/tap_b27-2.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for tap_b27-2.pdb #10
---
Chain | Description
A | No description available
B | No description available
C | No description available
> volume #7 level 0.864
> volume #7 level 0.8339
> volume #7 level 0.6764
> hide #10 models
> show #10 models
> hide #!7 models
> show #!8 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> hide #10 models
> show #10 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #10 models
> show #6 models
> hide #6 models
> show #1 models
> select add #1
8810 atoms, 8974 bonds, 1125 residues, 1 model selected
> view matrix models
> #1,0.99658,-0.050284,0.065615,15.738,0.024056,0.93578,0.35176,-67.451,-0.079089,-0.34898,0.93379,88.076
> view matrix models
> #1,0.99658,-0.050284,0.065615,-1.3835,0.024056,0.93578,0.35176,-57.795,-0.079089,-0.34898,0.93379,85.857
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.87431,-0.34446,-0.34195,141.26,0.40095,0.9096,0.10888,-72.164,0.27353,-0.2323,0.93339,8.059
> ui mousemode right "translate selected models"
> fitmap #1 inMap #2
Fit molecule tap_b27_atp_tm-
coot-12_real_space_refined_033_real_space_refined_145.pdb (#1) to map
cryosparc_P10_J42_006_volume_map.mrc (#2) using 8810 atoms
average map value = 0.2456, steps = 192
shifted from previous position = 4.65
rotated from previous position = 30.8 degrees
atoms outside contour = 2863, contour level = 0.17617
Position of tap_b27_atp_tm-
coot-12_real_space_refined_033_real_space_refined_145.pdb (#1) relative to
cryosparc_P10_J42_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99999997 0.00020147 0.00015613 -0.07023175
-0.00020150 0.99999995 0.00023847 -0.03855672
-0.00015608 -0.00023850 0.99999996 0.10167608
Axis -0.68322881 0.44722577 -0.57722396
Axis point 0.00000000 358.64708225 109.34029111
Rotation angle (degrees) 0.01999970
Shift along axis -0.02794907
> select subtract #1
Nothing selected
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/tap_b27-2-coot-0.pdb"
Summary of feedback from opening /Users/jameslee/Dropbox (Dropbox
@RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/tap_b27-2-coot-0.pdb
---
warning | PDB SEQRES record for chain A is incomplete. Ignoring input sequence
records as basis for sequence.
Chain information for tap_b27-2-coot-0.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #11 models
> show #11 models
> hide #1 models
> select add #2
2 models selected
> select subtract #2
Nothing selected
> select add #11
8868 atoms, 9032 bonds, 1132 residues, 1 model selected
> view matrix models #11,1,0,0,-6.5152,0,1,0,-41.863,0,0,1,-18.279
> view matrix models #11,1,0,0,-30.002,0,1,0,-41.916,0,0,1,-24.775
> ui mousemode right "rotate selected models"
> view matrix models
> #11,0.97502,-0.18371,0.12487,-15.537,0.21455,0.92445,-0.31521,-2.5944,-0.057525,0.33413,0.94077,-66.366
> ui mousemode right "translate selected models"
> view matrix models
> #11,0.97502,-0.18371,0.12487,-14.423,0.21455,0.92445,-0.31521,7.3553,-0.057525,0.33413,0.94077,-69.546
> ui tool show "Fit in Map"
> fitmap #11 inMap #2
Fit molecule tap_b27-2-coot-0.pdb (#11) to map
cryosparc_P10_J42_006_volume_map.mrc (#2) using 8868 atoms
average map value = 0.2443, steps = 136
shifted from previous position = 2.27
rotated from previous position = 16.9 degrees
atoms outside contour = 2914, contour level = 0.17617
Position of tap_b27-2-coot-0.pdb (#11) relative to
cryosparc_P10_J42_006_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
0.99655074 0.02451296 -0.07928265 -13.50163263
-0.05080451 0.93562880 -0.34931026 64.54272874
0.06561651 0.35213331 0.93364694 -95.14780418
Axis 0.97395332 -0.20119226 -0.10457818
Axis point 0.00000000 297.73237993 120.58342110
Rotation angle (degrees) 21.10641269
Shift along axis -16.18507290
> select subtract #11
Nothing selected
> close #11
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_B27_membrane/RealSpaceRefine_48/tap_b27-2-coot-3_real_space_refined_048.pdb"
Chain information for tap_b27-2-coot-3_real_space_refined_048.pdb #11
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!2 models
> show #!8 models
> hide #!8 models
> show #!7 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!7 models
> open /Users/jameslee/Downloads/cryosparc_P15_J186_003_volume_map.mrc
Opened cryosparc_P15_J186_003_volume_map.mrc as #12, grid size 100,100,100,
pixel 3.39, shown at level 0.887, step 1, values float32
> open /Users/jameslee/Downloads/cryosparc_P15_J186_003_volume_map_sharp.mrc
Opened cryosparc_P15_J186_003_volume_map_sharp.mrc as #13, grid size
100,100,100, pixel 3.39, shown at level 0.938, step 1, values float32
> show #!2 models
> hide #11 models
> hide #!7 models
> hide #!2 models
> hide #!12 models
> show #!12 models
> hide #!13 models
> hide #!12 models
> show #!13 models
> volume #13 level 1.526
> volume #13 level 0.7644
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_dimer_done_modeled/RealSpaceRefine_131/output_real_space_refined_082-coot-28_real_space_refined_131.pdb"
Chain information for
output_real_space_refined_082-coot-28_real_space_refined_131.pdb #14
---
Chain | Description
A | No description available
B | No description available
> fitmap #14 inMap #13
Fit molecule output_real_space_refined_082-coot-28_real_space_refined_131.pdb
(#14) to map cryosparc_P15_J186_003_volume_map_sharp.mrc (#13) using 8518
atoms
average map value = 1.351, steps = 136
shifted from previous position = 4.16
rotated from previous position = 29.4 degrees
atoms outside contour = 2222, contour level = 0.76438
Position of output_real_space_refined_082-coot-28_real_space_refined_131.pdb
(#14) relative to cryosparc_P15_J186_003_volume_map_sharp.mrc (#13)
coordinates:
Matrix rotation and translation
0.87386391 -0.47971117 0.07898770 90.60508556
0.48435390 0.87306368 -0.05622385 -48.60748913
-0.04199008 0.08739000 0.99528881 -4.77716008
Axis 0.14621914 0.12317243 0.98155413
Axis point 140.61320838 151.11718548 0.00000000
Rotation angle (degrees) 29.41232401
Shift along axis 2.57205399
> volume #13 level 2.142
> volume #13 level 1.32
> color #14 skyblue
> color #13 silver
> color zone #13 near #14 distance 3.5
> volume splitbyzone #13
Opened cryosparc_P15_J186_003_volume_map_sharp.mrc 0 as #15.1, grid size
100,100,100, pixel 3.39, shown at level 1.32, step 1, values float32
Opened cryosparc_P15_J186_003_volume_map_sharp.mrc 1 as #15.2, grid size
100,100,100, pixel 3.39, shown at level 1.32, step 1, values float32
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!15.1 models
> volume flip #14
> close #15
> show #!13 models
> volume flip #13
Opened cryosparc_P15_J186_003_volume_map_sharp.mrc z flip as #15, grid size
100,100,100, pixel 3.39, shown at step 1, values float32
> select add #15
2 models selected
> select subtract #15
Nothing selected
> select add #14
8518 atoms, 8669 bonds, 3 pseudobonds, 1093 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.77197,0.62445,-0.11887,214.31,0.62098,0.78079,0.068909,-75.63,0.13584,-0.02062,-0.99052,291.19
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.77197,0.62445,-0.11887,214.05,0.62098,0.78079,0.068909,-71.137,0.13584,-0.02062,-0.99052,315.44
> hide #!15 models
> show #!15 models
> fitmap #14 inMap #15
Fit molecule output_real_space_refined_082-coot-28_real_space_refined_131.pdb
(#14) to map cryosparc_P15_J186_003_volume_map_sharp.mrc z flip (#15) using
8518 atoms
average map value = 1.465, steps = 100
shifted from previous position = 6.16
rotated from previous position = 44.1 degrees
atoms outside contour = 3981, contour level = 1.3196
Position of output_real_space_refined_082-coot-28_real_space_refined_131.pdb
(#14) relative to cryosparc_P15_J186_003_volume_map_sharp.mrc z flip (#15)
coordinates:
Matrix rotation and translation
-0.99397837 -0.04572652 0.09957957 330.14053205
-0.05336414 0.99572167 -0.07543627 23.39015039
-0.09570410 -0.08029600 -0.99216595 361.96580060
Axis -0.02485879 0.99892727 -0.03906842
Axis point 174.23826797 0.00000000 173.34409631
Rotation angle (degrees) 174.39057057
Shift along axis 1.01673518
> fitmap #14 inMap #15
Fit molecule output_real_space_refined_082-coot-28_real_space_refined_131.pdb
(#14) to map cryosparc_P15_J186_003_volume_map_sharp.mrc z flip (#15) using
8518 atoms
average map value = 1.465, steps = 40
shifted from previous position = 0.0174
rotated from previous position = 0.0833 degrees
atoms outside contour = 3980, contour level = 1.3196
Position of output_real_space_refined_082-coot-28_real_space_refined_131.pdb
(#14) relative to cryosparc_P15_J186_003_volume_map_sharp.mrc z flip (#15)
coordinates:
Matrix rotation and translation
-0.99392165 -0.04717487 0.09947002 330.39231986
-0.05479035 0.99565661 -0.07527237 23.63554953
-0.09548702 -0.08026484 -0.99218939 361.92748845
Axis -0.02558014 0.99891096 -0.03901981
Axis point 174.36020510 0.00000000 173.33631918
Rotation angle (degrees) 174.39989092
Shift along axis 1.03598658
> volume #15 level 1.161
> color #15 silver
> color zone #15 near #14 distance 3.5
> volume splitbyzone #15
Opened cryosparc_P15_J186_003_volume_map_sharp.mrc z flip 0 as #16.1, grid
size 100,100,100, pixel 3.39, shown at level 1.16, step 1, values float32
Opened cryosparc_P15_J186_003_volume_map_sharp.mrc z flip 1 as #16.2, grid
size 100,100,100, pixel 3.39, shown at level 1.16, step 1, values float32
> select subtract #14
Nothing selected
> hide #!16.1 models
> show #!16.1 models
> hide #!16 models
> show #!16 models
> hide #!16.2 models
> show #!16.2 models
> select add #14
8518 atoms, 8669 bonds, 3 pseudobonds, 1093 residues, 2 models selected
> select subtract #14
Nothing selected
> hide #!16.1 models
> show #!16.1 models
> open /Users/jameslee/Downloads/cryosparc_P6_J57_011_volume_map.mrc
Opened cryosparc_P6_J57_011_volume_map.mrc as #17, grid size 256,256,256,
pixel 1.16, shown at level 0.231, step 1, values float32
> hide #!16 models
> close #9-11#7-8,12-13
> close #15
> close #2
> close #3
> close #4
> close #5
> close #16
> open /Users/jameslee/Downloads/cryosparc_P6_J57_011_volume_map_sharp.mrc
Opened cryosparc_P6_J57_011_volume_map_sharp.mrc as #2, grid size 256,256,256,
pixel 1.16, shown at level 0.232, step 1, values float32
> hide #!17 models
> volume #2 level 0.2409
> hide #!2 models
> show #!17 models
> volume #17 level 0.3664
> select add #14
8518 atoms, 8669 bonds, 3 pseudobonds, 1093 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.85702,-0.42201,0.29567,340.14,0.44063,-0.89768,-0.0040552,248.85,0.26713,0.12681,0.95528,-36.797
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.85702,-0.42201,0.29567,333.12,0.44063,-0.89768,-0.0040552,233.31,0.26713,0.12681,0.95528,-75.756
> view matrix models
> #14,-0.85702,-0.42201,0.29567,329.52,0.44063,-0.89768,-0.0040552,227,0.26713,0.12681,0.95528,-85.645
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.82049,0.54051,0.18612,-101.78,-0.56552,0.81504,0.12609,88.01,-0.08354,-0.20871,0.9744,27.839
> ui tool show "Fit in Map"
> fitmap #14 inMap #17
Fit molecule output_real_space_refined_082-coot-28_real_space_refined_131.pdb
(#14) to map cryosparc_P6_J57_011_volume_map.mrc (#17) using 8518 atoms
average map value = 0.445, steps = 148
shifted from previous position = 9.25
rotated from previous position = 26.5 degrees
atoms outside contour = 3073, contour level = 0.36642
Position of output_real_space_refined_082-coot-28_real_space_refined_131.pdb
(#14) relative to cryosparc_P6_J57_011_volume_map.mrc (#17) coordinates:
Matrix rotation and translation
0.98029025 0.19641836 -0.02123335 -47.19384021
-0.19629829 0.98051463 0.00761907 15.99364577
0.02231613 -0.00330083 0.99974552 -23.32877238
Axis -0.02762611 -0.11017519 -0.99352817
Axis point 69.99744237 244.10050781 0.00000000
Rotation angle (degrees) 11.39883455
Shift along axis 22.71947162
> select subtract #14
Nothing selected
> hide #!14 models
> show #!2 models
> hide #!17 models
> show #!14 models
> volume #2 level 0.3947
> open /Users/jameslee/Downloads/cryosparc_P18_J153_004_volume_map.mrc
Opened cryosparc_P18_J153_004_volume_map.mrc as #3, grid size 256,256,256,
pixel 1.31, shown at level 0.216, step 1, values float32
> show #6 models
> hide #!2 models
> hide #!3 models
> hide #6 models
> hide #!14 models
> show #!3 models
> volume #3 level 0.4335
> open /Users/jameslee/Downloads/cryosparc_P18_J153_004_volume_map_sharp.mrc
Opened cryosparc_P18_J153_004_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.31, shown at level 0.193, step 1, values float32
> hide #!3 models
> volume #4 level 0.6452
> volume #4 level 0.4026
> volume #4 level 0.7445
> volume #4 level 0.6122
> open /Users/jameslee/Downloads/cryosparc_P6_J113_003_volume_map.mrc
Opened cryosparc_P6_J113_003_volume_map.mrc as #5, grid size 256,256,256,
pixel 1.16, shown at level 0.216, step 1, values float32
> hide #!4 models
> hide #!5 models
> show #!5 models
> open /Users/jameslee/Downloads/cryosparc_P6_J113_003_volume_map_sharp.mrc
Opened cryosparc_P6_J113_003_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.16, shown at level 0.214, step 1, values float32
> hide #!7 models
> volume #5 level 0.3109
> show #!7 models
> hide #!5 models
> volume #7 level 0.2805
> volume #7 level 0.4327
> volume #7 level 0.393
> color #7 silver
> color #6 skyblue
> color zone # 7 near #6 distance 3
> show #6 models
> open /Users/jameslee/Downloads/cryosparc_P6_J122_001_volume_map_sharp.mrc
Opened cryosparc_P6_J122_001_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 1.16, shown at level 0.217, step 1, values float32
> hide #6 models
> hide #!7 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.3069
> volume #8 level 0.3963
> volume #8 level 0.3665
> volume #8 level 0.4485
> close #2-5
> close #7-8
> show #!14 models
> close #17
> rename #6 id #2
> rename #14 id #3
> rename #3
> dimer_output_real_space_refined_082-coot-28_real_space_refined_131.pdb
> open /Users/jameslee/Downloads/cryosparc_P6_J122_005_volume_map_sharp.mrc
Opened cryosparc_P6_J122_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.16, shown at level 0.229, step 1, values float32
> hide #!3 models
> volume #4 level 0.4764
> volume #4 level 0.6319
> volume #4 level 0.6044
> volume #4 level 0.5221
> volume #4 level 1.007
> show #!3 models
> volume #4 level 1.254
> volume #4 level 0.8057
> volume #4 level 0.6227
> open /Users/jameslee/Downloads/cryosparc_P6_J123_005_volume_map_sharp.mrc
Opened cryosparc_P6_J123_005_volume_map_sharp.mrc as #5, grid size
256,256,256, pixel 1.16, shown at level 0.233, step 1, values float32
> hide #!4 models
> volume #5 level 0.427
> open /Users/jameslee/Downloads/cryosparc_P6_J123_005_volume_map.mrc
Opened cryosparc_P6_J123_005_volume_map.mrc as #6, grid size 256,256,256,
pixel 1.16, shown at level 0.203, step 1, values float32
> hide #!5 models
> volume #6 level 0.3347
> hide #!6 models
> show #!6 models
> open /Users/jameslee/Downloads/cryosparc_P6_J122_006_volume_map_sharp.mrc
Opened cryosparc_P6_J122_006_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.16, shown at level 0.237, step 1, values float32
> volume #7 level 0.5159
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> volume #5 level 0.4
> volume #5 level 0.5
> volume #7 level 0.5
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> close #4-6
> show #2 models
> hide #2 models
> save "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/tap_ul495.pdb" models #3 relModel #7
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/j122_deepem_highres.mrc"
Opened j122_deepem_highres.mrc as #4, grid size 256,256,256, pixel 1.16, shown
at level 0.00182, step 1, values float32
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/j122_deepem_wide.mrc"
Opened j122_deepem_wide.mrc as #5, grid size 256,256,256, pixel 1.16, shown at
level 0.00311, step 1, values float32
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/j122_deepem.mrc"
Opened j122_deepem.mrc as #6, grid size 256,256,256, pixel 1.16, shown at
level 0.00022, step 1, values float32
> hide #!3 models
> hide #!7 models
> hide #!5 models
> hide #!4 models
> volume #6 level 0.05539
> hide #!6 models
> show #!4 models
> volume #4 level 0.01932
> hide #!4 models
> show #!5 models
> volume #5 level 0.02088
> volume #5 level 0.09196
> hide #!5 models
> show #!6 models
> close #4-6
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/j133_deepem_highres.mrc"
Opened j133_deepem_highres.mrc as #4, grid size 256,256,256, pixel 1.16, shown
at level 0.00303, step 1, values float32
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/j133_deepem_wide.mrc"
Opened j133_deepem_wide.mrc as #5, grid size 256,256,256, pixel 1.16, shown at
level 0.0319, step 1, values float32
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/j133_deepem.mrc"
Opened j133_deepem.mrc as #6, grid size 256,256,256, pixel 1.16, shown at
level 0.000131, step 1, values float32
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/cryosparc_P6_J133_005_volume_map_sharp.mrc"
Opened cryosparc_P6_J133_005_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 1.16, shown at level 0.226, step 1, values float32
> hide #!4 models
> hide #!5 models
> hide #!6 models
> volume #8 level 0.5741
> volume #8 level 0.4645
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/tap_ul495-coot-3.pdb"
Summary of feedback from opening /Users/jameslee/Dropbox (Dropbox
@RU)/TAP_Viral_Inhibitors/UL495/tap_ul495-coot-3.pdb
---
warnings | PDB SEQRES record for chain A is incomplete. Ignoring input
sequence records as basis for sequence.
PDB SEQRES record for chain B is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for tap_ul495-coot-3.pdb #9
---
Chain | Description
A | No description available
B | No description available
> color #9 skyblue
> color zone #8 near #9 distance 3
> volume splitbyzone #8
Opened cryosparc_P6_J133_005_volume_map_sharp.mrc 0 as #10.1, grid size
256,256,256, pixel 1.16, shown at level 0.465, step 1, values float32
Opened cryosparc_P6_J133_005_volume_map_sharp.mrc 1 as #10.2, grid size
256,256,256, pixel 1.16, shown at level 0.465, step 1, values float32
> hide #!10.2 models
> hide #!10 models
> hide #!9 models
> hide #!10.1 models
> show #!8 models
> hide #!8 models
> show #!8 models
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/tap_ul495-coot-4.pdb"
Summary of feedback from opening /Users/jameslee/Dropbox (Dropbox
@RU)/TAP_Viral_Inhibitors/UL495/tap_ul495-coot-4.pdb
---
warnings | PDB SEQRES record for chain A is incomplete. Ignoring input
sequence records as basis for sequence.
PDB SEQRES record for chain B is incomplete. Ignoring input sequence records
as basis for sequence.
Chain information for tap_ul495-coot-4.pdb #11
---
Chain | Description
A | No description available
B | No description available
D | No description available
> color #11 skyblue
> color #8 silver
> color zone #8 near #11 distance 3
> color #8/B gold
> color #11/B gold
> color #11/C violet
> color zone #8 near #11 distance 3
> color #11/D violet
> color zone #8 near #11 distance 3
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/RealSpaceRefine_170/tap_ul495-coot-29_real_space_refined_170.pdb"
Chain information for tap_ul495-coot-29_real_space_refined_170.pdb #12
---
Chain | Description
A | No description available
B | No description available
D | No description available
> close #4-11#10.1-2
> color #12/A skyblue
> color #12/B gold
> color #12/D magneta
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #12/D magenta
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/cryosparc_P6_J133_005_volume_map_sharp.mrc"
Opened cryosparc_P6_J133_005_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.16, shown at level 0.226, step 1, values float32
> color #12 silver
> color zone #4 near #12
> color #12/A skyblue
> color #12/B gold
> color #12/D magenta
> color zone #4 near #12
> volume splitbyxoner
Expected a density maps specifier or a keyword
> volume splitbyzone #4
Opened cryosparc_P6_J133_005_volume_map_sharp.mrc 0 as #5.1, grid size
256,256,256, pixel 1.16, shown at level 0.226, step 1, values float32
Opened cryosparc_P6_J133_005_volume_map_sharp.mrc 1 as #5.2, grid size
256,256,256, pixel 1.16, shown at level 0.226, step 1, values float32
Opened cryosparc_P6_J133_005_volume_map_sharp.mrc 2 as #5.3, grid size
256,256,256, pixel 1.16, shown at level 0.226, step 1, values float32
Opened cryosparc_P6_J133_005_volume_map_sharp.mrc 3 as #5.4, grid size
256,256,256, pixel 1.16, shown at level 0.226, step 1, values float32
Opened cryosparc_P6_J133_005_volume_map_sharp.mrc 4 as #5.5, grid size
256,256,256, pixel 1.16, shown at level 0.226, step 1, values float32
> hide #!5 models
> show #!4 models
> volume #4 level 0.4645
> hide #!4 models
> show #!5 models
> hide #!5.1 models
> hide #!5.2 models
> hide #!5.4 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!12 models
> transparency #5.3 50
> lighting soft
> lighting flat
> set bgColor white
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 1
[Repeated 1 time(s)]
> graphics silhouettes width 1
> lighting full
> show #!12 models
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting shadows false
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> lighting simple
> hide #12/A-B
> hide #12/A-B cartoons
> show #12/D sticks
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #12/D atoms
> color #12/D byhetero
> hide #!5.3 models
> show #!5.3 models
> show #!5.2 models
> hide #!5.2 models
> show #12/A-B
> show #12/A-B cartoons
> hide #12/A-B atoms
> show #12/A:242,246,308,309,312
> color #12/A byhetero
> show #!5.1 models
> volume #5.1 level 0.3345
> hide #!5.3 models
> show #2 models
> hide #2 models
> hide #!5 models
> show #2 models
> hide #2 models
> show #!4 models
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> open /Users/jameslee/Downloads/cryosparc_P17_J307_008_volume_map_sharp.mrc
Opened cryosparc_P17_J307_008_volume_map_sharp.mrc as #6, grid size
220,220,220, pixel 1.33, shown at level 0.274, step 1, values float32
> close #4-6,12#5.1-5
> open /Users/jameslee/Downloads/cryosparc_P17_J307_008_volume_map.mrc
Opened cryosparc_P17_J307_008_volume_map.mrc as #4, grid size 220,220,220,
pixel 1.33, shown at level 0.265, step 1, values float32
> open /Users/jameslee/Downloads/cryosparc_P17_J307_008_volume_map_sharp.mrc
Opened cryosparc_P17_J307_008_volume_map_sharp.mrc as #5, grid size
220,220,220, pixel 1.33, shown at level 0.274, step 1, values float32
> hide #!5 models
> volume #4 level 0.3382
> volume #4 level 0.3919
> show #!5 models
> hide #!4 models
> volume #5 level 0.2972
> volume #5 level 0.4346
> volume #5 level 0.5033
> volume #5 level 0.5491
> volume flip #5
Opened cryosparc_P17_J307_008_volume_map_sharp.mrc z flip as #6, grid size
220,220,220, pixel 1.33, shown at step 1, values float32
> show #!5 models
> hide #!5 models
> color #6 silver
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_dimer_done_modeled/cryosparc_P19_J115_004_volume_map_sharp.mrc"
MRC file is truncated. Failed reading 1 values, type int32
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_dimer_done_modeled/cryosparc_P19_J115_004_volume_map_sharp.mrc"
Opened cryosparc_P19_J115_004_volume_map_sharp.mrc as #7, grid size
400,400,400, pixel 0.847, shown at level 0.0849, step 2, values float32
> volume #7 level 0.1981
> volume #7 step 1
> show #!3 models
> volume flip #7
Opened cryosparc_P19_J115_004_volume_map_sharp.mrc z flip as #8, grid size
400,400,400, pixel 0.847, shown at step 1, values float32
> show #!7 models
> hide #!7 models
> hide #!6 models
> hide #!3 models
> close #7
> show #!6 models
> select add #8
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,-11.904,0,1,0,-26.071,0,0,1,-26.151
> ui mousemode right "rotate selected models"
> view matrix models
> #8,-0.98628,-0.040468,0.16002,324.7,0.012218,-0.98472,-0.17372,318.82,0.16461,-0.16939,0.97171,-23.852
> ui tool show "Fit in Map"
> fitmap #8 inMap #6
Fit map cryosparc_P19_J115_004_volume_map_sharp.mrc z flip in map
cryosparc_P17_J307_008_volume_map_sharp.mrc z flip using 104405 points
correlation = 0.8345, correlation about mean = 0.5438, overlap = 4.496e+04
steps = 308, shift = 33.5, angle = 16 degrees
Position of cryosparc_P19_J115_004_volume_map_sharp.mrc z flip (#8) relative
to cryosparc_P17_J307_008_volume_map_sharp.mrc z flip (#6) coordinates:
Matrix rotation and translation
-0.99316205 0.11548840 0.01707534 292.79901403
-0.11514964 -0.99315382 0.01964806 330.40736717
0.01922756 0.01754749 0.99966113 -27.58529751
Axis -0.00910688 -0.00933081 -0.99991500
Axis point 156.09009492 156.85561733 0.00000000
Rotation angle (degrees) 173.37740850
Shift along axis 21.83350023
> select subtract #8
Nothing selected
> hide #!8 models
> show #!8 models
> show #!3 models
> fitmap #3 inMap #8
Fit molecule
dimer_output_real_space_refined_082-coot-28_real_space_refined_131.pdb (#3) to
map cryosparc_P19_J115_004_volume_map_sharp.mrc z flip (#8) using 8518 atoms
average map value = 0.4224, steps = 2000
shifted from previous position = 6.03
rotated from previous position = 18.2 degrees
atoms outside contour = 3723, contour level = 0.19807
Position of
dimer_output_real_space_refined_082-coot-28_real_space_refined_131.pdb (#3)
relative to cryosparc_P19_J115_004_volume_map_sharp.mrc z flip (#8)
coordinates:
Matrix rotation and translation
-0.99999283 -0.00015036 0.00378333 338.59627543
0.00036557 -0.99837712 0.05694738 330.82290874
0.00376862 0.05694835 0.99837002 -10.25497915
Axis 0.00188840 0.02848955 0.99959231
Axis point 169.28647180 165.57944781 0.00000000
Rotation angle (degrees) 179.98521389
Shift along axis -0.18639904
> color #8 silver
> color zone #8 near #3
> hide #!6 models
> select add #3
8518 atoms, 8669 bonds, 3 pseudobonds, 1093 residues, 2 models selected
> view matrix models
> #3,-0.69493,0.71836,0.031948,138.89,-0.71674,-0.68841,-0.11125,400.16,-0.057924,-0.10021,0.99328,6.242
> fitmap #3 inMap #8
Fit molecule
dimer_output_real_space_refined_082-coot-28_real_space_refined_131.pdb (#3) to
map cryosparc_P19_J115_004_volume_map_sharp.mrc z flip (#8) using 8518 atoms
average map value = 0.08982, steps = 116
shifted from previous position = 1.54
rotated from previous position = 1.2 degrees
atoms outside contour = 6523, contour level = 0.19807
Position of
dimer_output_real_space_refined_082-coot-28_real_space_refined_131.pdb (#3)
relative to cryosparc_P19_J115_004_volume_map_sharp.mrc z flip (#8)
coordinates:
Matrix rotation and translation
0.77770658 -0.62841054 -0.01651263 146.69453619
0.62523769 0.77052184 0.12399161 -86.33020301
-0.06519430 -0.10675341 0.99214586 30.73862369
Axis -0.18088627 0.03816267 0.98276333
Axis point 198.09727254 163.47180301 0.00000000
Rotation angle (degrees) 39.62930300
Shift along axis 0.37917381
> select subtract #3
Nothing selected
> select add #3
8518 atoms, 8669 bonds, 3 pseudobonds, 1093 residues, 2 models selected
> view matrix models
> #3,-0.9031,0.42936,0.0083145,225.82,-0.42886,-0.90072,-0.069088,381.5,-0.022174,-0.065959,0.99758,-5.7181
> fitmap #3 inMap #8
Fit molecule
dimer_output_real_space_refined_082-coot-28_real_space_refined_131.pdb (#3) to
map cryosparc_P19_J115_004_volume_map_sharp.mrc z flip (#8) using 8518 atoms
average map value = 0.6435, steps = 168
shifted from previous position = 0.533
rotated from previous position = 19.5 degrees
atoms outside contour = 1242, contour level = 0.19807
Position of
dimer_output_real_space_refined_082-coot-28_real_space_refined_131.pdb (#3)
relative to cryosparc_P19_J115_004_volume_map_sharp.mrc z flip (#8)
coordinates:
Matrix rotation and translation
0.99999998 -0.00006440 0.00015905 -0.00790981
0.00006444 0.99999997 -0.00022577 0.01811203
-0.00015904 0.00022577 0.99999996 -0.00788181
Axis 0.79614624 0.56084532 0.22716448
Axis point 0.00000000 37.00565293 75.07783370
Rotation angle (degrees) 0.01624785
Shift along axis 0.00207021
> color zone #8 near #3
> color #3/A skyblue
> color #3/B gold
> color zone #8 near #3
> select subtract #3
Nothing selected
> hide #!3 models
> show #!6 models
> volume #8 level 0.2489
> volume #8 level 0.2319
> hide #!6 models
> show #!6 models
> show #!3 models
> hide #!8 models
> hide #!3 models
> show #!8 models
> hide #!8 models
> graphics silhouettes false
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> show #!8 models
> hide #!6 models
> volume #5 level 0.4899
> hide #!5 models
> show #!6 models
> hide #!6 models
> hide #!8 models
> show #!6 models
> volume #6 level 0.4571
> show #!8 models
> hide #!6 models
> volume #8 level 0.1529
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!8 models
> volume #6 level 0.3848
> open /Users/jameslee/Downloads/cryosparc_P32_J171_004_volume_map_sharp.mrc
Opened cryosparc_P32_J171_004_volume_map_sharp.mrc as #7, grid size
256,256,256, pixel 1.16, shown at level 0.153, step 1, values float32
> hide #!6 models
> volume #7 level 0.272
> graphics silhouettes true
> open /Users/jameslee/Downloads/cryosparc_P32_J173_003_volume_map_sharp.mrc
Opened cryosparc_P32_J173_003_volume_map_sharp.mrc as #9, grid size
256,256,256, pixel 1.16, shown at level 0.147, step 1, values float32
> volume #9 level 0.272
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> open /Users/jameslee/Downloads/cryosparc_P32_J176_003_volume_map_sharp.mrc
Opened cryosparc_P32_J176_003_volume_map_sharp.mrc as #10, grid size
256,256,256, pixel 1.16, shown at level 0.15, step 1, values float32
> hide #!7 models
> volume #10 level 0.2696
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> open /Users/jameslee/Downloads/cryosparc_P32_J178_003_volume_map_sharp.mrc
Opened cryosparc_P32_J178_003_volume_map_sharp.mrc as #11, grid size
256,256,256, pixel 1.16, shown at level 0.168, step 1, values float32
> volume #11 level 0.27
> hide #!10 models
> show #!7 models
> hide #!7 models
> close #4-10
> open /Users/jameslee/Downloads/cryosparc_P32_J181_004_volume_map_sharp.mrc
Opened cryosparc_P32_J181_004_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.16, shown at level 0.178, step 1, values float32
> volume #4 level 0.27
> close #4,11
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/tap_ul495-coot-30.pdb"
Chain information for tap_ul495-coot-30.pdb #4
---
Chain | Description
A | No description available
B | No description available
D | No description available
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/J178_003_volume_map_sharp.mrc"
Opened J178_003_volume_map_sharp.mrc as #5, grid size 256,256,256, pixel 1.16,
shown at level 0.168, step 1, values float32
> volume #5 level 0.3439
> lighting soft
> lighting simple
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/CPX/cryosparc_P33_J144_010_volume_map_sharp.mrc"
Opened cryosparc_P33_J144_010_volume_map_sharp.mrc as #6, grid size
220,220,220, pixel 1.36, shown at level 0.294, step 1, values float32
> hide #!4 models
> hide #!5 models
> save "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/CPX/cpx.cxs" includeMaps true
——— End of log from Tue Oct 24 11:12:09 2023 ———
opened ChimeraX session
> volume #6 level 0.6036
> ui tool show "Side View"
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/tap_ul495-coot-31.pdb"
Chain information for tap_ul495-coot-31.pdb #7
---
Chain | Description
A | No description available
B | No description available
D | No description available
> volume flip 6
Missing or invalid "volumes" argument: invalid density maps specifier
> volume flip #6
Opened cryosparc_P33_J144_010_volume_map_sharp.mrc z flip as #8, grid size
220,220,220, pixel 1.36, shown at step 1, values float32
> select add #7
8938 atoms, 9103 bonds, 2 pseudobonds, 1144 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.96582,-0.038143,-0.2564,45.425,-0.029053,-0.99881,0.03915,299.26,-0.25759,-0.030362,-0.96578,308.23
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.96582,-0.038143,-0.2564,46.414,-0.029053,-0.99881,0.03915,299.18,-0.25759,-0.030362,-0.96578,332.39
> view matrix models
> #7,0.96582,-0.038143,-0.2564,40.851,-0.029053,-0.99881,0.03915,301.53,-0.25759,-0.030362,-0.96578,330
> ui tool show "Fit in Map"
> fitmap #7 inMap #8
Fit molecule tap_ul495-coot-31.pdb (#7) to map
cryosparc_P33_J144_010_volume_map_sharp.mrc z flip (#8) using 8938 atoms
average map value = 0.559, steps = 120
shifted from previous position = 7.17
rotated from previous position = 22.1 degrees
atoms outside contour = 5086, contour level = 0.60364
Position of tap_ul495-coot-31.pdb (#7) relative to
cryosparc_P33_J144_010_volume_map_sharp.mrc z flip (#8) coordinates:
Matrix rotation and translation
0.96123664 -0.27199660 0.04518828 40.62597587
-0.27369340 -0.96111075 0.03685171 328.53779053
0.03340740 -0.04779095 -0.99829854 297.88371679
Axis -0.99025727 0.13782766 -0.01985130
Axis point 0.00000000 170.31144700 144.98697487
Rotation angle (degrees) 177.55056326
Shift along axis -0.86195179
> ui mousemode right translate
> lighting soft
> lighting simple
> lighting soft
> select subtract #7
Nothing selected
> hide #7
> show #7/A-B:701
> hide #7/A:701
> hide #7/B:801
> show #7/B:801
> show #7/B:801 atoms
> show #7/A:801
> color #7/A-B silver
> color #7/A:801 magenta
> color #7/B:701 magenta
> color #7/B:701 byhetero
> color #7/A:801 byhetero
> show #!8 models
> color #8 silver
> color zone #8 near #7 distance 3
> hide #!7 models
> show #!7 models
> hide #!8 models
> volume #8 level 0.7401
> color #7/A:801 mangeta
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color #7/A:801 magenta
> color #7/B:701 magenta
> color zone #8 near #7 distance 3
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> volume #8 level 0.9018
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> transparency #8 50
> volume #8 level 0.5965
> volume #8 level 0.4851
> lighting simple
> volume #8 level 0.3342
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_peptide_paper/20230524/Models/03_B27/cryosparc_P5_J186_006_volume_map_sharp.mrc"
Opened cryosparc_P5_J186_006_volume_map_sharp.mrc as #9, grid size
448,448,448, pixel 0.676, shown at level 0.0468, step 2, values float32
> hide #!7 models
> hide #!8 models
> volume #9 step 1
> volume #9 level 0.1347
> volume #9 level 0.1066
> lighting soft
> show #!8 models
> hide #!9 models
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_ATP/Models/TAP_EQ_ATP_dimer_done_modeled/cryosparc_P19_J115_004_volume_map_sharp.mrc"
Opened cryosparc_P19_J115_004_volume_map_sharp.mrc as #10, grid size
400,400,400, pixel 0.847, shown at level 0.0849, step 2, values float32
> hide #!8 models
> volume #10 step 1
> volume #10 level 0.007504
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/jameslee/Dropbox (Dropbox
> @RU)/TAP_Viral_Inhibitors/UL495/RealSpaceRefine_54/tap_ul495-coot-35_real_space_refined_054.pdb"
Chain information for tap_ul495-coot-35_real_space_refined_054.pdb #1
---
Chain | Description
A | No description available
B | No description available
D | No description available
OpenGL version: 4.1 INTEL-18.8.5
OpenGL renderer: Intel(R) Iris(TM) Graphics 550
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro13,2
Processor Name: Dual-Core Intel Core i5
Processor Speed: 3.1 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 499.40.2.0.0
OS Loader Version: 540.120.3~22
SMC Version (system): 2.37f25
Software:
System Software Overview:
System Version: macOS 12.6.2 (21G320)
Kernel Version: Darwin 21.6.0
Time since boot: 53 days 20:41
Graphics/Displays:
Intel Iris Graphics 550:
Chipset Model: Intel Iris Graphics 550
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x1927
Revision ID: 0x000a
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP VH240a:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 6CM150117N
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Apple USB-C Digital AV Adapter
Adapter Firmware Version: 2.35
DELL P2312H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: GFXN435FBKRM
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: Analog VGA or Analog Over DVI-I
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.19.0
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.5
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 12.6.2, Intel Iris Graphics 550 |
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Apple Intel graphics driver crash.