id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10224 ChimeraX bug report submission chimerax-bug-report@… "{{{ 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"" : 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""bfdb4b69bdd095b730f36e0edbc03a9c588672e4"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62c751b6bcb0435c2153fe92"", ""factorPackIds"" : { ""SIRI_UNDERSTANDING_ASR_ASSISTANT"" : ""653702d4f280c152252ea7ba"", ""SIRI_UNDERSTANDING_MORPHUN"" : ""64e514ddc83b9a3d50649ddc"" }, ""deploymentId"" : 240000359 }, { ""rolloutId"" : ""60356660bbe37970735c5624"", ""factorPackIds"" : { }, ""deploymentId"" : 240000027 } ], ""experiments"" : [ ] } } ===== 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 }}} " defect new normal Unassigned