id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
10055	Graphics crash, macOS 12.6.2, Intel Iris Graphics 550	chimerax-bug-report@…	Tom Goddard	"{{{
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,
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    ""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"",
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    ""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""
  },
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    ""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,
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    ""path"" : ""\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation"",
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    ""source"" : ""P"",
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    ""path"" : ""\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit"",
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],
  ""sharedCache"" : {
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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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  ""experiments"" : [
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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

}}}
"	defect	closed	normal		Graphics		nonchimerax						all	ChimeraX