Opened 2 years ago

Last modified 2 years ago

#10224 closed defect

ChimeraX bug report submission — at Initial Version

Reported by: chimerax-bug-report@… Owned by:
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.5.2-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00000002abedf000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002aaed3000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a9ec7000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a8ebb000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a7eaf000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a6ea3000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a5e97000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a4e8b000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a3e7f000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a2e73000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a1e67000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00000002a0e5b000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x000000029fe4f000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000294013000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000000293007000 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00000001dbfc6080 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.6.1.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":"2023-11-24 18:07:47.00 +0000","app_version":"1.6.1","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.5.2 (22G91)","roots_installed":0,"name":"ChimeraX","incident_id":"A684FB98-40D7-4903-8129-E2AE15A53AFF"}
{
  "uptime" : 100000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 503,
  "deployVersion" : 210,
  "modelCode" : "Mac14,9",
  "coalitionID" : 1900,
  "osVersion" : {
    "train" : "macOS 13.5.2",
    "build" : "22G91",
    "releaseType" : "User"
  },
  "captureTime" : "2023-11-24 18:07:45.7233 +0000",
  "incident" : "A684FB98-40D7-4903-8129-E2AE15A53AFF",
  "pid" : 53252,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-11-24 11:48:40.9858 +0000",
  "procStartAbsTime" : 2064626040653,
  "procExitAbsTime" : 2430710937210,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"F403C663-ED3D-5EBD-90E3-1907538C7ACC","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "BF2B3580-A1C4-5A90-B68E-2D28F156E60D",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 0,
  "sleepWakeUUID" : "E6ED89B5-1DF0-42AF-B078-86B7746AD977",
  "sip" : "enabled",
  "vmRegionInfo" : "0x18 is not in any region.  Bytes before following region: 105555129532392\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   600078000000-600080000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
  "exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":53252},
  "vmregioninfo" : "0x18 is not in any region.  Bytes before following region: 105555129532392\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   600078000000-600080000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
  "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" : [{"triggered":true,"id":1579077,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6458637741},{"value":5369363480},{"value":12979183233058688588},{"value":0},{"value":6124892200},{"value":15206481622518462668},{"value":15206481615414597708},{"value":78},{"value":0},{"value":49},{"value":16},{"value":14027849728},{"value":16},{"value":328},{"value":8064512928},{"value":0},{"value":11},{"value":7985717376,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":7985717600,"symbolLocation":224,"symbol":"_main_thread"},{"value":4813724592},{"value":1},{"value":32769},{"value":32768},{"value":7985723808,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6458457128},"cpsr":{"value":1073745920},"fp":{"value":5369363280},"sp":{"value":5369363248},"esr":{"value":1442840704,"description":" Address size 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  "vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=21.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=21.7G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               384K        3 \nActivity Tracing                   256K        1 \nCG backing stores                 6848K       12 \nCG image                          2368K      118 \nColorSync                          592K       30 \nCoreAnimation                     6272K      369 \nCoreGraphics                        64K        4 \nCoreServices                       624K        2 \nCoreUI image data                 5696K       53 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                            19.6G     1434 \nMALLOC guard page                  192K       11 \nMALLOC_LARGE (reserved)           43.9M        1         reserved VM address space (unallocated)\nMALLOC_MEDIUM (reserved)         808.0M       11         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           128.0M        1         reserved VM address space (unallocated)\nMach message                        64K        2 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        768K       48 \nStack                            393.2M       49 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      501.2M     1120 \nVM_ALLOCATE (reserved)           256.0M        3         reserved VM address space (unallocated)\n__AUTH                            1844K      369 \n__AUTH_CONST                      28.7M      602 \n__CTF                               824        1 \n__DATA                            20.3M      749 \n__DATA_CONST                      38.9M      758 \n__DATA_DIRTY                      1973K      229 \n__FONT_DATA                        2352        1 \n__GLSLBUILTINS                    5174K        1 \n__INFO_FILTER                         8        1 \n__LINKEDIT                       831.4M      155 \n__OBJC_RO                         66.4M        1 \n__OBJC_RW                         2012K        1 \n__TEXT                           851.2M      778 \ndyld private memory                272K        2 \nmapped file                      526.7M       74 \nshared memory                     3200K       29 \n===========                     =======  ======= \nTOTAL                             24.1G     7031 \nTOTAL, minus reserved VM space    22.8G     7031 \n",
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/2023_11_21_chimeraxsession.cxs

Opened emd_15829.map as #1, grid size 340,340,340, pixel 1.05, shown at level
0.904, step 2, values float32  
Opened cryosparc_P7_J649_008_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.48, shown at level 0.165, step 1, values float32  
Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 1.48, shown at level 0.178, step 1, values float32  
Opened emd_10585.map as #11, grid size 320,320,320, pixel 1.06, shown at level
0.0153, step 2, values float32  
Opened map series J684_series_000_frame_000.mrc as #12, 41 images, grid size
128,128,128, pixel 2.96, shown at level 0.00925, step 1, values float32  
Opened map series J684_series_001_frame_000.mrc as #13, 41 images, grid size
128,128,128, pixel 2.96, shown at level 0.0119, step 1, values float32  
Log from Tue Nov 21 10:52:47 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/2023_11_16_chimerasession-fittingmodels-
> preliminary.cxs

Opened emd_15829.map as #1, grid size 340,340,340, pixel 1.05, shown at level
0.674, step 2, values float32  
Opened cryosparc_P7_J649_008_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.48, shown at level 0.12, step 1, values float32  
Log from Sat Nov 18 13:53:42 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/ccrowe/Downloads/emd_15829.map

Opened emd_15829.map as #1, grid size 340,340,340, pixel 1.05, shown at level
0.319, step 2, values float32  

> open /Users/ccrowe/Downloads/cryosparc_P7_J649_008_volume_map_sharp.mrc

Opened cryosparc_P7_J649_008_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.48, shown at level 0.0675, step 1, values float32  

> volume #2 level 0.1569

> volume #1 level 1.422

> volume #2 level 0.2462

> fitmap #1 inMap #2

Fit map emd_15829.map in map cryosparc_P7_J649_008_volume_map_sharp.mrc using
8467 points  
correlation = 0.2699, correlation about mean = 0.02423, overlap = 792.2  
steps = 88, shift = 5.5, angle = 8.32 degrees  
  
Position of emd_15829.map (#1) relative to
cryosparc_P7_J649_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.98954429 -0.13805513 -0.04174771 37.60417190  
0.13857643 0.99030278 0.00984807 -22.08426146  
0.03998330 -0.01553035 0.99907965 -6.71417206  
Axis -0.08764266 -0.28225251 0.95532836  
Axis point 184.37562505 256.21425444 0.00000000  
Rotation angle (degrees) 8.32474228  
Shift along axis -3.47663053  
  

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.98954,-0.13806,-0.041748,35.375,0.13858,0.9903,0.0098481,-2.1466,0.039983,-0.01553,0.99908,24.804

> fitmap #1 inMap #2

Fit map emd_15829.map in map cryosparc_P7_J649_008_volume_map_sharp.mrc using
8467 points  
correlation = 0.4314, correlation about mean = 0.0793, overlap = 1491  
steps = 192, shift = 8.85, angle = 11.7 degrees  
  
Position of emd_15829.map (#1) relative to
cryosparc_P7_J649_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.95102599 -0.30734543 0.03299018 64.18837099  
0.30895288 0.94852311 -0.06965642 -9.87847425  
-0.00988337 0.07643748 0.99702539 10.52181670  
Axis 0.23013187 0.06753581 0.97081318  
Axis point 67.26780029 179.91918163 0.00000000  
Rotation angle (degrees) 18.50657282  
Shift along axis 24.31935726  
  

> select clear

> surface dust #1 size 10.5

> surface dust #2 size 14.8

> hide #!1 models

> volume #2 level 0.2409

> volume #2 level 0.2357

> volume #2 level 0.2094

> volume #2 level 0.2041

> volume #2 level 0.1884

> volume #2 level 0.1779

> volume #2 level 0.1674

> volume #2 level 0.1569

> volume #2 level 0.1621

> show #!1 models

> hide #!1 models

> open 5n4w

5n4w title:  
Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex [more
info...]  
  
Chain information for 5n4w #3  
---  
Chain | Description | UniProt  
A | Cullin-2 | CUL2_HUMAN 1-745  
B | Elongin-B | ELOB_HUMAN 1-104  
C | Elongin-C | ELOC_HUMAN 17-112  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-102  
V | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
  
Non-standard residues in 5n4w #3  
---  
ZN — zinc ion  
  

> select add #3

7719 atoms, 7841 bonds, 29 pseudobonds, 970 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,67.765,0,1,0,146.24,0,0,1,202.44

> view matrix models #3,1,0,0,86.717,0,1,0,171.74,0,0,1,261.01

> view matrix models #3,1,0,0,139.75,0,1,0,165.25,0,0,1,246.27

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.79454,-0.062119,-0.60402,123.9,0.10797,0.99335,0.039873,164.84,0.59753,-0.0969,0.79597,230.62

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.79454,-0.062119,-0.60402,166.64,0.10797,0.99335,0.039873,161.69,0.59753,-0.0969,0.79597,218.48

> ui mousemode right translate

> fitmap #3 inMap #2

Fit molecule 5n4w (#3) to map cryosparc_P7_J649_008_volume_map_sharp.mrc (#2)
using 7719 atoms  
average map value = 0.18, steps = 116  
shifted from previous position = 3.22  
rotated from previous position = 10.6 degrees  
atoms outside contour = 3991, contour level = 0.16211  
  
Position of 5n4w (#3) relative to cryosparc_P7_J649_008_volume_map_sharp.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.79478450 0.08379181 -0.60107948 162.30251961  
-0.07692658 0.99634346 0.03717539 161.31478949  
0.60199660 0.01669257 0.79832415 216.95739215  
Axis -0.01687306 -0.99105349 -0.13239439  
Axis point -206.08574593 0.00000000 335.00747620  
Rotation angle (degrees) 37.37061157  
Shift along axis -191.33406721  
  

> hide sel atoms

> show sel cartoons

> select /A

5384 atoms, 5468 bonds, 16 pseudobonds, 671 residues, 2 models selected  

> color (#!3 & sel) light sea green

> color (#!3 & sel) #4294a5ff

> select /R

693 atoms, 707 bonds, 6 pseudobonds, 89 residues, 2 models selected  

> color (#!3 & sel) #5ecd3cff

[Repeated 1 time(s)]

> select /V

315 atoms, 319 bonds, 37 residues, 1 model selected  

> color sel #3478f5ff

> color sel #429429ff

> select clear

> transparency #2.1 50

> select /B

627 atoms, 634 bonds, 5 pseudobonds, 82 residues, 2 models selected  

> color (#!3 & sel) #c5c53fff

> select /C

700 atoms, 713 bonds, 2 pseudobonds, 91 residues, 2 models selected  

> color (#!3 & sel) #b1d9aaff

> select #2

2 models selected  

> select clear

> open 5t35

5t35 title:  
The PROTAC MZ1 in complex with the second bromodomain of Brd4 and
pVHL:ElonginC:ElonginB [more info...]  
  
Chain information for 5t35 #4  
---  
Chain | Description | UniProt  
A E | Bromodomain-containing protein 4 | BRD4_HUMAN 333-460  
B F | Transcription elongation factor B polypeptide 2 | ELOB_HUMAN 1-104  
C G | Transcription elongation factor B polypeptide 1 | ELOC_HUMAN 17-112  
D H | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
  
Non-standard residues in 5t35 #4  
---  
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
  
5t35 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #4/E

910 atoms, 918 bonds, 126 residues, 1 model selected  

> delete sel

> select #4/G

693 atoms, 703 bonds, 1 pseudobond, 92 residues, 2 models selected  

> delete sel

> select #4/F

811 atoms, 826 bonds, 105 residues, 1 model selected  

> delete sel

> select #4/H

1265 atoms, 1294 bonds, 156 residues, 1 model selected  

> delete sel

> ui mousemode right "translate selected models"

> select add #4

3730 atoms, 3763 bonds, 1 pseudobond, 510 residues, 2 models selected  

> view matrix models #4,1,0,0,-5.3699,0,1,0,134.86,0,0,1,94.837

> view matrix models #4,1,0,0,2.1659,0,1,0,-62.339,0,0,1,-18.94

> view matrix models #4,1,0,0,2.3333,0,1,0,-67.77,0,0,1,-18.915

> view matrix models #4,1,0,0,2.5358,0,1,0,-69.072,0,0,1,-31.691

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,1.5607,0,1,0,-14.072,0,0,1,-88.646

> view matrix models #4,1,0,0,-5.8062,0,1,0,211.25,0,0,1,194

> view matrix models #4,1,0,0,172.88,0,1,0,205.94,0,0,1,213.38

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,170.43,0,1,0,219.02,0,0,1,201.75

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.87652,0.14211,-0.4599,186.86,0.47965,0.33829,-0.80963,203.87,0.040523,-0.93025,-0.36468,185.16

> view matrix models
> #4,-0.82238,-0.48607,0.29569,170.12,0.079795,-0.61313,-0.78595,185.13,0.56332,-0.62275,0.54301,185.81

> view matrix models
> #4,-0.42813,-0.10102,0.89806,174.29,-0.57519,-0.73601,-0.357,185.14,0.69704,-0.66939,0.257,184.85

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.42813,-0.10102,0.89806,169.91,-0.57519,-0.73601,-0.357,201.7,0.69704,-0.66939,0.257,150.37

> view matrix models
> #4,-0.42813,-0.10102,0.89806,196.15,-0.57519,-0.73601,-0.357,202.85,0.69704,-0.66939,0.257,152.15

> fitmap #4 inMap #2

Fit molecule 5t35 (#4) to map cryosparc_P7_J649_008_volume_map_sharp.mrc (#2)
using 3730 atoms  
average map value = 0.215, steps = 108  
shifted from previous position = 3.82  
rotated from previous position = 14.6 degrees  
atoms outside contour = 1669, contour level = 0.16211  
  
Position of 5t35 (#4) relative to cryosparc_P7_J649_008_volume_map_sharp.mrc
(#2) coordinates:  
Matrix rotation and translation  
-0.47918317 -0.26739413 0.83599275 190.99987496  
-0.36232349 -0.80726251 -0.46588511 200.32242340  
0.79944054 -0.52614411 0.28994343 151.75878688  
Axis -0.50966766 0.30915673 -0.80290784  
Axis point 51.91965946 127.33615507 0.00000000  
Rotation angle (degrees) 176.61092812  
Shift along axis -157.26375277  
  

> select clear

> ui mousemode right "translate selected models"

> select add #4

3730 atoms, 3763 bonds, 1 pseudobond, 510 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> select clear

> select #4/A

893 atoms, 908 bonds, 119 residues, 1 model selected  

> color sel #590df2ff

> select #4/D

1305 atoms, 1322 bonds, 171 residues, 1 model selected  

> color sel #429429ff

> select clear

> select #4/B

831 atoms, 830 bonds, 121 residues, 1 model selected  

> color sel #c5c53fff

> select clear

> select #4/C

701 atoms, 703 bonds, 1 pseudobond, 99 residues, 2 models selected  

> ui tool show "Color Actions"

> color (#!4 & sel) #b1d9aaff

> select clear

> volume #2 level 0.2199

> volume #2 level 0.3092

> volume #2 level 0.4143

> volume #2 level 0.2987

> volume #2 level 0.2567

> volume #2 level 0.2199

> volume #2 level 0.1201

> volume #2 level 0.1621

> volume #2 level 0.2567

> volume #2 level 0.4195

> volume #2 level 0.3092

> volume #2 level 0.304

> volume #2 level 0.2199

> volume #2 level 0.2567

> hide #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #2 level 0.3145

> volume #2 level 0.2882

> volume #2 level 0.388

> volume #2 level 0.698

> volume #2 level 0.5509

> volume #2 level 0.4038

> volume #2 level 0.2567

> volume #2 level 0.1726

> volume #2 level 0.2567

> volume #2 level 0.1989

> volume #2 level 0.2567

> volume #2 level 0.4143

> volume #2 level 0.2882

> show #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> volume #2 level 0.1884

> open 4wqo

Summary of feedback from opening 4wqo fetched from pdb  
---  
note | Fetching compressed mmCIF 4wqo from
http://files.rcsb.org/download/4wqo.cif  
  
4wqo title:  
Structure of VHL-EloB-EloC-Cul2 [more info...]  
  
Chain information for 4wqo #5  
---  
Chain | Description | UniProt  
A | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 1-213  
B | Transcription elongation factor B polypeptide 2 | ELOB_HUMAN 1-118  
C | Transcription elongation factor B polypeptide 1 | ELOC_HUMAN 17-112  
D | Cullin-2 | CUL2_HUMAN 1-163  
  

> select add #5

3902 atoms, 3993 bonds, 1 pseudobond, 489 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,180.02,0,1,0,177.54,0,0,1,282.36

> ui mousemode right translate

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.092227,-0.96275,0.25417,126.56,-0.93133,-0.006911,-0.36411,100,0.35231,-0.2703,-0.896,199.81

> view matrix models
> #5,0.16376,-0.64354,-0.74769,87.296,0.41354,-0.64333,0.64429,238.26,-0.89564,-0.41471,0.16078,180.97

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.16376,-0.64354,-0.74769,111.47,0.41354,-0.64333,0.64429,266.25,-0.89564,-0.41471,0.16078,190.29

> view matrix models
> #5,0.16376,-0.64354,-0.74769,123.34,0.41354,-0.64333,0.64429,258.18,-0.89564,-0.41471,0.16078,186.92

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.7722,-0.13503,-0.62087,167.87,0.44116,-0.58928,0.67685,261.68,-0.45727,-0.79656,-0.39547,183.32

> view matrix models
> #5,0.72947,-0.079516,-0.67938,162.03,0.5206,-0.5797,0.62684,263.82,-0.44368,-0.81094,-0.38147,184.92

> view matrix models
> #5,0.70928,-0.056381,-0.70267,159.51,0.5528,-0.57404,0.60407,264.56,-0.43741,-0.81689,-0.37599,185.61

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.70928,-0.056381,-0.70267,202.01,0.5528,-0.57404,0.60407,256.45,-0.43741,-0.81689,-0.37599,174.15

> view matrix models
> #5,0.70928,-0.056381,-0.70267,194.92,0.5528,-0.57404,0.60407,251.32,-0.43741,-0.81689,-0.37599,113.88

> fitmap #5 inMap #2

Fit molecule 4wqo (#5) to map cryosparc_P7_J649_008_volume_map_sharp.mrc (#2)
using 3902 atoms  
average map value = 0.2249, steps = 96  
shifted from previous position = 7.16  
rotated from previous position = 20.3 degrees  
atoms outside contour = 1821, contour level = 0.18838  
  
Position of 4wqo (#5) relative to cryosparc_P7_J649_008_volume_map_sharp.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.61111157 -0.06427886 -0.78893022 179.81366838  
0.74581173 -0.28711959 0.60110499 262.91204689  
-0.26515567 -0.95573562 -0.12752218 141.29348770  
Axis -0.85004254 -0.28598345 0.44231340  
Axis point 0.00000000 183.63820774 34.59377662  
Rotation angle (degrees) 113.68856996  
Shift along axis -165.54175955  
  

> select clear

> select ::name="759"

69 atoms, 75 bonds, 1 residue, 1 model selected  

> color sel yellow

> color sel byhetero

> show sel atoms

> select clear

> select #5/D

1168 atoms, 1197 bonds, 1 pseudobond, 141 residues, 2 models selected  

> color (#!5 & sel) #3e8a9aff

> select clear

> select #5/A

1197 atoms, 1228 bonds, 148 residues, 1 model selected  

> color sel #409028ff

> select clear

> select #3/B

627 atoms, 634 bonds, 5 pseudobonds, 82 residues, 2 models selected  

> color (#!3 & sel) #c0c03dff

> select #5/B

798 atoms, 813 bonds, 104 residues, 1 model selected  

> color sel #c0c03dff

> select #5/C

739 atoms, 755 bonds, 96 residues, 1 model selected  

> color sel #91b28bff

> select clear

> volume #2 level 0.1201

> open /Users/ccrowe/Downloads/AF-Q13617-F1-model_v4.pdb

AF-Q13617-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for cullin-2 (Q13617) [more info...]  
  
Chain information for AF-Q13617-F1-model_v4.pdb #6  
---  
Chain | Description | UniProt  
A | cullin-2 | CUL2_HUMAN 1-745  
  

> select add #6

6101 atoms, 6220 bonds, 745 residues, 1 model selected  

> color sel #39808fff

> ui mousemode right "translate selected models"

> view matrix models #6,1,0,0,17.593,0,1,0,199.75,0,0,1,200.97

> view matrix models #6,1,0,0,156.95,0,1,0,177.05,0,0,1,231.02

> ui mousemode right translate

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.17819,-0.97355,-0.14301,180.77,0.48079,-0.21295,0.85058,183.71,-0.85854,0.082807,0.50602,240.32

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.17819,-0.97355,-0.14301,182.97,0.48079,-0.21295,0.85058,171.99,-0.85854,0.082807,0.50602,209.51

> fitmap #6 inMap #2

Fit molecule AF-Q13617-F1-model_v4.pdb (#6) to map
cryosparc_P7_J649_008_volume_map_sharp.mrc (#2) using 6101 atoms  
average map value = 0.1704, steps = 248  
shifted from previous position = 16.5  
rotated from previous position = 17.7 degrees  
atoms outside contour = 2691, contour level = 0.12007  
  
Position of AF-Q13617-F1-model_v4.pdb (#6) relative to
cryosparc_P7_J649_008_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.08107301 -0.98653713 0.14202696 193.35932442  
0.46251136 0.08898798 0.88213626 175.29744761  
-0.88289887 0.13720652 0.44907010 221.70078625  
Axis -0.38700209 0.53246422 0.75280225  
Axis point 115.16845768 142.52512290 0.00000000  
Rotation angle (degrees) 105.75398941  
Shift along axis 185.40600949  
  

> select clear

> hide #!3 models

> show #!3 models

> show #!1 models

> hide #!2 models

> volume #1 level 0.884

> open 6ttu

6ttu title:  
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...]  
  
Chain information for 6ttu #7  
---  
Chain | Description | UniProt  
C | Cullin-1 | CUL1_HUMAN 1-776  
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 1-147  
I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY |  
N | NEDD8 | NEDD8_HUMAN 1-76  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108  
S | S-phase kinase-associated protein 1 | SKP1_HUMAN 1-145  
T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN 1-605  
U | Polyubiquitin-C | UBC_HUMAN 1-76  
  
Non-standard residues in 6ttu #7  
---  
ZN — zinc ion  
  

> ui tool show Matchmaker

> matchmaker #!7 to #3/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 5n4w, chain A (#3) with 6ttu, chain C (#7), sequence alignment
score = 1558.4  
RMSD between 318 pruned atom pairs is 1.340 angstroms; (across all 640 pairs:
9.463)  
  

> select add #7

12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> color (#!7 & sel) orange

> select clear

> volume #1 level 1.015

[Repeated 1 time(s)]

> volume #1 level 0.6739

> save "/Users/ccrowe/OneDrive - University of Dundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/2023_11_16_chimerasession-fittingmodels-
> preliminary.cxs"

——— End of log from Sat Nov 18 13:53:42 2023 ———

opened ChimeraX session  

> save /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-EM/CRL2/2023_11_16_mapCRL2/AF-
> cul2-docked-chimera.pdb models #6

> hide #!7 models

> hide #!1 models

> show #!2 models

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/DockInMap_1/placed_model.pdb

Summary of feedback from opening /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-
EM/CRL2/2023_11_16_mapCRL2/DockInMap_1/placed_model.pdb  
---  
warning | Ignored bad PDB record found on line 6108  
  
Chain information for placed_model.pdb #8  
---  
Chain | Description  
A | No description available  
  

> volume #2 level 0.2567

> close #8

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J710_006_volume_map_sharp.mrc

Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #8, grid size
256,256,256, pixel 1.48, shown at level 0.0524, step 1, values float32  

> volume #8 level 0.1539

> surface dust #2 size 14.8

> surface dust #8 size 14.8

> volume #8 level 0.2007

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/DockInMap_3/placed_model.pdb

Summary of feedback from opening /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-
EM/CRL2/2023_11_16_mapCRL2/DockInMap_3/placed_model.pdb  
---  
warning | Ignored bad PDB record found on line 6108  
  
Chain information for placed_model.pdb #9  
---  
Chain | Description  
A | No description available  
  

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model.pdb

Summary of feedback from opening /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-
EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
  
  
Ignored bad PDB record found on line 2  
REMARK MODEL FROM PHENIX.MAP_TO_MODEL  
  
Ignored bad PDB record found on line 3  
REMARK MAP FILE: /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-
EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J710_006_volume_map_sharp.mrc  
  
Ignored bad PDB record found on line 4  
  
  
Ignored bad PDB record found on line 90  
  
Chain information for map_to_model.pdb #10  
---  
Chain | Description  
U | No description available  
  

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> color #10 #d783ffff

> select add #10

84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected  

> select subtract #10

Nothing selected  

> hide #9 models

> hide #!8 models

> select add #10

84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected  

> select subtract #10

Nothing selected  

> select add #10

84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected  

> select subtract #10

Nothing selected  

> select add #10

84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected  

> select subtract #10

Nothing selected  

> select add #10

84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected  

> close #10

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model_0/model_PROTEIN.pdb

Summary of feedback from opening /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-
EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model_0/model_PROTEIN.pdb  
---  
warning | Ignored bad PDB record found on line 87  
  
Chain information for model_PROTEIN.pdb #10  
---  
Chain | Description  
U | No description available  
  

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> select add #10

84 atoms, 85 bonds, 1 pseudobond, 12 residues, 2 models selected  

> close #10

> show #!8 models

> transparency #2.1#8.1 0

> transparency #2.1#8.1 50

> color #8 #8efa00ff models

> transparency #2.1#8.1 0

> transparency #2.1#8.1 50

> color #8 #ff2600ff models

> transparency #2.1#8.1 0

> transparency #2.1#8.1 50

> hide #6 models

> show #6 models

> hide #6 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!1 models

> transparency 0

> transparency 50

> volume #2 level 0.1864

> volume #8 level 0.1461

> volume #1 level 0.9037

> volume #2 level 0.2026

> volume #8 level 0.1851

> open 8bei

Fetching url http://files.rcsb.org/download/8bei.cif failed:  
HTTP Error 404: Not Found  

> open 8b3i

Summary of feedback from opening 8b3i fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /N:1  
Atom H1 is not in the residue template for MET /U:1  
Atom H1 is not in the residue template for MET /a:1  
Atom H1 is not in the residue template for MET /d:1  
  
8b3i title:  
CRL4CSA-E2-Ub (state 2) [more info...]  
  
Chain information for 8b3i #10  
---  
Chain | Description | UniProt  
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 1-147  
N | NEDD8 | NEDD8_HUMAN 1-76  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108  
U | Ubiquitin | UBC_HUMAN 1-76  
a | DNA excision repair protein ERCC-8 | ERCC8_HUMAN 1-396  
d | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140  
e | Cullin-4A | CUL4A_HUMAN 1-759  
  
Non-standard residues in 8b3i #10  
---  
ZN — zinc ion  
  

> select add #10

40377 atoms, 40760 bonds, 21 pseudobonds, 2540 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.99993,0.010671,0.005056,-2.7845,-0.011717,0.94982,0.31259,-45.787,-0.0014665,-0.31263,0.94987,64.421

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.99993,0.010671,0.005056,-3.3622,-0.011717,0.94982,0.31259,-29.739,-0.0014665,-0.31263,0.94987,85.229

> view matrix models
> #10,0.99993,0.010671,0.005056,2.5399,-0.011717,0.94982,0.31259,-31.225,-0.0014665,-0.31263,0.94987,80.291

> view matrix models
> #10,0.99993,0.010671,0.005056,2.5336,-0.011717,0.94982,0.31259,-36.105,-0.0014665,-0.31263,0.94987,81.646

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 4 atomic models, 3 maps.  

> hide #!8 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> fitmap #10 inMap #1

Fit molecule 8b3i (#10) to map emd_15829.map (#1) using 40377 atoms  
average map value = 1.297, steps = 256  
shifted from previous position = 17.3  
rotated from previous position = 29.2 degrees  
atoms outside contour = 17017, contour level = 0.90374  
  
Position of 8b3i (#10) relative to emd_15829.map (#1) coordinates:  
Matrix rotation and translation  
0.99999997 -0.00023490 0.00007996 0.02149465  
0.00023488 0.99999994 0.00024868 -0.07820052  
-0.00008002 -0.00024866 0.99999997 0.06914071  
Axis -0.70786977 0.22770737 0.66863274  
Axis point 0.00000000 242.49058258 326.60984678  
Rotation angle (degrees) 0.02012788  
Shift along axis 0.01320749  
  

> select clear

> show #6 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #!8 models

> hide #!10 models

> show #!10 models

> hide #6 models

> show #6 models

> hide #6 models

> show #!3 models

> hide #!3 models

> show #6 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/emd_10585.map

Opened emd_10585.map as #11, grid size 320,320,320, pixel 1.06, shown at level
0.000884, step 2, values float32  

> volume #2 level 0.1647

> volume #11 color #ff9300

> transparency 0

> transparency 50

> volume #11 level 0.01017

> fitmap #11 inMap #8

Fit map emd_10585.map in map cryosparc_P7_J710_006_volume_map_sharp.mrc using
13478 points  
correlation = 0.2383, correlation about mean = 0.01468, overlap = 11.76  
steps = 180, shift = 10.8, angle = 11.3 degrees  
  
Position of emd_10585.map (#11) relative to
cryosparc_P7_J710_006_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.98403384 0.07388692 -0.16192012 28.38530521  
-0.08713715 0.99326921 -0.07631113 32.01277931  
0.15519188 0.08920200 0.98384881 -35.82899321  
Axis 0.42192631 -0.80838238 -0.41048279  
Axis point 244.25883800 0.00000000 149.12121744  
Rotation angle (degrees) 11.31131831  
Shift along axis 0.80512552  
  

> select add #11

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.1087,0.9264,0.36051,-22.476,0.81709,0.28981,-0.49836,71.941,-0.56616,0.2404,-0.78846,376.31

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.1087,0.9264,0.36051,-27.473,0.81709,0.28981,-0.49836,90.516,-0.56616,0.2404,-0.78846,400.2

> fitmap #11 inMap #8

Fit map emd_10585.map in map cryosparc_P7_J710_006_volume_map_sharp.mrc using
13478 points  
correlation = 0.4738, correlation about mean = 0.1259, overlap = 30.17  
steps = 372, shift = 5.18, angle = 30 degrees  
  
Position of emd_10585.map (#11) relative to
cryosparc_P7_J710_006_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
-0.55622647 0.82178426 0.12362336 113.90601365  
0.71361529 0.54855645 -0.43570522 50.69802278  
-0.42587008 -0.15413125 -0.89155944 462.06282433  
Axis 0.44919643 0.87660980 -0.17256253  
Axis point 86.58312572 0.00000000 226.23073896  
Rotation angle (degrees) 161.73456499  
Shift along axis 15.87382737  
  

> select clear

> volume #11 level 0.01189

> hide #!2 models

> hide #6 models

> hide #!8 models

> hide #!10 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 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 0.2397

> volume #11 level 0.01286

> volume #11 level 0.01629

> volume #8 level 0.2085

> volume #11 level 0.01531

> show #!7 models

> hide #!8 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!8 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!1 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!11 models

> hide #!11 models

> show #!11 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #!11 models

> hide #!8 models

> show #!8 models

> show #6 models

> show #!5 models

> hide #!5 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!7 models

> hide #!3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #6/A #9/A

Alignment identifier is 1  

> select
> #6/A:10-25,32-46,54-104,106-116,120-124,139-172,178-192,201-229,232-253,256-272,275-287,291-303,308-328,332-357,362-376,387-399,408-424,428-444,451-465,467-496,531-547,557-559,579-589,596-603,607-619,656-658,662-691,696-707,715-727
> #9/A:10-25,32-46,54-104,106-116,120-124,139-172,178-192,201-229,232-253,256-272,275-287,291-303,308-328,332-357,362-376,387-399,408-424,428-444,451-465,467-496,531-547,557-559,579-589,596-603,607-619,656-658,662-691,696-707,715-727

8398 atoms, 8498 bonds, 1010 residues, 2 models selected  

> view matrix models
> #6,-0.081073,-0.98654,0.14203,193.19,0.46251,0.088988,0.88214,174.98,-0.8829,0.13721,0.44907,219.29,#9,1,0,0,-0.1681,0,1,0,-0.31576,0,0,1,-2.4148

> select clear

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> save /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/MapToModel_2/map_to_model_0/2023_11_20.cxs
> includeMaps true

> select add #8

2 models selected  

> vop gaussian #8 sdev 4.44

Opened cryosparc_P7_J710_006_volume_map_sharp.mrc gaussian as #12, grid size
256,256,256, pixel 1.48, shown at step 1, values float32  

> volume #12 level 0.07218

> volume #12 level 0.08236

> volume #12 step 4

> volume #12 step 16

> volume #12 step 1

> volume #12 level 0.0271

> hide #!12 models

> show #!8 models

> select subtract #8

Nothing selected  

> close #12

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl  
[Repeated 2 time(s)]

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.6.0-cp39-cp39-macosx_10_13_universal2.whl  
[Repeated 1 time(s)]

> hide #!10 models

> show #!10 models

> hide #!1 models

> hide #!10 models

> hide #!1 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> volume #8 level 0.1175

> volume #!8 style surface

> transparency #8.1 0

> transparency #8.1 50

> show #!2 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!8 models

> show #!8 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #8 level 0.1782

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_000.mrc

Opened J684_series_000_frame_000.mrc as #12, grid size 128,128,128, pixel
2.96, shown at level 0.000154, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_001.mrc

Opened J684_series_000_frame_001.mrc as #13, grid size 128,128,128, pixel
2.96, shown at level 0.000181, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_002.mrc

Opened J684_series_000_frame_002.mrc as #14, grid size 128,128,128, pixel
2.96, shown at level 2.51e-06, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_003.mrc

Opened J684_series_000_frame_003.mrc as #15, grid size 128,128,128, pixel
2.96, shown at level 2.19e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_004.mrc

Opened J684_series_000_frame_004.mrc as #16, grid size 128,128,128, pixel
2.96, shown at level 4.29e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_005.mrc

Opened J684_series_000_frame_005.mrc as #17, grid size 128,128,128, pixel
2.96, shown at level 9.98e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_006.mrc

Opened J684_series_000_frame_006.mrc as #18, grid size 128,128,128, pixel
2.96, shown at level 0.000141, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_007.mrc

Opened J684_series_000_frame_007.mrc as #19, grid size 128,128,128, pixel
2.96, shown at level 0.000188, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_008.mrc

Opened J684_series_000_frame_008.mrc as #20, grid size 128,128,128, pixel
2.96, shown at level 0.000132, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_009.mrc

Opened J684_series_000_frame_009.mrc as #21, grid size 128,128,128, pixel
2.96, shown at level 3.05e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_010.mrc

Opened J684_series_000_frame_010.mrc as #22, grid size 128,128,128, pixel
2.96, shown at level 0.000104, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_011.mrc

Opened J684_series_000_frame_011.mrc as #23, grid size 128,128,128, pixel
2.96, shown at level 0.00013, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_012.mrc

Opened J684_series_000_frame_012.mrc as #24, grid size 128,128,128, pixel
2.96, shown at level 0.00012, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_013.mrc

Opened J684_series_000_frame_013.mrc as #25, grid size 128,128,128, pixel
2.96, shown at level 5.42e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_014.mrc

Opened J684_series_000_frame_014.mrc as #26, grid size 128,128,128, pixel
2.96, shown at level 0.000165, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_015.mrc

Opened J684_series_000_frame_015.mrc as #27, grid size 128,128,128, pixel
2.96, shown at level 0.000171, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_016.mrc

Opened J684_series_000_frame_016.mrc as #28, grid size 128,128,128, pixel
2.96, shown at level 2.93e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_017.mrc

Opened J684_series_000_frame_017.mrc as #29, grid size 128,128,128, pixel
2.96, shown at level 0.00017, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_018.mrc

Opened J684_series_000_frame_018.mrc as #30, grid size 128,128,128, pixel
2.96, shown at level 0.000176, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_019.mrc

Opened J684_series_000_frame_019.mrc as #31, grid size 128,128,128, pixel
2.96, shown at level 6.17e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_020.mrc

Opened J684_series_000_frame_020.mrc as #32, grid size 128,128,128, pixel
2.96, shown at level 0.000205, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_021.mrc

Opened J684_series_000_frame_021.mrc as #33, grid size 128,128,128, pixel
2.96, shown at level 6.87e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_022.mrc

Opened J684_series_000_frame_022.mrc as #34, grid size 128,128,128, pixel
2.96, shown at level 9.07e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_023.mrc

Opened J684_series_000_frame_023.mrc as #35, grid size 128,128,128, pixel
2.96, shown at level 9.5e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_024.mrc

Opened J684_series_000_frame_024.mrc as #36, grid size 128,128,128, pixel
2.96, shown at level 0.000158, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_025.mrc

Opened J684_series_000_frame_025.mrc as #37, grid size 128,128,128, pixel
2.96, shown at level 6.33e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_026.mrc

Opened J684_series_000_frame_026.mrc as #38, grid size 128,128,128, pixel
2.96, shown at level 0.000131, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_027.mrc

Opened J684_series_000_frame_027.mrc as #39, grid size 128,128,128, pixel
2.96, shown at level 7.92e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_028.mrc

Opened J684_series_000_frame_028.mrc as #40, grid size 128,128,128, pixel
2.96, shown at level 0.000171, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_029.mrc

Opened J684_series_000_frame_029.mrc as #41, grid size 128,128,128, pixel
2.96, shown at level 8.69e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_030.mrc

Opened J684_series_000_frame_030.mrc as #42, grid size 128,128,128, pixel
2.96, shown at level 0.000128, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_031.mrc

Opened J684_series_000_frame_031.mrc as #43, grid size 128,128,128, pixel
2.96, shown at level 0.000183, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_032.mrc

Opened J684_series_000_frame_032.mrc as #44, grid size 128,128,128, pixel
2.96, shown at level 9.78e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_033.mrc

Opened J684_series_000_frame_033.mrc as #45, grid size 128,128,128, pixel
2.96, shown at level 7.4e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_034.mrc

Opened J684_series_000_frame_034.mrc as #46, grid size 128,128,128, pixel
2.96, shown at level 8.13e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_035.mrc

Opened J684_series_000_frame_035.mrc as #47, grid size 128,128,128, pixel
2.96, shown at level 0.000108, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_036.mrc

Opened J684_series_000_frame_036.mrc as #48, grid size 128,128,128, pixel
2.96, shown at level 8.72e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_037.mrc

Opened J684_series_000_frame_037.mrc as #49, grid size 128,128,128, pixel
2.96, shown at level 9.87e-05, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_038.mrc

Opened J684_series_000_frame_038.mrc as #50, grid size 128,128,128, pixel
2.96, shown at level 0.000132, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_039.mrc

Opened J684_series_000_frame_039.mrc as #51, grid size 128,128,128, pixel
2.96, shown at level 0.000167, step 1, values float32  

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_040.mrc

Opened J684_series_000_frame_040.mrc as #52, grid size 128,128,128, pixel
2.96, shown at level 0.000203, step 1, values float32  

> close #12

> close #13-23

> close #24-38

> close #39-52

> ui tool show "Volume Viewer"

> hide #6 models

> open /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_000.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_001.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_002.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_003.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_004.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_005.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_006.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_007.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_008.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_009.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_010.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_011.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_012.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_013.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_014.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_015.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_016.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_017.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_018.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_019.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_020.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_021.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_022.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_023.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_024.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_025.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_026.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_027.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_028.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_029.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_030.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_031.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_032.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_033.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_034.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_035.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_036.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_037.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_038.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_039.mrc
> /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/J684_series_000_frame_040.mrc

Opened J684_series_000_frame_000.mrc as #12.1, grid size 128,128,128, pixel
2.96, shown at level 0.000154, step 1, values float32  
Opened J684_series_000_frame_001.mrc as #12.2, grid size 128,128,128, pixel
2.96, shown at level 0.000181, step 1, values float32  
Opened J684_series_000_frame_002.mrc as #12.3, grid size 128,128,128, pixel
2.96, shown at level 2.51e-06, step 1, values float32  
Opened J684_series_000_frame_003.mrc as #12.4, grid size 128,128,128, pixel
2.96, shown at level 2.19e-05, step 1, values float32  
Opened J684_series_000_frame_004.mrc as #12.5, grid size 128,128,128, pixel
2.96, shown at level 4.29e-05, step 1, values float32  
Opened J684_series_000_frame_005.mrc as #12.6, grid size 128,128,128, pixel
2.96, shown at level 9.98e-05, step 1, values float32  
Opened J684_series_000_frame_006.mrc as #12.7, grid size 128,128,128, pixel
2.96, shown at level 0.000141, step 1, values float32  
Opened J684_series_000_frame_007.mrc as #12.8, grid size 128,128,128, pixel
2.96, shown at level 0.000188, step 1, values float32  
Opened J684_series_000_frame_008.mrc as #12.9, grid size 128,128,128, pixel
2.96, shown at level 0.000132, step 1, values float32  
Opened J684_series_000_frame_009.mrc as #12.10, grid size 128,128,128, pixel
2.96, shown at level 3.05e-05, step 1, values float32  
Opened J684_series_000_frame_010.mrc as #12.11, grid size 128,128,128, pixel
2.96, shown at level 0.000104, step 1, values float32  
Opened J684_series_000_frame_011.mrc as #12.12, grid size 128,128,128, pixel
2.96, shown at level 0.00013, step 1, values float32  
Opened J684_series_000_frame_012.mrc as #12.13, grid size 128,128,128, pixel
2.96, shown at level 0.00012, step 1, values float32  
Opened J684_series_000_frame_013.mrc as #12.14, grid size 128,128,128, pixel
2.96, shown at level 5.42e-05, step 1, values float32  
Opened J684_series_000_frame_014.mrc as #12.15, grid size 128,128,128, pixel
2.96, shown at level 0.000165, step 1, values float32  
Opened J684_series_000_frame_015.mrc as #12.16, grid size 128,128,128, pixel
2.96, shown at level 0.000171, step 1, values float32  
Opened J684_series_000_frame_016.mrc as #12.17, grid size 128,128,128, pixel
2.96, shown at level 2.93e-05, step 1, values float32  
Opened J684_series_000_frame_017.mrc as #12.18, grid size 128,128,128, pixel
2.96, shown at level 0.00017, step 1, values float32  
Opened J684_series_000_frame_018.mrc as #12.19, grid size 128,128,128, pixel
2.96, shown at level 0.000176, step 1, values float32  
Opened J684_series_000_frame_019.mrc as #12.20, grid size 128,128,128, pixel
2.96, shown at level 6.17e-05, step 1, values float32  
Opened J684_series_000_frame_020.mrc as #12.21, grid size 128,128,128, pixel
2.96, shown at level 0.000205, step 1, values float32  
Opened J684_series_000_frame_021.mrc as #12.22, grid size 128,128,128, pixel
2.96, shown at level 6.87e-05, step 1, values float32  
Opened J684_series_000_frame_022.mrc as #12.23, grid size 128,128,128, pixel
2.96, shown at level 9.07e-05, step 1, values float32  
Opened J684_series_000_frame_023.mrc as #12.24, grid size 128,128,128, pixel
2.96, shown at level 9.5e-05, step 1, values float32  
Opened J684_series_000_frame_024.mrc as #12.25, grid size 128,128,128, pixel
2.96, shown at level 0.000158, step 1, values float32  
Opened J684_series_000_frame_025.mrc as #12.26, grid size 128,128,128, pixel
2.96, shown at level 6.33e-05, step 1, values float32  
Opened J684_series_000_frame_026.mrc as #12.27, grid size 128,128,128, pixel
2.96, shown at level 0.000131, step 1, values float32  
Opened J684_series_000_frame_027.mrc as #12.28, grid size 128,128,128, pixel
2.96, shown at level 7.92e-05, step 1, values float32  
Opened J684_series_000_frame_028.mrc as #12.29, grid size 128,128,128, pixel
2.96, shown at level 0.000171, step 1, values float32  
Opened J684_series_000_frame_029.mrc as #12.30, grid size 128,128,128, pixel
2.96, shown at level 8.69e-05, step 1, values float32  
Opened J684_series_000_frame_030.mrc as #12.31, grid size 128,128,128, pixel
2.96, shown at level 0.000128, step 1, values float32  
Opened J684_series_000_frame_031.mrc as #12.32, grid size 128,128,128, pixel
2.96, shown at level 0.000183, step 1, values float32  
Opened J684_series_000_frame_032.mrc as #12.33, grid size 128,128,128, pixel
2.96, shown at level 9.78e-05, step 1, values float32  
Opened J684_series_000_frame_033.mrc as #12.34, grid size 128,128,128, pixel
2.96, shown at level 7.4e-05, step 1, values float32  
Opened J684_series_000_frame_034.mrc as #12.35, grid size 128,128,128, pixel
2.96, shown at level 8.13e-05, step 1, values float32  
Opened J684_series_000_frame_035.mrc as #12.36, grid size 128,128,128, pixel
2.96, shown at level 0.000108, step 1, values float32  
Opened J684_series_000_frame_036.mrc as #12.37, grid size 128,128,128, pixel
2.96, shown at level 8.72e-05, step 1, values float32  
Opened J684_series_000_frame_037.mrc as #12.38, grid size 128,128,128, pixel
2.96, shown at level 9.87e-05, step 1, values float32  
Opened J684_series_000_frame_038.mrc as #12.39, grid size 128,128,128, pixel
2.96, shown at level 0.000132, step 1, values float32  
Opened J684_series_000_frame_039.mrc as #12.40, grid size 128,128,128, pixel
2.96, shown at level 0.000167, step 1, values float32  
Opened J684_series_000_frame_040.mrc as #12.41, grid size 128,128,128, pixel
2.96, shown at level 0.000203, step 1, values float32  

> volume #12.1 level 0.004131

> close #12

> cd /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-EM/CRL2/2023_11_16_mapCRL2/

Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-EM/CRL2/2023_11_16_mapCRL2  

> pwd

Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-EM/CRL2/2023_11_16_mapCRL2  

> open *.mrc vseries true

Cannot make series from volumes with different sizes:  
5t35map.mrc 256 256 256  
cryosparc_P13_J404_004_volume_map_sharp.mrc 324 324 324  
cryosparc_P7_J649_008_volume_map_sharp.mrc 256 256 256  
cryosparc_P7_J710_006_volume_map_sharp.mrc 256 256 256  
ctermcullin.mrc 256 256 256  
cullinmap.mrc 256 256 256  

> open *.mrc vseries true

Cannot make series from volumes with different sizes:  
5t35map.mrc 256 256 256  
cryosparc_P13_J404_004_volume_map_sharp.mrc 324 324 324  
cryosparc_P7_J649_008_volume_map_sharp.mrc 256 256 256  
cryosparc_P7_J710_006_volume_map_sharp.mrc 256 256 256  
ctermcullin.mrc 256 256 256  
cullinmap.mrc 256 256 256  

> cd /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2//Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> cd /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2//Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/

Expected name of a folder to open/read; a name of 'browse' will bring up a
file browser or a keyword  

> cd /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000/

Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-
EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000  

> pwd

Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-
EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_000  

> open *.mrc vseries true

Opened map series J684_series_000_frame_000.mrc as #12, 41 images, grid size
128,128,128, pixel 2.96, shown at level 0.000154, step 1, values float32  

> volume #12.1 level 0.004131

> volume #12.20 level 0.009246

> cd /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_001/

Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-
EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_001  

> pwd

Current working directory is: /Users/ccrowe/Library/CloudStorage/OneDrive-
UniversityofDundee/Documents/Biology/cryo-
EM/CRL2/2023_11_16_mapCRL2/cryosparc_P7_J684_series_001  

> open *.mrc vseries true

Opened map series J684_series_001_frame_000.mrc as #13, 41 images, grid size
128,128,128, pixel 2.96, shown at level 0.000195, step 1, values float32  

> volume #13.15 level 0.01189

> hide #!12 models

> hide #!13 models

> show #!12 models

> save /Users/ccrowe/Library/CloudStorage/OneDrive-
> UniversityofDundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/2023_11_21_chimeraxsession.cxs includeMaps true

——— End of log from Tue Nov 21 10:52:47 2023 ———

opened ChimeraX session  

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #!12 models

> show #!10 models

> hide #!10 models

> show #9 models

> hide #9 models

> show #!12 models

> volume #12.5 level 0.08829

> show #!13 models

> volume #13.7 level 0.06315

> volume #12.7 level 0.07226

> hide #!12 models

> hide #!13 models

> show #!12 models

> show #!13 models

> hide #!13 models

> hide #!12 models

> show #!8 models

> volume #8 level 0.1157

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #9 models

> show #6 models

> hide #6 models

> hide #!8 models

> show #!8 models

> hide #9 models

> open /Users/ccrowe/Downloads/cryosparc_P14_J395_003_volume_map_sharp.mrc

Opened cryosparc_P14_J395_003_volume_map_sharp.mrc as #14, grid size
128,128,128, pixel 3.38, shown at level 0.124, step 1, values float32  

> open /Users/ccrowe/Downloads/cryosparc_P14_J396_003_volume_map_sharp.mrc

Opened cryosparc_P14_J396_003_volume_map_sharp.mrc as #15, grid size
128,128,128, pixel 3.38, shown at level 0.152, step 1, values float32  

> volume #14 level 0.2547

> volume #15 level 0.4279

> volume #14 level 0.3449

> surface dust #14 size 33.8

> surface dust #15 size 33.8

> open /Users/ccrowe/Downloads/cryosparc_P14_J427_003_volume_map_sharp.mrc

Opened cryosparc_P14_J427_003_volume_map_sharp.mrc as #16, grid size
128,128,128, pixel 3.38, shown at level 0.134, step 1, values float32  

> volume #16 level 0.1674

> surface dust #14 size 33.8

> surface dust #16 size 33.8

> volume #16 level 0.3324

> volume #16 level 0.6514

> volume #16 level 0.3104

> show #!8 models

> ui mousemode right "rotate selected models"

> select add #14

2 models selected  

> view matrix models
> #14,-0.83202,-0.54997,0.072621,494.21,0.52167,-0.82021,-0.23477,322.91,0.18868,-0.15745,0.96933,-0.68575

> view matrix models
> #14,-0.86702,-0.49747,0.028397,501.16,0.49797,-0.86303,0.084876,262.05,-0.017716,0.08773,0.99599,-13.576

> volume #14 flipNormals

Missing "flipNormals" keyword's argument  

> volume flip #14

Opened cryosparc_P14_J395_003_volume_map_sharp.mrc z flip as #17, grid size
128,128,128, pixel 3.38, shown at step 1, values float32  

> show #!14 models

> hide #!14 models

> select subtract #14

Nothing selected  

> select add #17

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.98445,-0.096336,0.14692,-6.4957,-0.081978,-0.99152,-0.10084,450.89,0.15539,0.087225,-0.98399,338.63

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.98445,-0.096336,0.14692,-8.2028,-0.081978,-0.99152,-0.10084,441.44,0.15539,0.087225,-0.98399,350.39

> ui mousemode right rotate

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.98445,-0.096336,0.14692,-38.071,-0.081978,-0.99152,-0.10084,445.18,0.15539,0.087225,-0.98399,346.35

> fitmap #17 inMap #8

Fit map cryosparc_P14_J395_003_volume_map_sharp.mrc z flip in map
cryosparc_P7_J710_006_volume_map_sharp.mrc using 6377 points  
correlation = 0.6796, correlation about mean = 0.4352, overlap = 909.3  
steps = 92, shift = 6.71, angle = 11.6 degrees  
  
Position of cryosparc_P14_J395_003_volume_map_sharp.mrc z flip (#17) relative
to cryosparc_P7_J710_006_volume_map_sharp.mrc (#8) coordinates:  
Matrix rotation and translation  
0.99965078 -0.00283677 -0.02627309 -20.41884302  
-0.00432054 -0.99838806 -0.05659173 418.32860816  
-0.02607021 0.05668549 -0.99805165 396.56551922  
Axis 0.99991262 -0.00179092 -0.01309749  
Axis point 0.00000000 203.53018816 204.07754379  
Rotation angle (degrees) 176.75282512  
Shift along axis -26.36026434  
  

> select clear

> hide #!17 models

> show #!17 models

> show #6 models

> hide #6 models

> show #6 models

> hide #6 models

> surface dust #8 size 14.8

> surface dust #17 size 33.8

> volume #17 level 0.2747

> transparency #8.1#17.1 0

> transparency #8.1#17.1 50

> volume #17 level 0.776

> volume #17 level 0.9565

> volume #8 level 0.1548

> volume #17 level 0.2647

> show #!3 models

> hide #!3 models

> show #!7 models

> hide #!7 models

> show #9 models

> show #!7 models

> hide #9 models

> select #7/D

1135 atoms, 1171 bonds, 146 residues, 1 model selected  

> color sel #ff2600ff

> select clear

> select #7/N

605 atoms, 610 bonds, 77 residues, 1 model selected  

> color sel cyan

> select clear

> volume #17 level 0.1444

> volume #17 level 0.3449

> save "/Users/ccrowe/OneDrive - University of Dundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/2023_11_24_chimeraxsession.cxs" includeMaps true

> open 8pc2

Summary of feedback from opening 8pc2 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /C:16  
Atom H1 is not in the residue template for MET /D:1  
Atom H1 is not in the residue template for MET /E:16  
Atom H1 is not in the residue template for MET /F:1  
note | Fetching compressed mmCIF 8pc2 from
http://files.rcsb.org/download/8pc2.cif  
  
8pc2 title:  
SelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC [more info...]  
  
Chain information for 8pc2 #18  
---  
Chain | Description | UniProt  
A B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
C E | Elongin-C | ELOC_HUMAN 17-112  
D F | Elongin-B | ELOB_HUMAN 1-104  
G H | Peptidyl-prolyl cis-trans isomerase FKBP5 | FKBP5_HUMAN 16-140  
  
Non-standard residues in 8pc2 #18  
---  
XZW —
[(1~{R})-3-(3,4-dimethoxyphenyl)-1-[4-[[1-[3-[2-[[[(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-
butanoyl]-4-oxidanyl-
pyrrolidin-2-yl]carbonylamino]methyl]-5-(4-methyl-1,3-thiazol-5-yl)phenoxy]propyl]-1,2,3-triazol-4-yl]methoxy]phenyl]propyl]
(2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate  
  
8pc2 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select add #18

14339 atoms, 14505 bonds, 2 pseudobonds, 934 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #18,0.28252,0.45894,0.84235,-27.049,-0.48448,0.82616,-0.28763,-24.16,-0.82792,-0.32684,0.45576,-41.649

> view matrix models
> #18,-0.79648,0.26486,0.54357,-78.503,-0.3288,0.56473,-0.75695,-20.263,-0.50745,-0.78162,-0.36271,-32.611

> view matrix models
> #18,-0.99423,0.013299,0.10643,-90.565,-0.084286,0.51682,-0.85194,-9.7222,-0.066335,-0.85599,-0.51272,-13.448

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.99423,0.013299,0.10643,135.52,-0.084286,0.51682,-0.85194,117.45,-0.066335,-0.85599,-0.51272,202.3

> view matrix models
> #18,-0.99423,0.013299,0.10643,138.57,-0.084286,0.51682,-0.85194,118.64,-0.066335,-0.85599,-0.51272,204.28

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.99423,0.013299,0.10643,127.01,-0.084286,0.51682,-0.85194,153.95,-0.066335,-0.85599,-0.51272,200.24

> ui mousemode right "rotate selected models"

> view matrix models
> #18,0.28745,0.93692,-0.19889,163.2,0.33926,-0.29379,-0.89364,188.3,-0.8957,0.1894,-0.40231,143.86

> select #18/B

2587 atoms, 2621 bonds, 157 residues, 1 model selected  

> delete sel

> select #18/H

1585 atoms, 1604 bonds, 118 residues, 1 model selected  

> delete sel

> select #18/E

1369 atoms, 1382 bonds, 1 pseudobond, 88 residues, 2 models selected  

> delete sel

> select #18/F

1550 atoms, 1566 bonds, 104 residues, 1 model selected  

> delete sel

> select add #18

7248 atoms, 7332 bonds, 1 pseudobond, 467 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.77662,0.181,0.60341,138.68,-0.45828,0.4949,-0.73828,134.8,-0.43226,-0.84989,-0.3014,190.01

> view matrix models
> #18,-0.80062,0.59389,-0.079453,117.09,0.044137,-0.073789,-0.9963,167.11,-0.59755,-0.80116,0.032864,186.57

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.80062,0.59389,-0.079453,119.76,0.044137,-0.073789,-0.9963,134.26,-0.59755,-0.80116,0.032864,132.67

> delete sel

> open 8pc2

Summary of feedback from opening 8pc2 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /C:16  
Atom H1 is not in the residue template for MET /D:1  
Atom H1 is not in the residue template for MET /E:16  
Atom H1 is not in the residue template for MET /F:1  
  
8pc2 title:  
SelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC [more info...]  
  
Chain information for 8pc2 #18  
---  
Chain | Description | UniProt  
A B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
C E | Elongin-C | ELOC_HUMAN 17-112  
D F | Elongin-B | ELOB_HUMAN 1-104  
G H | Peptidyl-prolyl cis-trans isomerase FKBP5 | FKBP5_HUMAN 16-140  
  
Non-standard residues in 8pc2 #18  
---  
XZW —
[(1~{R})-3-(3,4-dimethoxyphenyl)-1-[4-[[1-[3-[2-[[[(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-
butanoyl]-4-oxidanyl-
pyrrolidin-2-yl]carbonylamino]methyl]-5-(4-methyl-1,3-thiazol-5-yl)phenoxy]propyl]-1,2,3-triazol-4-yl]methoxy]phenyl]propyl]
(2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate  
  
8pc2 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui mousemode right "translate selected models"

> select add #17

2 models selected  

> select subtract #17

Nothing selected  

> select add #18

14339 atoms, 14505 bonds, 2 pseudobonds, 934 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #18,1,0,0,38.073,0,1,0,177.57,0,0,1,134.03

> view matrix models #18,1,0,0,81.788,0,1,0,204.91,0,0,1,132.51

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models #18,1,0,0,212.24,0,1,0,179.99,0,0,1,133.55

> hide sel atoms

> show sel cartoons

> color (#!18 & sel) hot pink

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.13447,-0.72061,0.68017,184.69,-0.91032,-0.18131,-0.37207,152.86,0.39144,-0.66921,-0.63161,135.41

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.13447,-0.72061,0.68017,184.63,-0.91032,-0.18131,-0.37207,153.56,0.39144,-0.66921,-0.63161,135.65

> view matrix models
> #18,-0.13447,-0.72061,0.68017,188.16,-0.91032,-0.18131,-0.37207,135.84,0.39144,-0.66921,-0.63161,96.836

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.18052,-0.71423,0.67623,185.86,-0.56832,-0.48539,-0.66438,151.95,0.80276,-0.50425,-0.31828,118.18

> view matrix models
> #18,-0.0075376,-0.97404,-0.22623,182.92,-0.055407,0.2263,-0.97248,157.5,0.99844,0.0052047,-0.055674,122.59

> view matrix models
> #18,0.013282,0.24818,0.96862,182.61,-0.98845,-0.143,0.050191,138.83,0.15097,-0.9581,0.24341,106.01

> ui tool show Matchmaker

> matchmaker #!18 to #3/V pairing bs

Parameters  
---  
Chain pairing | bs  
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 5n4w, chain V (#3) with 8pc2, chain B (#18), sequence alignment
score = 612.8  
RMSD between 33 pruned atom pairs is 0.971 angstroms; (across all 37 pairs:
1.565)  
  

> show #!4 models

> select subtract #18

Nothing selected  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> select ::name="XZW"

374 atoms, 392 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> hide #!7 models

> hide #!4 models

> select clear

> hide #!17 models

> show #!17 models

> select #18/B

2587 atoms, 2621 bonds, 157 residues, 1 model selected  

> select clear

> select #18/A

2575 atoms, 2613 bonds, 153 residues, 1 model selected  

> delete sel

> select #18/E

1369 atoms, 1382 bonds, 1 pseudobond, 88 residues, 2 models selected  

> delete sel

> select #18/D

1590 atoms, 1606 bonds, 104 residues, 1 model selected  

> select #18/F

1550 atoms, 1566 bonds, 104 residues, 1 model selected  

> delete sel

> select clear

> select #18/G

1724 atoms, 1740 bonds, 123 residues, 1 model selected  

> select clear

> select #18/H

1585 atoms, 1604 bonds, 118 residues, 1 model selected  

> delete sel

> select clear

> open 83wv

Fetching url http://files.rcsb.org/download/83wv.cif failed:  
HTTP Error 404: Not Found  

> open 8ewv

Summary of feedback from opening 8ewv fetched from pdb  
---  
note | Fetching compressed mmCIF 8ewv from
http://files.rcsb.org/download/8ewv.cif  
  
8ewv title:  
DNA-encoded library (DEL)-enabled discovery of proximity inducing small
molecules [more info...]  
  
Chain information for 8ewv #19  
---  
Chain | Description | UniProt  
A E I M Q U | Elongin-B | ELOB_HUMAN 1-118  
B F J N R V | Elongin-C | ELOC_HUMAN 17-112  
C G K O S W | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
D H L P T X | Bromodomain-containing protein 4 | BRD4_HUMAN 44-168  
  
Non-standard residues in 8ewv #19  
---  
X5K —
N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-
L-
valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide  
  
8ewv mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
5| author_defined_assembly  
6| author_defined_assembly  
  

> select add #19

22123 atoms, 22675 bonds, 6 pseudobonds, 2688 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #19,1,0,0,297.32,0,1,0,102.43,0,0,1,267.63

> ui mousemode right translate

> ui tool show Matchmaker

> matchmaker #!19 to #3/V pairing bs

Parameters  
---  
Chain pairing | bs  
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 5n4w, chain V (#3) with 8ewv, chain C (#19), sequence alignment
score = 624.8  
RMSD between 33 pruned atom pairs is 1.042 angstroms; (across all 37 pairs:
1.645)  
  

> matchmaker #!19 to #3/V pairing bs

Parameters  
---  
Chain pairing | bs  
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 5n4w, chain V (#3) with 8ewv, chain C (#19), sequence alignment
score = 624.8  
RMSD between 33 pruned atom pairs is 1.042 angstroms; (across all 37 pairs:
1.645)  
  

> hide sel atoms

> show sel cartoons

> select clear

> select ::name="X5K"

402 atoms, 438 bonds, 6 residues, 1 model selected  

> show sel atoms

> select clear

> select #19/K

1260 atoms, 1297 bonds, 147 residues, 1 model selected  

> delete sel

> select #19/W

1256 atoms, 1293 bonds, 147 residues, 1 model selected  

> delete sel

Drag select of 67 atoms, 537 residues, 1 pseudobonds, 73 bonds  

> delete sel

Drag select of 17 cryosparc_P14_J395_003_volume_map_sharp.mrc z flip , 134
atoms, 817 residues, 1 pseudobonds, 146 bonds  

> select subtract #17

6801 atoms, 146 bonds, 1 pseudobond, 819 residues, 2 models selected  

> delete sel

> select #19/G

353 atoms, 357 bonds, 2 pseudobonds, 41 residues, 2 models selected  

> delete sel

> select #19/C

1256 atoms, 1293 bonds, 147 residues, 1 model selected  

> select clear

> select #19/S

142 atoms, 144 bonds, 16 residues, 1 model selected  

> delete sel

Drag select of 93 residues, 5 pseudobonds  

> delete sel

Drag select of 2 pseudobonds  

> delete sel

> select clear

Drag select of 2 pseudobonds  

> delete sel

> select clear

Drag select of 17 cryosparc_P14_J395_003_volume_map_sharp.mrc z flip , 190
residues, 10 pseudobonds  

> select clear

> select #19/V

43 atoms, 43 bonds, 6 residues, 1 model selected  

> delete sel

> select #19/R

23 atoms, 20 bonds, 2 pseudobonds, 3 residues, 2 models selected  

> delete sel

> select #19/J

698 atoms, 713 bonds, 1 pseudobond, 90 residues, 2 models selected  

> delete sel

> select #19/F

603 atoms, 615 bonds, 2 pseudobonds, 77 residues, 2 models selected  

> delete sel

> select #19/B

706 atoms, 721 bonds, 1 pseudobond, 90 residues, 2 models selected  

> select #18/C

1359 atoms, 1373 bonds, 1 pseudobond, 87 residues, 2 models selected  

> select clear

> select #19/U

372 atoms, 371 bonds, 5 pseudobonds, 47 residues, 2 models selected  

> delete sel

> select #19/I

759 atoms, 774 bonds, 1 pseudobond, 97 residues, 2 models selected  

> delete sel

> select #19/E

545 atoms, 554 bonds, 3 pseudobonds, 68 residues, 2 models selected  

> delete sel

Drag select of 17 cryosparc_P14_J395_003_volume_map_sharp.mrc z flip , 51
residues, 2 pseudobonds  

> select subtract #17

414 atoms, 2 pseudobonds, 51 residues, 2 models selected  

> delete sel

> open 8bds

Summary of feedback from opening 8bds fetched from pdb  
---  
notes | Fetching compressed mmCIF 8bds from
http://files.rcsb.org/download/8bds.cif  
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif  
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif  
Fetching CCD QIY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/QIY/QIY.cif  
  
8bds title:  
Ternary complex between VCB, BRD4-BD1 and PROTAC 48 [more info...]  
  
Chain information for 8bds #20  
---  
Chain | Description | UniProt  
A | Elongin-B | ELOB_HUMAN 1-104  
B | Elongin-C | ELOC_HUMAN 17-112  
C | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
D | Bromodomain-containing protein 4 | BRD4_HUMAN 44-168  
  
Non-standard residues in 8bds #20  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
QIY —
(2~{S},4~{R})-~{N}-[(1~{S})-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-
propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
SO4 — sulfate ion  
  

> select add #20

4274 atoms, 3966 bonds, 1 pseudobond, 876 residues, 2 models selected  

> hide #!18 models

> hide #!19 models

> ui mousemode right "translate selected models"

> view matrix models #20,1,0,0,194.58,0,1,0,158.32,0,0,1,128.98

> view matrix models #20,1,0,0,166.57,0,1,0,215.73,0,0,1,136.45

> ui mousemode right translate

> ui tool show Matchmaker

> matchmaker #!20 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 5t35, chain D (#4) with 8bds, chain C (#20), sequence alignment
score = 822.6  
RMSD between 147 pruned atom pairs is 0.548 angstroms; (across all 147 pairs:
0.548)  
  

> matchmaker #!20 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 5t35, chain D (#4) with 8bds, chain C (#20), sequence alignment
score = 822.6  
RMSD between 147 pruned atom pairs is 0.548 angstroms; (across all 147 pairs:
0.548)  
  

> select clear

> open 7khh

Summary of feedback from opening 7khh fetched from pdb  
---  
note | Fetching compressed mmCIF 7khh from
http://files.rcsb.org/download/7khh.cif  
  
7khh title:  
Ternary complex of VHL/BRD4-BD1/Compound9
(4-(3,5-difluoropyridin-2-yl)-N-(11-(((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)amino)-11-oxoundecyl)-10-methyl-7-((methylsulfonyl)methyl)-11-oxo-3,4,10,11-tetrahydro-1H-1,4,10-triazadibenzo[cd,f]azulene-6-carboxamide)
[more info...]  
  
Chain information for 7khh #21  
---  
Chain | Description | UniProt  
A | Elongin-B | ELOB_HUMAN 1-118  
B | Elongin-C | ELOC_HUMAN 17-112  
C | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 55-213  
D | Bromodomain-containing protein 4 | BRD4_HUMAN 44-168  
  
Non-standard residues in 7khh #21  
---  
CSX — S-oxy cysteine  
WEP —
N-[11-({7-(3,5-difluoropyridin-2-yl)-2-methyl-10-[(methylsulfonyl)methyl]-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[cd,f]azulene-9-carbonyl}amino)undecanoyl]-3-methyl-
L-
valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide  
  

> ui tool show Matchmaker

> matchmaker #!21 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 5t35, chain D (#4) with 7khh, chain C (#21), sequence alignment
score = 801.3  
RMSD between 148 pruned atom pairs is 0.456 angstroms; (across all 148 pairs:
0.456)  
  

> matchmaker #!21 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 5t35, chain D (#4) with 7khh, chain C (#21), sequence alignment
score = 801.3  
RMSD between 148 pruned atom pairs is 0.456 angstroms; (across all 148 pairs:
0.456)  
  

> color #21 #fffb00ff

> save "/Users/ccrowe/OneDrive - University of Dundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/2023_11_24_chimeraxsession_withothersubs.cxs"
> includeMaps true

> open 6sis

Summary of feedback from opening 6sis fetched from pdb  
---  
notes | Fetching compressed mmCIF 6sis from
http://files.rcsb.org/download/6sis.cif  
Fetching CCD LFE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/LFE/LFE.cif  
  
6sis title:  
Crystal structure of macrocyclic PROTAC 1 in complex with the second
bromodomain of human Brd4 and pVHL:ElonginC:ElonginB [more info...]  
  
Chain information for 6sis #22  
---  
Chain | Description | UniProt  
A E | Bromodomain-containing protein 4 | BRD4_HUMAN 333-460  
B F | Elongin-B | ELOB_HUMAN 1-104  
C G | Elongin-C | ELOC_HUMAN 17-112  
D H | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
  
Non-standard residues in 6sis #22  
---  
LFE —
~{N}-[(5~{S},7~{R},11~{S},23~{S})-11-~{tert}-butyl-34-(4-methyl-1,3-thiazol-5-yl)-7-oxidanyl-4,10,13-tris(oxidanylidene)-15,18,21,25,28,31-hexaoxa-3,9,12-triazatricyclo[30.4.0.0^{5,9}]hexatriaconta-1(32),33,35-trien-23-yl]-2-[(7~{S},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanamide  
  
6sis mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #!22 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 5t35, chain D (#4) with 6sis, chain D (#22), sequence alignment
score = 822.6  
RMSD between 149 pruned atom pairs is 0.412 angstroms; (across all 149 pairs:
0.412)  
  

> matchmaker #!22 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 5t35, chain D (#4) with 6sis, chain D (#22), sequence alignment
score = 822.6  
RMSD between 149 pruned atom pairs is 0.412 angstroms; (across all 149 pairs:
0.412)  
  

> select add #22

7369 atoms, 7546 bonds, 2 pseudobonds, 911 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> hide #!20 models

> hide #!21 models

> hide #!17 models

> show #!17 models

> select ::name="SO4"

20 atoms, 16 bonds, 4 residues, 1 model selected  

> select clear

> select ::name="EDO"

24 atoms, 18 bonds, 6 residues, 1 model selected  

> select clear

> select ::name="LFE"

154 atoms, 168 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select #22/E

885 atoms, 908 bonds, 111 residues, 1 model selected  

> delete sel

> select #22/H

1292 atoms, 1331 bonds, 150 residues, 1 model selected  

> delete sel

> select #22/G

689 atoms, 703 bonds, 1 pseudobond, 87 residues, 2 models selected  

> delete sel

> select #22/F

817 atoms, 833 bonds, 104 residues, 1 model selected  

> delete sel

> select clear

> open 7znt

Summary of feedback from opening 7znt fetched from pdb  
---  
notes | Fetching compressed mmCIF 7znt from
http://files.rcsb.org/download/7znt.cif  
Fetching CCD IZR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/IZR/IZR.cif  
  
7znt title:  
Crystal structure of AT7 In complex with the second bromodomain of human BRD4
and PVHL:elonginc:elonginb [more info...]  
  
Chain information for 7znt #23  
---  
Chain | Description | UniProt  
A D | Elongin-B | ELOB_HUMAN 1-104  
B E | Elongin-C | ELOC_HUMAN 17-112  
C F | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
G H | Bromodomain-containing protein 4 | BRD4_HUMAN 333-460  
  
Non-standard residues in 7znt #23  
---  
IZR —
(2~{S},4~{R})-1-[(2~{R})-3-[6-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]hexylsulfanyl]-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-
butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
  
7znt mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #!23 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 5t35, chain D (#4) with 7znt, chain C (#23), sequence alignment
score = 799.2  
RMSD between 148 pruned atom pairs is 0.458 angstroms; (across all 149 pairs:
0.490)  
  

> matchmaker #!23 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 5t35, chain D (#4) with 7znt, chain C (#23), sequence alignment
score = 799.2  
RMSD between 148 pruned atom pairs is 0.458 angstroms; (across all 149 pairs:
0.490)  
  

> select add #23

7333 atoms, 7482 bonds, 4 pseudobonds, 921 residues, 2 models selected  

> hide #!22 models

> hide sel atoms

> show sel cartoons

> select ::name="WEP"

81 atoms, 88 bonds, 1 residue, 1 model selected  

> select ::name="QIY"

71 atoms, 77 bonds, 1 residue, 1 model selected  

> select ::name="IZR"

138 atoms, 152 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select #23/F

1279 atoms, 1309 bonds, 156 residues, 1 model selected  

> delete sel

> select #23/E

691 atoms, 702 bonds, 1 pseudobond, 89 residues, 2 models selected  

> delete sel

> select #23/D

765 atoms, 776 bonds, 1 pseudobond, 99 residues, 2 models selected  

> delete sel

> select #23/H

897 atoms, 919 bonds, 111 residues, 1 model selected  

> select #23/G

890 atoms, 911 bonds, 111 residues, 1 model selected  

> delete sel

> show #!22 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> show #!8 models

> hide #!8 models

> show #!14 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> show #!16 models

> hide #!16 models

> show #!14 models

> hide #!14 models

> hide #!17 models

> show #!17 models

> hide #!23 models

> show #!4 models

> show #!3 models

> open 6ttu

6ttu title:  
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...]  
  
Chain information for 6ttu #24  
---  
Chain | Description | UniProt  
C | Cullin-1 | CUL1_HUMAN 1-776  
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 1-147  
I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY |  
N | NEDD8 | NEDD8_HUMAN 1-76  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108  
S | S-phase kinase-associated protein 1 | SKP1_HUMAN 1-145  
T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN 1-605  
U | Polyubiquitin-C | UBC_HUMAN 1-76  
  
Non-standard residues in 6ttu #24  
---  
ZN — zinc ion  
  

> select add #24

12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #!24 to #3/R pairing bs

Parameters  
---  
Chain pairing | bs  
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 5n4w, chain R (#3) with 6ttu, chain R (#24), sequence alignment
score = 461.5  
RMSD between 49 pruned atom pairs is 1.112 angstroms; (across all 77 pairs:
6.151)  
  

> matchmaker #24/R to #3/R pairing ss

Parameters  
---  
Chain pairing | ss  
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 5n4w, chain R (#3) with 6ttu, chain R (#24), sequence alignment
score = 461.5  
RMSD between 49 pruned atom pairs is 1.112 angstroms; (across all 77 pairs:
6.151)  
  

> matchmaker #24/R to #3/R pairing ss

Parameters  
---  
Chain pairing | ss  
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 5n4w, chain R (#3) with 6ttu, chain R (#24), sequence alignment
score = 461.5  
RMSD between 49 pruned atom pairs is 1.112 angstroms; (across all 77 pairs:
6.151)  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #24,-0.65214,0.60199,-0.46078,247.01,-0.1752,-0.71104,-0.68098,435.72,-0.73758,-0.36336,0.56916,344.36

> view matrix models
> #24,-0.63481,0.76499,0.1087,115.75,0.57213,0.55992,-0.5993,82.934,-0.51932,-0.31825,-0.79311,541.88

> ui mousemode right "translate selected models"

> view matrix models
> #24,-0.63481,0.76499,0.1087,105.88,0.57213,0.55992,-0.5993,94.41,-0.51932,-0.31825,-0.79311,492.62

> view matrix models
> #24,-0.63481,0.76499,0.1087,136.55,0.57213,0.55992,-0.5993,105.61,-0.51932,-0.31825,-0.79311,487.62

> ui mousemode right "translate selected models"

> view matrix models
> #24,-0.63481,0.76499,0.1087,137.76,0.57213,0.55992,-0.5993,97.297,-0.51932,-0.31825,-0.79311,489.09

> ui mousemode right "rotate selected models"

> view matrix models
> #24,-0.63599,0.76676,0.087117,141.49,0.64527,0.59032,-0.48492,59.631,-0.42325,-0.25219,-0.87021,475.58

> ui mousemode right "translate selected models"

> view matrix models
> #24,-0.63599,0.76676,0.087117,140.79,0.64527,0.59032,-0.48492,65.754,-0.42325,-0.25219,-0.87021,476.75

> open 5ait

Summary of feedback from opening 5ait fetched from pdb  
---  
note | Fetching compressed mmCIF 5ait from
http://files.rcsb.org/download/5ait.cif  
  
5ait title:  
A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink) [more
info...]  
  
Chain information for 5ait #25  
---  
Chain | Description | UniProt  
A | E3 UBIQUITIN-PROTEIN LIGASE RNF4 | RNF4_RAT 131-194 196-259  
B E | UBIQUITIN-CONJUGATING ENZYME E2 N | UBE2N_HUMAN 1-152  
C F | POLYUBIQUITIN-C | UBC_BOVIN 1-76  
D G | UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2 | UB2V2_HUMAN 1-145  
  
Non-standard residues in 5ait #25  
---  
ZN — zinc ion  
  

> select subtract #24

Nothing selected  

> hide #!24 models

> ui tool show Matchmaker

> matchmaker #!25 to #3/R pairing bs

Parameters  
---  
Chain pairing | bs  
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 5n4w, chain R (#3) with 5ait, chain A (#25), sequence alignment
score = 82.7  
RMSD between 25 pruned atom pairs is 0.790 angstroms; (across all 72 pairs:
21.329)  
  

> matchmaker #!25 to #3/R pairing bs

Parameters  
---  
Chain pairing | bs  
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 5n4w, chain R (#3) with 5ait, chain A (#25), sequence alignment
score = 82.7  
RMSD between 25 pruned atom pairs is 0.790 angstroms; (across all 72 pairs:
21.329)  
  

> select add #25

6742 atoms, 6875 bonds, 16 pseudobonds, 855 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #25/A to #3/R pairing ss

Parameters  
---  
Chain pairing | ss  
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 5n4w, chain R (#3) with 5ait, chain A (#25), sequence alignment
score = 82.7  
RMSD between 25 pruned atom pairs is 0.790 angstroms; (across all 72 pairs:
21.329)  
  

> matchmaker #25/A to #3/R pairing ss

Parameters  
---  
Chain pairing | ss  
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 5n4w, chain R (#3) with 5ait, chain A (#25), sequence alignment
score = 82.7  
RMSD between 25 pruned atom pairs is 0.790 angstroms; (across all 72 pairs:
21.329)  
  

> select clear

> select #25/E

1173 atoms, 1203 bonds, 147 residues, 1 model selected  

> select clear

> hide #!25 models

> show #!24 models

> select add #24

12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected  

> hide #!17 models

> close #24

> show #!17 models

> show #!7 models

> select #7/R

669 atoms, 685 bonds, 13 pseudobonds, 82 residues, 3 models selected  

> color (#!7 & sel) medium blue

> select clear

> hide #!4 models

> hide #!3 models

> ui tool show Matchmaker

> matchmaker #25/A to #7/R pairing ss

Parameters  
---  
Chain pairing | ss  
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 6ttu, chain R (#7) with 5ait, chain A (#25), sequence alignment
score = 89.3  
RMSD between 31 pruned atom pairs is 0.837 angstroms; (across all 50 pairs:
5.656)  
  

> matchmaker #25/A to #7/R pairing ss

Parameters  
---  
Chain pairing | ss  
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 6ttu, chain R (#7) with 5ait, chain A (#25), sequence alignment
score = 89.3  
RMSD between 31 pruned atom pairs is 0.837 angstroms; (across all 50 pairs:
5.656)  
  

> show #!25 models

> hide #!7 models

> open 6nyo

6nyo title:  
Crystal structure of a human Cdc34-ubiquitin thioester mimetic [more info...]  
  
Chain information for 6nyo #24  
---  
Chain | Description | UniProt  
A | Ubiquitin-conjugating enzyme E2 R2 | UB2R2_HUMAN 1-202  
E | Ubiquitin |  
  
Non-standard residues in 6nyo #24  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
PO4 — phosphate ion  
U94 —
4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic
acid  
  

> ui tool show Matchmaker

> matchmaker #24 to #7/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 6ttu, chain D (#7) with 6nyo, chain A (#24), sequence alignment
score = 333.4  
RMSD between 113 pruned atom pairs is 1.226 angstroms; (across all 146 pairs:
1.958)  
  

> matchmaker #24 to #7/D pairing bs

Parameters  
---  
Chain pairing | bs  
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 6ttu, chain D (#7) with 6nyo, chain A (#24), sequence alignment
score = 333.4  
RMSD between 113 pruned atom pairs is 1.226 angstroms; (across all 146 pairs:
1.958)  
  

> hide #24 models

> hide #!25 models

> hide #!17 models

> open /Users/ccrowe/Downloads/cryosparc_P14_J425_009_volume_map_sharp.mrc

Opened cryosparc_P14_J425_009_volume_map_sharp.mrc as #26, grid size
128,128,128, pixel 3.38, shown at level 0.158, step 1, values float32  

> open /Users/ccrowe/Downloads/cryosparc_P14_J409_009_volume_map_sharp.mrc

Opened cryosparc_P14_J409_009_volume_map_sharp.mrc as #27, grid size
128,128,128, pixel 3.38, shown at level 0.192, step 1, values float32  

> volume #26 level 0.4433

> volume #27 level 0.7354

> surface dust #26 size 33.8

> surface dust #27 size 33.8

> select add #27

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #27,0.92656,0.21156,-0.31103,45.037,0.13982,-0.9613,-0.23738,430.97,-0.34921,0.17646,-0.92028,489.13

> ui mousemode right "translate selected models"

> view matrix models
> #27,0.92656,0.21156,-0.31103,34.762,0.13982,-0.9613,-0.23738,437.75,-0.34921,0.17646,-0.92028,465.65

> select clear

> fitmap #26 inMap #27

Fit map cryosparc_P14_J425_009_volume_map_sharp.mrc in map
cryosparc_P14_J409_009_volume_map_sharp.mrc using 5304 points  
correlation = 0.4684, correlation about mean = 0.1235, overlap = 2971  
steps = 116, shift = 11.3, angle = 18.4 degrees  
  
Position of cryosparc_P14_J425_009_volume_map_sharp.mrc (#26) relative to
cryosparc_P14_J409_009_volume_map_sharp.mrc (#27) coordinates:  
Matrix rotation and translation  
0.99690210 0.01498710 -0.07721130 12.27385432  
0.03774770 -0.95239895 0.30250843 340.77892525  
-0.06900224 -0.30448584 -0.95001424 507.98636675  
Axis -0.99920647 -0.01351339 0.03746748  
Axis point 0.00000000 209.83848448 227.69702793  
Rotation angle (degrees) 162.31773513  
Shift along axis 2.16377737  
  

> select clear

> volume #26 level 0.4652

> volume #27 level 0.9165

> hide #!27 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!17 models

> volume #17 level 0.3048

> hide #!17 models

> show #!8 models

> hide #!8 models

> show #!8 models

> volume #8 level 0.1548

> show #9 models

> hide #9 models

> show #!12 models

> show #!13 models

> hide #!8 models

> hide #!13 models

> show #!13 models

> hide #!12 models

> volume #13.2 level -0.009403

> volume #13.2 level 0.01816

> show #!12 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #!12 models

> show #!13 models

> show #!12 models

> hide #!13 models

> hide #!12 models

> show #!17 models

> show #!26 models

> show #!27 models

> hide #!17 models

> hide #!27 models

> show #!27 models

> hide #!26 models

> show #!26 models

> hide #!27 models

> show #!27 models

> hide #!26 models

> hide #!27 models

> show #!17 models

> hide #!17 models

> show #!27 models

> show #!26 models

> hide #!27 models

> hide #!26 models

> show #!1 models

> show #!7 models

> hide #!7 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> hide #!1 models

> show #!27 models

> show #!26 models

> hide #!27 models

> hide #!26 models

> show #!7 models

> select #7/I

58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected  

> hide #!7 models

> show #!7 models

> select add #7

12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected  

> select subtract #7

Nothing selected  

> hide #!7 models

> show #!17 models

> hide #!17 models

> show #!17 models

> show #!8 models

> transparency #8.1#17.1 0

> volume #8 level 0.1235

> volume #17 level 0.4251

> volume #17 level 0.2948

> hide #!17 models

> show #!18 models

> transparency #8.1 50

> hide #!18 models

> show #!4 models

> show #!18 models

> show #!19 models

> show #!20 models

> show #!21 models

> show #!22 models

> hide #!22 models

> hide #!21 models

> show #!21 models

> show #!22 models

> show #!23 models

> show #24 models

> hide #24 models

> hide #!23 models

> show #!23 models

> hide #!22 models

> show #!22 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> show #!17 models

> hide #!8 models

> show #!8 models

> hide #!17 models

> show #9 models

> show #!3 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #!8 models

> show #!8 models

> volume #8 level 0.1938

> volume #8 level 0.1548

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> volume #8 level 0.186

> show #!3 models

> volume #8 level 0.1157

> show #!25 models

> hide #!25 models

> show #!25 models

> hide #!25 models

> show #24 models

> hide #24 models

> show #!7 models

> hide #!7 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!10 models

> volume #8 level 0.1001

> show #!3 models

> hide #!3 models

> show #!17 models

> hide #!8 models

> show #!8 models

> hide #9 models

> transparency #8.1#17.1 0

> transparency #8.1#17.1 50

> show #!10 models

> hide #!10 models

> show #!7 models

> hide #!7 models

> volume #17 level 0.2246

> hide #!17 models

> show #9 models

> volume #8 level 0.1313

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> show #6 models

> hide #6 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 #!7 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!25 models

> hide #!25 models

> show #!7 models

> show #!25 models

> show #!10 models

> hide #!10 models

> volume #16 level 0.2884

> volume #17 level 0.3248

> hide #!25 models

> hide #!7 models

> show #24 models

> hide #24 models

> show #!10 models

> hide #!10 models

> show #!7 models

> hide #!7 models

> show #!3 models

Unsupported scale factor (0.000000) detected on Display0  

QPainter::begin: Paint device returned engine == 0, type: 3  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,9
      Model Number: Z17K001SWB/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5.2 (22G91)
      Kernel Version: Darwin 22.6.0
      Time since boot: 4 days, 6 hours, 26 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        TH-65EQ2:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 30.00Hz
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
          Television: Yes
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

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