id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15609 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 zhangtia22@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-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 Current thread 0x00000001e0411000 (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"":""2024-07-15 08:14:30.00 +0800"",""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 14.2.1 (23C71)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""8885AD82-1116-450F-BD5F-39EA44D3BBD1""} { ""uptime"" : 1200000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro17,1"", ""coalitionID"" : 1742, ""osVersion"" : { ""train"" : ""macOS 14.2.1"", ""build"" : ""23C71"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-07-15 08:14:15.2765 +0800"", ""codeSigningMonitor"" : 1, ""incident"" : ""8885AD82-1116-450F-BD5F-39EA44D3BBD1"", ""pid"" : 1333, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-07-14 23:30:42.0635 +0800"", ""procStartAbsTime"" : 31039746369346, ""procExitAbsTime"" : 31132906947324, ""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"":""CE645537-3544-5E42-AB3E-5FA35C462179"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""8026ABDA-C978-978E-4C7F-184163BBA1EE"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""wakeTime"" : 25, ""sleepWakeUUID"" : ""1EA78313-3086-4F8A-B5FD-2D0361A57179"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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All rights reserved. > open /Users/zhangtianyi/T/LiuLab/课题/ASXL/质谱送样-zty/PR-DUB-Ub-HDXlow- > blueed.cxs Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.008, step 2, values float32 Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at level 0.008, step 1, values float32 Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown at level 0.00982, step 1, values float32 Log from Wed Jul 10 17:09:03 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > ""/Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/job151_map_and_model-002 > interaction analysis.cxs"" Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.008, step 2, values float32 Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at level 0.008, step 1, values float32 Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown at level 0.00982, step 1, values float32 Log from Sat Jul 1 11:38:15 2023UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:\\\Users\\\Lenovo\\\Desktop\\\20230617_H2AK119Ub-AT2-Ub-PR- > DUB\\\job151 Refine bin1 57.8Ww 3.43A, 3.34A\\\job151_map and model.cxs"" Updating list of available bundles failed: Internal Server Error Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.147, step 2, values float32 Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at level 0.00661, step 1, values float32 Log from Thu Jun 29 10:10:27 2023UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:\\\Users\\\Lenovo\\\Desktop\\\20230617_H2AK119Ub-AT2-Ub-PR- > DUB\\\xuruiming_map and model.cxs"" Opened run_it011_half1_class001.mrc as #1, grid size 128,128,128, pixel 2.2, shown at level 0.0245, step 1, values float32 Opened emdb 34431 as #3, grid size 352,352,352, pixel 1, shown at level 9.44, step 2, values float32 Opened emdb 34432 as #4, grid size 104,112,143, pixel 1.04,1.04,1.04, shown at level 0.0819, step 1, values float32 Opened emdb 35179 as #5, grid size 352,352,352, pixel 1, shown at level 0.271, step 2, values float32 Opened emdb 35180 as #6, grid size 352,352,352, pixel 1, shown at level 0.222, step 2, values float32 Opened emdb 35181 as #7, grid size 352,352,352, pixel 1, shown at level 0.00557, step 2, values float32 Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.14, step 2, values float32 Log from Wed Jun 28 16:03:29 2023UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:\\\Users\\\Lenovo\\\Desktop\\\20230617_H2AK119Ub-AT2-Ub-PR- > DUB\\\job149 Refine bin2\\\run_it011_half1_class001.mrc"" Opened run_it011_half1_class001.mrc as #1, grid size 128,128,128, pixel 2.2, shown at level 0.0284, step 1, values float32 > volume #1 level 0.0258 > volume #1 level 0.02467 > graphics silhouettes true > lighting soft > lighting simple > lighting soft > lighting full > lighting shadows false > set bgColor white > volume #1 level 0.02317 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job139 Refine > bin2 89W/job139_run_class001.mrc"" Opened job139_run_class001.mrc as #2, grid size 128,128,128, pixel 2.2, shown at level 0.0272, step 1, values float32 > ui tool show ""Command Line Interface"" > volume all level 0.034 > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > ui tool show ""Fit in Map"" Fit map run_it011_half1_class001.mrc in map job139_run_class001.mrc using 17425 points correlation = 0.9972, correlation about mean = 0.9785, overlap = 74.41 steps = 80, shift = 0.498, angle = 0.827 degrees Position of run_it011_half1_class001.mrc (#1) relative to job139_run_class001.mrc (#2) coordinates: Matrix rotation and translation 0.99989599 0.01380768 -0.00416533 -1.49573984 -0.01380653 0.99990464 0.00030410 1.81571435 0.00416913 -0.00024656 0.99999128 -0.08487031 Axis -0.01908692 -0.28889124 -0.95717164 Axis point 122.07421022 109.81952662 0.00000000 Rotation angle (degrees) 0.82651459 Shift along axis -0.41475944 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > lighting soft > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > volume #1 level 0.02741 > volume all level 0.03 > volume all level 0.026 > open emdb-34431 'emdb-34431' has no suffix > open emd-34431 'emd-34431' has no suffix > open emdb:34431 Opened emdb 34431 as #3, grid size 352,352,352, pixel 1, shown at level 1.98, step 2, values float32 > open emdb:34432 Summary of feedback from opening 34432 fetched from emdb --- note | Fetching compressed map 34432 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-34432/map/emd_34432.map.gz Opened emdb 34432 as #4, grid size 104,112,143, pixel 1.04,1.04,1.04, shown at level 0.515, step 1, values float32 > open emdb:35179 Summary of feedback from opening 35179 fetched from emdb --- note | Fetching compressed map 35179 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35179/map/emd_35179.map.gz Opened emdb 35179 as #5, grid size 352,352,352, pixel 1, shown at level 0.152, step 2, values float32 > hide #!1 models > show #!2 models > hide #!2 models > volume all level 0.026 > hide #!3 models > volume all level 0.26 > show #!3 models > volume all level 0.26 > volume all level 0.26 > volume #3 level 10.22 > select #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,64.535,0,1,0,-30.598,0,0,1,-35.187 > volume #4 level 0.1143 > view matrix models #4,1,0,0,51.454,0,1,0,57.822,0,0,1,9.7514 > view matrix models #4,1,0,0,42.295,0,1,0,38.932,0,0,1,29.293 Fit map emdb 34432 in map emdb 34431 using 83018 points correlation = 0.4644, correlation about mean = 0.04404, overlap = 1.204e+05 steps = 84, shift = 3.53, angle = 3.55 degrees Position of emdb 34432 (#4) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99890937 0.03123120 -0.03470859 45.72282835 -0.03261495 0.99866550 -0.04004359 48.84191918 0.03341167 0.04113194 0.99859492 21.64673436 Axis 0.65613302 -0.55060868 -0.51606157 Axis point 0.00000000 -386.78737202 1121.73286361 Rotation angle (degrees) 3.54652680 Shift along axis -8.06357459 Fit map emdb 34432 in map emdb 35179 using 83018 points correlation = 0.341, correlation about mean = 0.07392, overlap = 5453 steps = 100, shift = 0.913, angle = 1.96 degrees Position of emdb 34432 (#4) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99895234 0.03147412 -0.03322041 44.67487050 -0.03386640 0.99667610 -0.07409328 53.99915515 0.03077796 0.07514071 0.99669784 17.51778732 Axis 0.85261312 -0.36563957 -0.37330762 Axis point 0.00000000 -256.69518956 798.57926733 Rotation angle (degrees) 5.02070032 Shift along axis 11.80662940 Fit map emdb 34432 in map emdb 35179 using 83018 points correlation = 0.341, correlation about mean = 0.07394, overlap = 5452 steps = 44, shift = 0.0146, angle = 0.0403 degrees Position of emdb 34432 (#4) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99896681 0.03149240 -0.03276494 44.60844069 -0.03386663 0.99663623 -0.07462758 54.07082246 0.03030453 0.07566012 0.99667306 17.50011789 Axis 0.85584426 -0.35916209 -0.37220047 Axis point 0.00000000 -256.57318302 795.03454053 Rotation angle (degrees) 5.03710382 Shift along axis 12.24413623 Fit map emdb 34432 in map emdb 35179 using 83018 points correlation = 0.341, correlation about mean = 0.07394, overlap = 5452 steps = 44, shift = 0.00596, angle = 0.0177 degrees Position of emdb 34432 (#4) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99896062 0.03148124 -0.03296380 44.63846152 -0.03386334 0.99665396 -0.07439188 54.03788776 0.03051155 0.07543082 0.99668412 17.50755650 Axis 0.85444513 -0.36200262 -0.37266288 Axis point 0.00000000 -256.63943020 796.59903642 Rotation angle (degrees) 5.02972229 Shift along axis 12.05484243 Fit map emdb 34432 in map emdb 34431 using 83018 points correlation = 0.4644, correlation about mean = 0.0441, overlap = 1.204e+05 steps = 64, shift = 0.919, angle = 1.97 degrees Position of emdb 34432 (#4) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99892127 0.03122111 -0.03437357 45.68426787 -0.03259126 0.99866604 -0.04004939 48.83024008 0.03307733 0.04112646 0.99860628 21.67062546 Axis 0.65818149 -0.54689834 -0.51739669 Axis point 0.00000000 -390.05511420 1125.06043205 Rotation angle (degrees) 3.53548883 Shift along axis -7.84894767 Fit map emdb 35179 in map emdb 34431 using 14429 points correlation = 0.8366, correlation about mean = 0.5508, overlap = 1.227e+05 steps = 52, shift = 0.454, angle = 0.791 degrees Position of emdb 35179 (#5) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99999272 0.00214134 0.00315901 -0.47875128 -0.00218307 0.99990963 0.01326523 -1.99764456 -0.00313032 -0.01327203 0.99990702 2.89389585 Axis -0.96103935 0.22776623 -0.15660754 Axis point 0.00000000 211.74601648 144.34107449 Rotation angle (degrees) 0.79108162 Shift along axis -0.44810305 > select #5 2 models selected > view matrix models > #5,0.99999,0.0021413,0.003159,1.2511,-0.0021831,0.99991,0.013265,-5.7327,-0.0031303,-0.013272,0.99991,-7.6705 Fit map emdb 35179 in map emdb 34431 using 14429 points correlation = 0.4433, correlation about mean = 0.04557, overlap = 4.107e+04 steps = 112, shift = 1.17, angle = 3.83 degrees Position of emdb 35179 (#5) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99773017 0.06338782 -0.02272660 -4.62359927 -0.06321197 0.99796498 0.00837475 5.72175057 0.02321121 -0.00691915 0.99970664 -12.16494231 Axis -0.11283492 -0.33891882 -0.93402479 Axis point 141.89552302 60.31997900 0.00000000 Rotation angle (degrees) 3.88597703 Shift along axis 9.94485223 > select clear > hide #!3 models > hide #!5 models > volume #4 level 0.03876 > volume #4 level 0.08193 > show #!3 models > hide #!4 models > volume #3 level 4.363 > volume #3 level 8.661 > show #!5 models > hide #!3 models > select #5 2 models selected > view sel > volume #5 level 0.3157 > open emdb:35180 Summary of feedback from opening 35180 fetched from emdb --- note | Fetching compressed map 35180 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35180/map/emd_35180.map.gz Opened emdb 35180 as #6, grid size 352,352,352, pixel 1, shown at level 0.128, step 2, values float32 > volume #6 level 0.2169 Fit map emdb 35180 in map emdb 34431 using 16962 points correlation = 0.8659, correlation about mean = 0.5218, overlap = 1.141e+05 steps = 48, shift = 0.0239, angle = 0.0661 degrees Position of emdb 35180 (#6) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99999971 -0.00075739 -0.00000082 0.13211717 0.00075739 0.99999933 0.00087070 -0.26277045 0.00000016 -0.00087070 0.99999962 0.15962417 Axis -0.75449292 -0.00042428 0.65630805 Axis point 0.00000000 179.28267107 301.92626454 Rotation angle (degrees) 0.06612062 Shift along axis 0.00519265 Fit map emdb 35180 in map emdb 34431 using 16962 points correlation = 0.866, correlation about mean = 0.522, overlap = 1.141e+05 steps = 28, shift = 0.00571, angle = 0.00356 degrees Position of emdb 35180 (#6) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99999972 -0.00074902 -0.00004045 0.13504859 0.00074905 0.99999938 0.00082350 -0.25553678 0.00003983 -0.00082353 0.99999966 0.14874632 Axis -0.73928609 -0.03603432 0.67242666 Axis point 0.00000000 172.82599236 310.02542270 Rotation angle (degrees) 0.06382356 Shift along axis 0.00938954 > select #6 2 models selected > view matrix models > #6,1,-0.00074902,-4.0448e-05,1.5687,0.00074905,1,0.0008235,-5.4821,3.9831e-05,-0.00082353,1,-6.6841 Fit map emdb 35180 in map emdb 34431 using 16962 points correlation = 0.4546, correlation about mean = 0.01254, overlap = 3.337e+04 steps = 136, shift = 2.43, angle = 5.15 degrees Position of emdb 35180 (#6) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99603630 0.07637558 -0.04559006 -2.54488492 -0.07661283 0.99705486 -0.00347703 10.51923386 0.04519023 0.00695603 0.99895418 -17.89003642 Axis 0.05854684 -0.50942829 -0.85851912 Axis point 200.83602946 51.29508390 0.00000000 Rotation angle (degrees) 5.11184277 Shift along axis 9.85114802 > surface dust #6 size 10 > select clear > surface dust #5 size 10 > surface dust #6 size 10 > select clear > volume #6 level 0.1575 > show #!1 models > volume #1 level 0.02912 > hide #!1 models > show #!1 models > hide #!1 models > volume #6 level 0.1971 > select #1 2 models selected > ~select #1 Nothing selected > select #1 2 models selected > show #!1 models > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.3119,-0.84096,-0.44216,361.9,-0.58855,-0.19432,0.78476,149.8,-0.74587,0.505,-0.43434,221.31 > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.3119,-0.84096,-0.44216,371.72,-0.58855,-0.19432,0.78476,164.27,-0.74587,0.505,-0.43434,266.26 > view matrix models > #1,-0.3119,-0.84096,-0.44216,400.86,-0.58855,-0.19432,0.78476,174.21,-0.74587,0.505,-0.43434,259.27 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.432, correlation about mean = -0.04102, overlap = 4048 steps = 176, shift = 7.2, angle = 16.4 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.41318297 -0.66529648 -0.62182025 411.95520538 -0.68732521 -0.22010093 0.69219913 209.11148816 -0.59738086 0.71339762 -0.36633309 204.01510017 Axis 0.54160944 -0.62441265 -0.56282151 Axis point 295.16780503 0.00000000 11.08768828 Rotation angle (degrees) 178.87865551 Shift along axis -22.27712010 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.41318,-0.6653,-0.62182,411.87,-0.68733,-0.2201,0.6922,199.3,-0.59738,0.7134,-0.36633,194.99 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.5482, correlation about mean = 0.08959, overlap = 6083 steps = 208, shift = 15.5, angle = 25.8 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.31694377 -0.32364929 -0.89151432 395.98909173 -0.79495142 -0.42202924 0.43582515 285.38972157 -0.51729961 0.84684263 -0.12352593 141.68444046 Axis 0.56399218 -0.51349195 -0.64671388 Axis point 300.29452266 27.46076670 0.00000000 Rotation angle (degrees) 158.63042959 Shift along axis -14.83986794 > view matrix models > #1,-0.31694,-0.32365,-0.89151,393.73,-0.79495,-0.42203,0.43583,283.47,-0.5173,0.84684,-0.12353,142.06 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.5482, correlation about mean = 0.08953, overlap = 6083 steps = 76, shift = 2.99, angle = 0.0146 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.31679506 -0.32384501 -0.89149610 395.98156900 -0.79492845 -0.42209014 0.43580807 285.40112818 -0.51742598 0.84673746 -0.12371755 141.73337945 Axis 0.56407668 -0.51348051 -0.64664926 Axis point 300.31774210 27.46109397 0.00000000 Rotation angle (degrees) 158.63859217 Shift along axis -14.83573259 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.19243,-0.42355,-0.8852,391.99,-0.42557,-0.7768,0.4642,280.65,-0.88423,0.46604,-0.030769,235.27 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.7122, correlation about mean = 0.235, overlap = 1.022e+04 steps = 112, shift = 1.88, angle = 13.5 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.20178070 -0.29779480 -0.93306099 380.47497501 -0.60749948 -0.70920833 0.35772605 311.11430563 -0.76826359 0.63901627 -0.03780564 194.14708143 Axis 0.62555392 -0.36648861 -0.68874407 Axis point 303.82924212 71.94693846 0.00000000 Rotation angle (degrees) 167.00694694 Shift along axis -9.72988983 > view matrix models > #1,-0.16656,-0.30219,-0.93858,376.9,-0.60955,-0.71665,0.33891,314.94,-0.77505,0.62856,-0.064835,200.15 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.16656,-0.30219,-0.93858,376.2,-0.60955,-0.71665,0.33891,311.95,-0.77505,0.62856,-0.064835,196.38 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.7121, correlation about mean = 0.2346, overlap = 1.022e+04 steps = 64, shift = 5.09, angle = 2.06 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.20176299 -0.29769584 -0.93309640 380.45281193 -0.60751348 -0.70924027 0.35763895 311.14795448 -0.76825717 0.63902694 -0.03775580 194.13599866 Axis 0.62555670 -0.36645589 -0.68875896 Axis point 303.82251702 71.96317881 0.00000000 Rotation angle (degrees) 167.00241071 Shift along axis -9.74010388 > hide #!6 models Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.7121, correlation about mean = 0.2346, overlap = 1.022e+04 steps = 64, shift = 5.09, angle = 2.06 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.20176299 -0.29769584 -0.93309640 380.45281193 -0.60751348 -0.70924027 0.35763895 311.14795448 -0.76825717 0.63902694 -0.03775580 194.13599866 Axis 0.62555670 -0.36645589 -0.68875896 Axis point 303.82251702 71.96317881 0.00000000 Rotation angle (degrees) 167.00241071 Shift along axis -9.74010388 > view matrix models > #1,-0.16656,-0.30219,-0.93858,378.11,-0.60955,-0.71665,0.33891,308.63,-0.77505,0.62856,-0.064835,192.89 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.7121, correlation about mean = 0.2348, overlap = 1.022e+04 steps = 84, shift = 9.91, angle = 2.06 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.20180659 -0.29771230 -0.93308172 380.46420720 -0.60745123 -0.70927184 0.35768208 311.13089585 -0.76829494 0.63898423 -0.03770997 194.14017512 Axis 0.62554266 -0.36644285 -0.68877864 Axis point 303.81627391 71.96638447 0.00000000 Rotation angle (degrees) 167.00614810 Shift along axis -9.73470558 > show #!3 models > hide #!5 models > hide #!3 models > show #!5 models Fit map run_it011_half1_class001.mrc in map emdb 35179 using 20495 points correlation = 0.5641, correlation about mean = 0.3443, overlap = 396.5 steps = 124, shift = 10.3, angle = 4.26 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation -0.19831167 -0.30563080 -0.93126919 380.58367178 -0.59680949 -0.71603997 0.36208451 310.04870405 -0.77749014 0.62759587 -0.04040428 197.62893854 Axis 0.62768588 -0.36354354 -0.68836511 Axis point 304.20513642 72.78850850 0.00000000 Rotation angle (degrees) 167.78971868 Shift along axis -9.87007366 > transparency #1.1 60 > close #2 > show #!3 models Fit map emdb 34431 in map emdb 35179 using 12029 points correlation = 0.3497, correlation about mean = 0.01267, overlap = 3.078e+04 steps = 96, shift = 0.776, angle = 1.66 degrees Position of emdb 34431 (#3) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99625963 -0.06990513 0.05079393 1.50664356 0.07004571 0.99754329 -0.00099064 -7.95886029 -0.05059989 0.00454483 0.99870866 17.42013605 Axis 0.03201378 0.58639926 0.80938929 Axis point 193.23518824 6.87152612 0.00000000 Rotation angle (degrees) 4.95967493 Shift along axis 9.48083508 > select #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.99959,-0.0066177,0.027919,-4.062,0.0065039,0.99997,0.0041645,-7.2656,-0.027945,-0.0039812,0.9996,0.47012 Fit map emdb 34431 in map emdb 35179 using 12029 points correlation = 0.7124, correlation about mean = 0.1294, overlap = 1.149e+05 steps = 112, shift = 4.05, angle = 5 degrees Position of emdb 34431 (#3) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99999218 -0.00227110 -0.00323698 0.51422483 0.00222815 0.99991028 -0.01320851 2.01866916 0.00326669 0.01320119 0.99990752 -2.86268567 Axis 0.95797217 -0.23591082 0.16320358 Axis point 0.00000000 212.28134970 143.33731474 Rotation angle (degrees) 0.78979960 Shift along axis -0.45081335 > hide #!3 models > show #!4 models Fit map emdb 34432 in map emdb 35179 using 99027 points correlation = 0.7726, correlation about mean = 0.5611, overlap = 2.08e+04 steps = 52, shift = 0.211, angle = 1.42 degrees Position of emdb 34432 (#4) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99852213 -0.05371313 -0.00827333 51.26289725 0.05334807 0.99779961 -0.03936905 41.61501505 0.01036976 0.03886950 0.99919049 34.37988091 Axis 0.58427765 -0.13922477 0.79952242 Axis point -897.63552058 417.29504737 0.00000000 Rotation angle (degrees) 3.83900892 Shift along axis 51.64540936 > hide #!4 models > show #!4 models > hide #!4 models Fit map emdb 35180 in map emdb 35179 using 19722 points correlation = 0.9292, correlation about mean = 0.8881, overlap = 5539 steps = 64, shift = 0.721, angle = 1.42 degrees Position of emdb 35180 (#6) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99999156 -0.00263646 -0.00315049 0.55269862 0.00259706 0.99991921 -0.01244286 1.82961033 0.00318304 0.01243457 0.99991762 -2.72705004 Axis 0.94955487 -0.24174675 0.19975998 Axis point 0.00000000 212.79164492 136.67877369 Rotation angle (degrees) 0.75056863 Shift along axis -0.46224015 > show #!6 models > hide #!6 models > show #!3 models > hide #!5 models > open 7XD1 7xd1 title: cryo-EM structure of unmodified nucleosome [more info...] Chain information for #2 --- Chain | Description A E | Histone H3 B F | Histone H4 C G | Histone H2A type 1-B/E D H | Histone H2B type 1-K I | DNA (147-mer) J | DNA (147-mer) > select #2 12048 atoms, 12861 bonds, 367 pseudobonds, 1054 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,39.425,0,1,0,35.345,0,0,1,9.204 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.28926,0.44394,-0.84808,200.55,-0.58378,-0.62032,-0.52383,407.67,-0.75864,0.64662,0.079727,160.31 > view matrix models > #2,0.048879,0.13582,-0.98953,295.06,-0.74597,-0.65384,-0.12659,376.27,-0.66419,0.74434,0.06936,135.91 > close #2 > open 8h1t 8h1t title: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome [more info...] Chain information for #2 --- Chain | Description A E | Histone H3.1 B F | Histone H4 C G | Histone H2A type 1-D D H | Histone H2B type 2-E I | DNA (187-mer) J | DNA (187-mer) K | Histone H1.4 L | Ubiquitin carboxyl-terminal hydrolase BAP1 M | Ubiquitin N | Polycomb group protein ASXL1 Fit molecule 8h1t (#2) to map emdb 35179 (#5) using 17365 atoms average map value = 0.1604, steps = 128 shifted from previous position = 2.03 rotated from previous position = 2 degrees atoms outside contour = 14706, contour level = 0.31574 Position of 8h1t (#2) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99939008 -0.02855745 0.02009832 1.18268568 0.02874245 0.99954654 -0.00897655 0.21120242 -0.01983286 0.00954875 0.99975771 11.97689886 Axis 0.25638336 0.55263300 0.79300967 Axis point 182.52799773 -51.52365080 0.00000000 Rotation angle (degrees) 2.07043952 Shift along axis 9.91773502 Fit molecule 8h1t (#2) to map emdb 35179 (#5) using 17365 atoms average map value = 0.1604, steps = 44 shifted from previous position = 0.00155 rotated from previous position = 0.00382 degrees atoms outside contour = 14707, contour level = 0.31574 Position of 8h1t (#2) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99939193 -0.02850881 0.02007543 1.17883432 0.02869282 0.99954831 -0.00893804 0.21332593 -0.01981155 0.00950863 0.99975852 11.98113743 Axis 0.25572879 0.55295861 0.79299405 Axis point 182.93641222 -51.53965694 0.00000000 Rotation angle (degrees) 2.06692781 Shift along axis 9.92039298 Fit molecule 8h1t (#2) to map run_it011_half1_class001.mrc (#1) using 17365 atoms average map value = 0.05027, steps = 96 shifted from previous position = 10.7 rotated from previous position = 2.21 degrees atoms outside contour = 4557, contour level = 0.02912 Position of 8h1t (#2) relative to run_it011_half1_class001.mrc (#1) coordinates: Matrix rotation and translation -0.20207793 -0.60739316 -0.76826952 415.09666474 -0.30219656 -0.70750415 0.63883888 210.30924230 -0.93158024 0.36126365 -0.04058115 250.74357678 Axis -0.62560219 0.36807154 0.68785553 Axis point 304.10787251 71.45893239 0.00000000 Rotation angle (degrees) 167.18249364 Shift along axis -9.80117958 > select clear > hide atoms > show cartoons > select clear > hide #!1 models > select #5 2 models selected > volume #5 level 0.2711 > hide #!5 models > show #!6 models > volume #6 level 0.3258 > select clear > transparency #6.1 50 > show #!5 models > hide #!5 models > volume #6 level 0.2664 > volume #6 level 0.2218 > transparency #5.1 50 > select clear > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting soft > lighting simple > lighting shadows true > lighting soft > lighting full > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > volume #1 level 0.03573 > transparency #4.1 50 > volume #3 level 5.925 > volume #3 level 9.442 > open emdb:35181 Summary of feedback from opening 35181 fetched from emdb --- note | Fetching compressed map 35181 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35181/map/emd_35181.map.gz Opened emdb 35181 as #7, grid size 352,352,352, pixel 1, shown at level 6.52e-06, step 2, values float32 > volume #7 level 0.007306 Fit map emdb 35181 in map run_it011_half1_class001.mrc using 4083 points correlation = 0.9093, correlation about mean = 0.3586, overlap = 2.248 steps = 68, shift = 10, angle = 3.45 degrees Position of emdb 35181 (#7) relative to run_it011_half1_class001.mrc (#1) coordinates: Matrix rotation and translation -0.23841936 -0.54780454 -0.80191420 417.02093533 -0.34619902 -0.72353752 0.59719318 227.06691731 -0.90736015 0.42000433 -0.01714404 231.26374693 Axis -0.61444130 0.36565700 0.69911147 Axis point 298.15032473 74.30215138 0.00000000 Rotation angle (degrees) 171.70979887 Shift along axis -11.52713835 Fit map emdb 35181 in map emdb 35180 using 4083 points correlation = 0.9073, correlation about mean = 0.5724, overlap = 17.33 steps = 84, shift = 1.3, angle = 1.74 degrees Position of emdb 35181 (#7) relative to emdb 35180 (#6) coordinates: Matrix rotation and translation 0.99718736 -0.07337531 0.01527862 10.74241755 0.07273164 0.99658427 0.03911391 -18.50292298 -0.01809643 -0.03789266 0.99911794 8.76555365 Axis -0.45702121 0.19807540 0.86712038 Axis point 257.87475932 130.45408627 0.00000000 Rotation angle (degrees) 4.83280414 Shift along axis -0.97369621 Fit map emdb 35181 in map emdb 34431 using 4083 points correlation = 0.9745, correlation about mean = 0.8424, overlap = 1313 steps = 48, shift = 0.157, angle = 0.0606 degrees Position of emdb 35181 (#7) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99715241 -0.07391523 0.01495331 10.95867242 0.07325251 0.99647639 0.04085177 -18.86344708 -0.01792019 -0.03964007 0.99905332 9.17345895 Axis -0.47089821 0.19231851 0.86096949 Axis point 261.54982201 132.51289479 0.00000000 Rotation angle (degrees) 4.90283886 Shift along axis -0.89014094 > surface dust #7 size 10 > volume #7 level 0.005574 > transparency #7.1 50 > volume #!7 style mesh > volume #!7 style surface > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting full > lighting shadows false > open emdb:35182 Summary of feedback from opening 35182 fetched from emdb --- note | Fetching compressed map 35182 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35182/map/emd_35182.map.gz Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.0644, step 2, values float32 > volume #8 level 0.1449 Fit map emdb 35182 in map emdb 34431 using 24046 points correlation = 0.4763, correlation about mean = -0.0003831, overlap = 3.117e+04 steps = 76, shift = 1.36, angle = 2.22 degrees Position of emdb 35182 (#8) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99572611 -0.06863698 0.06179381 1.64201538 0.06920377 0.99757745 -0.00707662 -6.61213603 -0.06115839 0.01132274 0.99806385 18.46918095 Axis 0.09912224 0.66237632 0.74258494 Axis point 186.40569216 -1.40044242 0.00000000 Rotation angle (degrees) 5.32536780 Shift along axis 9.49797358 Fit map emdb 35182 in map emdb 35180 using 24046 points correlation = 0.522, correlation about mean = 0.0978, overlap = 1120 steps = 56, shift = 1.14, angle = 1.27 degrees Position of emdb 35182 (#8) relative to emdb 35180 (#6) coordinates: Matrix rotation and translation 0.99619357 -0.07481814 0.04472832 4.53077775 0.07465857 0.99719544 0.00522997 -9.78343870 -0.04499417 -0.00187071 0.99898550 17.63317633 Axis -0.04069583 0.51422317 0.85669037 Axis point 201.26003236 55.69790579 0.00000000 Rotation angle (degrees) 5.00489231 Shift along axis 9.89091767 Fit map emdb 35182 in map emdb 35181 using 24046 points correlation = 0.3573, correlation about mean = -0.056, overlap = 16.2 steps = 316, shift = 9.92, angle = 4.98 degrees Position of emdb 35182 (#8) relative to emdb 35181 (#7) coordinates: Matrix rotation and translation 0.99721407 0.07252112 -0.01745822 -9.22927511 -0.07313472 0.99661547 -0.03753556 19.45060867 0.01467701 0.03870779 0.99914278 -8.01226063 Axis 0.45514287 -0.19183472 -0.86950814 Axis point 257.35740018 131.09208266 0.00000000 Rotation angle (degrees) 4.80458616 Shift along axis -0.96521509 > hide #!7 models > transparency #8.1 50 > volume #8 level 0.1159 > surface dust #8 size 10 > volume #8 level 0.1405 > volume #1 level 0.03184 > volume #1 level 0.02057 > volume #1 level 0.02523 > volume #1 level 0.02484 > lighting flat > lighting full > lighting simple > volume #1 level 0.02445 > show #!8 models > hide #!1 models > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/xuruiming_map > and model.cxs"" includeMaps true ——— End of log from Wed Jun 28 16:03:29 2023 ——— opened ChimeraX session > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job149 Refine > bin2/job149_run_class001_4.46A.mrc"" Opened job149_run_class001_4.46A.mrc as #9, grid size 128,128,128, pixel 2.2, shown at level 0.0276, step 1, values float32 > select #9 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #9,1,0,0,45.835,0,1,0,26.249,0,0,1,37.401 > ui mousemode right ""rotate selected models"" > view matrix models > #9,-0.17169,-0.11728,-0.97815,354.61,-0.71105,-0.67246,0.20544,337.48,-0.68186,0.73078,0.032062,155.29 > ui tool show ""Fit in Map"" Fit map job149_run_class001_4.46A.mrc in map run_it011_half1_class001.mrc using 20966 points correlation = 0.9966, correlation about mean = 0.9805, overlap = 82.65 steps = 100, shift = 6.36, angle = 16.2 degrees Position of job149_run_class001_4.46A.mrc (#9) relative to run_it011_half1_class001.mrc (#1) coordinates: Matrix rotation and translation 0.99999989 0.00020928 0.00041884 -0.06994052 -0.00020930 0.99999998 0.00004826 0.03452944 -0.00041883 -0.00004834 0.99999991 0.09029170 Axis -0.10261362 0.88981477 -0.44463481 Axis point 213.16237377 0.00000000 167.59255835 Rotation angle (degrees) 0.02696899 Shift along axis -0.00224518 Fit map job149_run_class001_4.46A.mrc in map emdb 35182 using 20966 points correlation = 0.9308, correlation about mean = 0.7175, overlap = 355.2 steps = 48, shift = 0.147, angle = 0.181 degrees Position of job149_run_class001_4.46A.mrc (#9) relative to emdb 35182 (#8) coordinates: Matrix rotation and translation -0.20298928 -0.30337753 -0.93099808 381.28750314 -0.60618210 -0.70775669 0.36279983 309.94973019 -0.76898544 0.63799885 -0.04023501 194.86601834 Axis 0.62533410 -0.36814095 -0.68806214 Axis point 303.99138854 71.48857777 0.00000000 Rotation angle (degrees) 167.28852422 Shift along axis -9.75304006 > hide #!8 models > transparency sel 50 > select clear > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job149 Refine > bin2/job149_map and model.cxs"" includeMaps true > select /L 2433 atoms, 2487 bonds, 2 pseudobonds, 301 residues, 2 models selected Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 2433 atoms average map value = 0.03568, steps = 64 shifted from previous position = 2.35 rotated from previous position = 1.97 degrees atoms outside contour = 748, contour level = 0.027568 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.20794411 -0.61149238 -0.76343717 414.87568309 -0.26697774 -0.71538055 0.64571942 203.42240837 -0.94100060 0.33809428 -0.01449568 250.07835222 Axis -0.62168400 0.35884046 0.69623453 Axis point 300.38077372 74.09859277 0.00000000 Rotation angle (degrees) 165.67553333 Shift along axis -10.81220027 > volume #9 level 0.03066 Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 2433 atoms average map value = 0.03568, steps = 64 shifted from previous position = 2.35 rotated from previous position = 1.97 degrees atoms outside contour = 943, contour level = 0.03066 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.20794411 -0.61149238 -0.76343717 414.87568309 -0.26697774 -0.71538055 0.64571942 203.42240837 -0.94100060 0.33809428 -0.01449568 250.07835222 Axis -0.62168400 0.35884046 0.69623453 Axis point 300.38077372 74.09859277 0.00000000 Rotation angle (degrees) 165.67553333 Shift along axis -10.81220027 Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 2433 atoms average map value = 0.03568, steps = 64 shifted from previous position = 2.35 rotated from previous position = 1.97 degrees atoms outside contour = 943, contour level = 0.03066 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.20794411 -0.61149238 -0.76343717 414.87568309 -0.26697774 -0.71538055 0.64571942 203.42240837 -0.94100060 0.33809428 -0.01449568 250.07835222 Axis -0.62168400 0.35884046 0.69623453 Axis point 300.38077372 74.09859277 0.00000000 Rotation angle (degrees) 165.67553333 Shift along axis -10.81220027 > select /N 903 atoms, 922 bonds, 109 residues, 1 model selected Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 903 atoms average map value = 0.03434, steps = 52 shifted from previous position = 0.869 rotated from previous position = 4.69 degrees atoms outside contour = 365, contour level = 0.03066 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.24163876 -0.58278597 -0.77586805 418.23265163 -0.33389716 -0.70080060 0.63038973 216.87762884 -0.91111108 0.41138673 -0.02524999 233.48173602 Axis -0.61165760 0.37772280 0.69512623 Axis point 297.47750506 71.69030385 0.00000000 Rotation angle (degrees) 169.68707388 Shift along axis -11.59627505 Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 903 atoms average map value = 0.03434, steps = 52 shifted from previous position = 0.869 rotated from previous position = 4.69 degrees atoms outside contour = 365, contour level = 0.03066 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.24163876 -0.58278597 -0.77586805 418.23265163 -0.33389716 -0.70080060 0.63038973 216.87762884 -0.91111108 0.41138673 -0.02524999 233.48173602 Axis -0.61165760 0.37772280 0.69512623 Axis point 297.47750506 71.69030385 0.00000000 Rotation angle (degrees) 169.68707388 Shift along axis -11.59627505 > volume #9 level 0.02315 Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 17365 atoms average map value = 0.05218, steps = 68 shifted from previous position = 2.31 rotated from previous position = 3.26 degrees atoms outside contour = 3341, contour level = 0.02315 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.20213510 -0.60700163 -0.76856388 415.10301458 -0.30219766 -0.70781072 0.63849867 210.40308740 -0.93156748 0.36132120 -0.04036108 250.71966046 Axis -0.62559675 0.36790337 0.68795045 Axis point 304.10399410 71.49954857 0.00000000 Rotation angle (degrees) 167.20105962 Shift along axis -9.79638843 > ui tool show ""Command Line Interface"" > open 1ubq 1ubq title: Structure of ubiquitin refined At 1.8 angstroms resolution [more info...] Chain information for #10 --- Chain | Description A | ubiquitin > select #10 660 atoms, 608 bonds, 134 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #10,1,0,0,174.52,0,1,0,181.95,0,0,1,110.84 > view matrix models #10,1,0,0,185.05,0,1,0,89.206,0,0,1,127.17 > view matrix models #10,1,0,0,196.16,0,1,0,101.46,0,0,1,174.23 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.82351,-0.0038313,-0.56729,261.61,-0.56355,-0.10936,0.81881,138.19,-0.065176,0.99399,0.087899,161.77 > view matrix models > #10,-0.76264,0.12736,0.63416,234.39,0.63668,-0.025136,0.77072,100.07,0.1141,0.99154,-0.061916,159.07 Fit molecule 1ubq (#10) to map job149_run_class001_4.46A.mrc (#9) using 660 atoms average map value = 0.03339, steps = 116 shifted from previous position = 15.3 rotated from previous position = 43.1 degrees atoms outside contour = 193, contour level = 0.02315 Position of 1ubq (#10) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation 0.36567514 -0.66574960 -0.65042998 142.72529105 -0.35843437 0.54420056 -0.75853184 170.72600300 0.85895663 0.51051270 -0.03962692 52.18360007 Axis 0.63586180 -0.75628653 0.15398200 Axis point 107.91005288 0.00000000 143.84367550 Rotation angle (degrees) 93.71971072 Shift along axis -30.32888044 > volume #9 level 0.03331 > view matrix models > #10,-0.89195,0.43544,-0.12175,242.23,0.020557,0.30806,0.95115,105.27,0.45167,0.84587,-0.28372,157.27 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.89195,0.43544,-0.12175,242.21,0.020557,0.30806,0.95115,109.67,0.45167,0.84587,-0.28372,155.88 Fit molecule 1ubq (#10) to map job149_run_class001_4.46A.mrc (#9) using 660 atoms average map value = 0.03427, steps = 92 shifted from previous position = 3.06 rotated from previous position = 39.7 degrees atoms outside contour = 288, contour level = 0.033311 Position of 1ubq (#10) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.13258148 -0.93511642 0.32860222 157.62955614 0.68580230 -0.32590484 -0.65073900 166.84812706 0.71560978 0.13908022 0.68451394 49.29275993 Axis 0.42827873 -0.20985448 0.87894165 Axis point -2.31223012 136.64161231 0.00000000 Rotation angle (degrees) 112.76710095 Shift along axis 75.82101791 > select clear > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job149 Refine > bin2/job149_map and model.cxs"" includeMaps true > close #1,3-7 > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job149 Refine > bin2/job149_map and model.cxs"" includeMaps true > volume #9 level 0.02475 > volume #8 level 0.1448 > volume #8 level 0.09928 > volume #8 level 0.1708 > volume #8 level 0.147 > select ::name=""CYS"" 48 atoms, 40 bonds, 8 residues, 1 model selected > select clear > volume #9 level 0.02989 > volume #9 level 0.02175 > volume #9 level 0.05772 > volume #9 level 0.04402 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job151 Refine > bin1 57.8Ww 3.43W/run_class001.mrc"" Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at level 0.00696, step 1, values float32 > select #1 2 models selected > view matrix models #1,1,0,0,8.7638,0,1,0,1.6233,0,0,1,22.107 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.03523,-0.50961,-0.85969,339.24,-0.659,-0.63485,0.40334,273.55,-0.75132,0.58074,-0.31347,217.31 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.03523,-0.50961,-0.85969,368.01,-0.659,-0.63485,0.40334,264.77,-0.75132,0.58074,-0.31347,230.22 > view matrix models > #1,-0.03523,-0.50961,-0.85969,378.65,-0.659,-0.63485,0.40334,299.13,-0.75132,0.58074,-0.31347,237.58 > view matrix models > #1,-0.03523,-0.50961,-0.85969,381.77,-0.659,-0.63485,0.40334,297.49,-0.75132,0.58074,-0.31347,234.6 Fit map run_class001.mrc in map job149_run_class001_4.46A.mrc using 167671 points correlation = 0.9884, correlation about mean = 0.937, overlap = 162.2 steps = 100, shift = 5.97, angle = 15.1 degrees Position of run_class001.mrc (#1) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation 0.99989284 -0.01348029 -0.00570862 2.81034906 0.01349390 0.99990619 0.00235266 -2.30743279 0.00567637 -0.00242944 0.99998094 -0.93663428 Axis -0.16119593 -0.38376750 0.90925155 Axis point 184.32278969 202.00113952 0.00000000 Rotation angle (degrees) 0.84991014 Shift along axis -0.41913528 > hide #!9 models > transparency sel 50 > select clear > close #9 > show #!8 models > hide #!1 models > show #!1 models Fit map run_class001.mrc in map emdb 35182 using 167671 points correlation = 0.9392, correlation about mean = 0.7508, overlap = 746.6 steps = 48, shift = 0.0393, angle = 0.0285 degrees Position of run_class001.mrc (#1) relative to emdb 35182 (#8) coordinates: Matrix rotation and translation -0.21231165 -0.29847789 -0.93050240 382.32214675 -0.61322651 -0.70068711 0.36467906 309.49276413 -0.76083967 0.64803436 -0.03427052 191.37941737 Axis 0.62108509 -0.37188290 -0.68989595 Axis point 302.93039272 70.63664063 0.00000000 Rotation angle (degrees) 166.81399207 Shift along axis -9.67236664 Fit map run_class001.mrc in map emdb 35182 using 167671 points correlation = 0.9392, correlation about mean = 0.7507, overlap = 746.6 steps = 48, shift = 0.0228, angle = 0.0172 degrees Position of run_class001.mrc (#1) relative to emdb 35182 (#8) coordinates: Matrix rotation and translation -0.21221175 -0.29829448 -0.93058400 382.27801023 -0.61342455 -0.70062361 0.36446795 309.55502898 -0.76070789 0.64818745 -0.03430060 191.33446074 Axis 0.62110914 -0.37188703 -0.68987207 Axis point 302.93309814 70.63807057 -0.00000000 Rotation angle (degrees) 166.79725799 Shift along axis -9.67943583 Fit molecule 8h1t (#2) to map emdb 35182 (#8) using 17365 atoms average map value = 0.3408, steps = 44 shifted from previous position = 0.057 rotated from previous position = 0.047 degrees atoms outside contour = 2653, contour level = 0.14697 Position of 8h1t (#2) relative to emdb 35182 (#8) coordinates: Matrix rotation and translation 0.99999864 0.00149315 0.00069727 -0.37820928 -0.00149268 0.99999866 -0.00066961 0.35972914 -0.00069827 0.00066857 0.99999953 0.00332282 Axis 0.37619080 0.39231738 -0.83938522 Axis point 241.80430793 252.52367144 0.00000000 Rotation angle (degrees) 0.10190529 Shift along axis -0.00393999 Fit molecule 1ubq (#10) to map run_class001.mrc (#1) using 660 atoms average map value = 0.009062, steps = 80 shifted from previous position = 0.291 rotated from previous position = 1.61 degrees atoms outside contour = 209, contour level = 0.0069642 Position of 1ubq (#10) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.11608350 -0.94174178 0.31566918 157.53510623 0.70546341 -0.30189800 -0.64123237 165.89216253 0.69917521 0.14825657 0.69940975 49.66349923 Axis 0.42298845 -0.20547295 0.88253138 Axis point -3.76561599 137.43736452 0.00000000 Rotation angle (degrees) 111.05634547 Shift along axis 76.37877478 > hide #!1 models > show #!1 models > volume #1 level 0.009643 > volume #1 level 0.01034 > hide #!8 models > volume #1 level 0.008478 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.01526, steps = 40 shifted from previous position = 0.0317 rotated from previous position = 0.0681 degrees atoms outside contour = 4776, contour level = 0.0084782 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.21145685 -0.61351649 -0.76084396 416.48603296 -0.29827318 -0.70080529 0.64800081 206.94115048 -0.93076265 0.36396356 -0.03480543 249.69291717 Axis -0.62140839 0.37174315 0.68968010 Axis point 303.05533602 70.63883455 0.00000000 Rotation angle (degrees) 166.78868456 Shift along axis -9.67072658 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.01526, steps = 44 shifted from previous position = 0.0124 rotated from previous position = 0.0115 degrees atoms outside contour = 4773, contour level = 0.0084782 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.21143857 -0.61367434 -0.76072173 416.48544831 -0.29822791 -0.70069461 0.64814132 206.89677658 -0.93078131 0.36391053 -0.03486095 249.70691032 Axis -0.62140666 0.37179700 0.68965263 Axis point 303.05602496 70.62591450 -0.00000000 Rotation angle (degrees) 166.77948178 Shift along axis -9.67220051 > select #2/L 2433 atoms, 2487 bonds, 2 pseudobonds, 301 residues, 2 models selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 2433 atoms average map value = 0.009533, steps = 68 shifted from previous position = 2.2 rotated from previous position = 2.15 degrees atoms outside contour = 1032, contour level = 0.0084782 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.21986908 -0.61430897 -0.75781401 416.58755140 -0.26308600 -0.71070142 0.65244865 200.88172401 -0.93938455 0.34282355 -0.00535482 247.90702448 Axis -0.61655174 0.36155864 0.69938494 Axis point 298.88551366 73.75135875 0.00000000 Rotation angle (degrees) 165.45773086 Shift along axis -10.83481508 > select clear > select #2/N 903 atoms, 922 bonds, 109 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 903 atoms average map value = 0.009329, steps = 68 shifted from previous position = 0.812 rotated from previous position = 3.38 degrees atoms outside contour = 389, contour level = 0.0084782 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.24506651 -0.59430236 -0.76599420 419.01621102 -0.31120687 -0.70005479 0.64270799 210.42817241 -0.91820078 0.39588887 -0.01339100 236.25229875 Axis -0.60905023 0.37558458 0.69856570 Axis point 296.77188620 71.91015579 0.00000000 Rotation angle (degrees) 168.30942308 Shift along axis -11.13059129 > select clear > volume #1 level 0.002306 > volume #1 level 0.008245 > volume #1 level 0.006848 > volume #1 level 0.007081 > volume #1 level 0.007896 > volume #1 level 0.006615 > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job151 Refine > bin1 57.8Ww 3.43W/job151_map and model.cxs"" includeMaps true ——— End of log from Thu Jun 29 10:10:27 2023 ——— opened ChimeraX session > select #2/K 520 atoms, 523 bonds, 73 residues, 1 model selected > hide sel cartoons > select clear > lighting soft > lighting simple > select #1 2 models selected > transparency #1.1 40 > select clear > volume #1 level 0.007896 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class006.mrc"" Opened run_it021_class006.mrc as #3, grid size 256,256,256, pixel 1.1, shown at level 4.31e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class001.mrc"" Opened run_it021_class001.mrc as #4, grid size 256,256,256, pixel 1.1, shown at level 4.04e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class002.mrc"" Opened run_it021_class002.mrc as #5, grid size 256,256,256, pixel 1.1, shown at level 4.76e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class003.mrc"" Opened run_it021_class003.mrc as #6, grid size 256,256,256, pixel 1.1, shown at level 2.76e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class004.mrc"" Opened run_it021_class004.mrc as #7, grid size 256,256,256, pixel 1.1, shown at level 1.85e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class005.mrc"" Opened run_it021_class005.mrc as #9, grid size 256,256,256, pixel 1.1, shown at level 2.1e-06, step 1, values float32 > ui tool show ""Command Line Interface"" > volume all level 0.008 > close #3-7,9 > volume #1 level 0.01027 > volume #1 level 0.009071 > select #2/L 2433 atoms, 2487 bonds, 2 pseudobonds, 301 residues, 2 models selected > ui tool show ""Fit in Map"" Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 2433 atoms average map value = 0.009533, steps = 72 shifted from previous position = 1.32 rotated from previous position = 3.38 degrees atoms outside contour = 1167, contour level = 0.0090706 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.22006435 -0.61436338 -0.75771322 416.60394012 -0.26306176 -0.71060204 0.65256666 200.84393052 -0.93934562 0.34293203 -0.00523734 247.86391439 Axis -0.61646851 0.36162188 0.69942562 Axis point 298.85499338 73.74213259 0.00000000 Rotation angle (degrees) 165.45526674 Shift along axis -10.83127884 > select clear > select #2/L:126 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #10/A:11 15 atoms, 13 bonds, 2 residues, 2 models selected > select add #2/L:118 26 atoms, 24 bonds, 3 residues, 2 models selected > select add #2/L:114 37 atoms, 34 bonds, 4 residues, 2 models selected > cofr sel > volume #1 level 0.01081 > select #10/A:8 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/A:9 15 atoms, 13 bonds, 2 residues, 1 model selected Fit molecule 1ubq (#10) to map run_class001.mrc (#1) using 660 atoms average map value = 0.009062, steps = 44 shifted from previous position = 0.0103 rotated from previous position = 0.0333 degrees atoms outside contour = 430, contour level = 0.01081 Position of 1ubq (#10) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.11634722 -0.94156449 0.31610067 157.52391787 0.70524706 -0.30241731 -0.64122566 165.90768674 0.69934962 0.14832426 0.69922100 49.66305610 Axis 0.42310599 -0.20537641 0.88249751 Axis point -3.74330323 137.40539977 0.00000000 Rotation angle (degrees) 111.08617962 Shift along axis 76.40331190 Fit molecule 1ubq (#10) to map run_class001.mrc (#1) using 660 atoms average map value = 0.009062, steps = 40 shifted from previous position = 0.0219 rotated from previous position = 0.0604 degrees atoms outside contour = 430, contour level = 0.01081 Position of 1ubq (#10) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.11655578 -0.94186914 0.31511468 157.56738459 0.70527226 -0.30188253 -0.64144989 165.91215464 0.69928948 0.14747696 0.69946034 49.68385481 Axis 0.42272272 -0.20584851 0.88257118 Axis point -3.73963179 137.47920654 0.00000000 Rotation angle (degrees) 111.06881635 Shift along axis 76.30408258 > select clear > select #10/A:8 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/A:9 15 atoms, 13 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > select #2/L:115 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select add #2/L:114 19 atoms, 17 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 19 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:115 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > ~label sel residues > select clear > select #2/L:111 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #2/L:118 18 atoms, 17 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 18 atom styles > volume #1 level 0.01068 > volume #1 level 0.01054 > volume #1 level 0.00974 > volume #1 level 0.009204 > volume #1 level 0.009071 > volume #1 level 0.009204 > volume #1 level 0.009338 > volume #1 level 0.009606 > volume #1 level 0.009071 > select #10/A:69 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > color sel byhetero > hide sel atoms > select #10/A:7 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/L:118 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel byhetero > select #10/A:7 7 atoms, 6 bonds, 1 residue, 1 model selected > select #10/A:8 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > color sel byhetero > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:118 11 atoms, 11 bonds, 1 residue, 1 model selected > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:9 7 atoms, 6 bonds, 1 residue, 1 model selected > select #10/A:7 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select #10/A:9 7 atoms, 6 bonds, 1 residue, 1 model selected > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:47 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #10/A:46 9 atoms, 7 bonds, 2 residues, 1 model selected > show sel atoms > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:48 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > volume #1 level 0.007465 > volume #1 level 0.008134 > select #10/A:68 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/L:117 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > color sel byhetero > volume #1 level 0.0085 > select #2/L:117 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #2/L:117 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #10/A:68 10 atoms, 10 bonds, 1 residue, 1 model selected > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > volume #1 level 0.0084 > volume #1 level 0.0083 > volume #1 level 0.0082 > select #2/L:122 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:121 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > show sel atoms > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:123 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 6 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > color sel byhetero > color sel byhetero > select clear > volume #1 level 0.008 > volume #1 level 0.007866 > select #2/L:123 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > volume #1 level 0.008535 > volume #1 level 0.01215 > volume #1 level 0.009472 > select #10/A:71 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #10/A:72 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #10/A:70 18 atoms, 16 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:71 8 atoms, 7 bonds, 1 residue, 1 model selected > cofr sel > select #2/L:129 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #2/L:130 17 atoms, 16 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 17 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > color sel byhetero > select #10/A:71 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:70 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:130 5 atoms, 4 bonds, 1 residue, 1 model selected > volume #1 level 0.01081 > select #10/A:35 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > show sel atoms > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select clear > volume #1 level 0.009472 > ui tool show ""Side View"" > select #2/L:126 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 6 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select clear > select #2/N:345 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > select add #2/N:331 19 atoms, 18 bonds, 2 residues, 1 model selected > select add #2/N:335 26 atoms, 24 bonds, 3 residues, 1 model selected > select add #2/N:338 37 atoms, 34 bonds, 4 residues, 1 model selected > select add #2/N:342 46 atoms, 42 bonds, 5 residues, 1 model selected > select add #2/N:349 55 atoms, 50 bonds, 6 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 55 atoms average map value = 0.01109, steps = 132 shifted from previous position = 6.72 rotated from previous position = 14.5 degrees atoms outside contour = 16, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.22679911 -0.46135157 -0.85773941 416.21434935 -0.45848542 -0.72642649 0.51195279 269.58911283 -0.85927485 0.50937146 -0.04677008 207.75394959 Axis -0.62177001 0.36984489 0.69037440 Axis point 301.45461119 79.45150457 0.00000000 Rotation angle (degrees) 179.88106587 Shift along axis -15.65543721 > select add #2/N:324 63 atoms, 57 bonds, 7 residues, 1 model selected > select add #2/N:334 72 atoms, 65 bonds, 8 residues, 1 model selected > select add #2/N:336 83 atoms, 75 bonds, 9 residues, 1 model selected > select add #2/N:339 92 atoms, 83 bonds, 10 residues, 1 model selected > select add #2/N:340 101 atoms, 91 bonds, 11 residues, 1 model selected > select add #2/N:341 109 atoms, 98 bonds, 12 residues, 1 model selected > select add #2/N:343 118 atoms, 106 bonds, 13 residues, 1 model selected > select add #2/N:344 127 atoms, 114 bonds, 14 residues, 1 model selected > select add #2/N:346 136 atoms, 122 bonds, 15 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 136 atoms average map value = 0.009299, steps = 112 shifted from previous position = 3.31 rotated from previous position = 31.3 degrees atoms outside contour = 72, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.54854460 -0.68144385 -0.48449263 434.37846586 -0.26493939 -0.40793243 0.87372664 103.58900598 -0.79303590 0.60763922 0.04322781 157.52609050 Axis -0.45668726 0.52955445 0.71484882 Axis point 255.01502382 37.21410113 0.00000000 Rotation angle (degrees) 163.06279391 Shift along axis -30.91175146 > select subtract #2/N:324 128 atoms, 115 bonds, 14 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 128 atoms average map value = 0.009396, steps = 164 shifted from previous position = 0.48 rotated from previous position = 26.3 degrees atoms outside contour = 65, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.58314546 -0.80979090 -0.06465348 373.75155416 0.08263785 -0.13830574 0.98693591 -31.07419828 -0.80815367 0.57018438 0.14757174 144.42595520 Axis -0.33770775 0.60248314 0.72316495 Axis point 222.19196350 10.26599477 0.00000000 Rotation angle (degrees) 141.90043719 Shift along axis -40.49668693 > select add #2/N:332 137 atoms, 123 bonds, 15 residues, 1 model selected > select add #2/N:333 145 atoms, 130 bonds, 16 residues, 1 model selected > select add #2/N:337 153 atoms, 137 bonds, 17 residues, 1 model selected > select add #2/N:347 160 atoms, 143 bonds, 18 residues, 1 model selected > select add #2/N:348 169 atoms, 151 bonds, 19 residues, 1 model selected > select add #2/N:330 176 atoms, 157 bonds, 20 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 176 atoms average map value = 0.009365, steps = 268 shifted from previous position = 5.34 rotated from previous position = 11 degrees atoms outside contour = 97, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.53769066 -0.83474919 0.11866990 332.11649342 0.20514812 0.00699217 0.97870596 -74.88971818 -0.81780376 0.55058597 0.16748760 140.53317326 Axis -0.29254363 0.63991266 0.71058427 Axis point 209.05625591 -3.08645029 0.00000000 Rotation angle (degrees) 132.96922611 Shift along axis -45.22078002 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.79044,-0.3104,-0.52808,209.19,-0.16217,0.7253,-0.66906,207.84,0.59069,0.61449,0.52297,-121.67 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 176 atoms average map value = 0.009364, steps = 184 shifted from previous position = 6.68 rotated from previous position = 0.618 degrees atoms outside contour = 97, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.53955657 -0.83493074 0.10848677 334.63450154 0.19710722 0.00000955 0.98038193 -72.54681288 -0.81855205 0.55035504 0.16456571 141.33905594 Axis -0.29608297 0.63828660 0.71058081 Axis point 210.04307592 -2.45330610 0.00000000 Rotation angle (degrees) 133.43179879 Shift along axis -44.95241310 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.00913, steps = 344 shifted from previous position = 39.6 rotated from previous position = 27.8 degrees atoms outside contour = 10500, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.42319264 -0.90134436 -0.09212134 391.69050858 -0.26615742 0.02648366 0.96356569 20.28057429 -0.86606478 0.43229269 -0.25110718 266.35591441 Axis -0.46872332 0.68282284 0.56040290 Axis point 266.02012591 0.00000000 37.92016898 Rotation angle (degrees) 145.47794330 Shift along axis -20.47980838 > select clear > undo > undo > undo > select clear Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.00913, steps = 348 shifted from previous position = 39.9 rotated from previous position = 28.2 degrees atoms outside contour = 10507, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.42309183 -0.90136967 -0.09233647 391.72527440 -0.26619746 0.02624242 0.96356123 20.34755272 -0.86610173 0.43225462 -0.25104528 266.34013870 Axis -0.46880019 0.68273440 0.56044635 Axis point 266.05958798 0.00000000 37.87485409 Rotation angle (degrees) 145.48191253 Shift along axis -20.47954876 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.00913, steps = 40 shifted from previous position = 0.0192 rotated from previous position = 0.0135 degrees atoms outside contour = 10503, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.42320873 -0.90133480 -0.09214096 391.69900415 -0.26614795 0.02646294 0.96356887 20.28617899 -0.86605983 0.43231389 -0.25108776 266.34317035 Axis -0.46871788 0.68281639 0.56041532 Axis point 266.02258135 0.00000000 37.91101818 Rotation angle (degrees) 145.47882181 Shift along axis -20.48179714 > select #2 17365 atoms, 18360 bonds, 434 pseudobonds, 1657 residues, 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.99418,-0.057605,-0.091013,24.765,-0.024208,0.70385,-0.70994,174.14,0.10496,0.70801,0.69836,-100.68 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.00913, steps = 96 shifted from previous position = 0.979 rotated from previous position = 7.99 degrees atoms outside contour = 10497, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.42318072 -0.90135053 -0.09211574 391.69024564 -0.26616934 0.02649190 0.96356217 20.28315134 -0.86606695 0.43227932 -0.25112275 266.35812727 Axis -0.46872924 0.68282566 0.56039452 Axis point 266.02177032 0.00000000 37.92034576 Rotation angle (degrees) 145.47771035 Shift along axis -20.48118161 > select clear > view > select #2 17365 atoms, 18360 bonds, 434 pseudobonds, 1657 residues, 4 models selected > view matrix models > #2,0.92475,0.059199,-0.37594,69.837,-0.1112,0.98675,-0.11816,30.193,0.36397,0.15107,0.91908,-90.907 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.01526, steps = 160 shifted from previous position = 9.71 rotated from previous position = 21.8 degrees atoms outside contour = 5484, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.21139736 -0.61362839 -0.76077024 416.48922441 -0.29826333 -0.70073363 0.64808283 206.91982160 -0.93077931 0.36391287 -0.03488961 249.70846855 Axis -0.62142677 0.37177819 0.68964465 Axis point 303.06569089 70.63125323 0.00000000 Rotation angle (degrees) 166.78279792 Shift along axis -9.67916697 > select clear > select #2/K 520 atoms, 523 bonds, 73 residues, 1 model selected > select #2/N 903 atoms, 922 bonds, 109 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 903 atoms average map value = 0.009329, steps = 56 shifted from previous position = 1.84 rotated from previous position = 2.36 degrees atoms outside contour = 474, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.24500346 -0.59414162 -0.76613905 419.01021599 -0.31141625 -0.70012214 0.64253318 210.50677733 -0.91814662 0.39601101 -0.01349301 236.24865723 Axis -0.60909025 0.37556999 0.69853866 Axis point 296.79220093 71.91220442 0.00000000 Rotation angle (degrees) 168.32446430 Shift along axis -11.12618967 > cofr sel > select clear > select #2/N:334 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > select #2/N:345 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > volume #1 level 0.008 > select #2/L:3 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/L:4 13 atoms, 11 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 13 atom styles > color sel byhetero > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job162 3D > bin1 no alignment mask UPD T=6/run_it051_class004.mrc"" Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown at level 0.000119, step 1, values float32 > volume all level 0.008 > select #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,87.213,0,1,0,38.442,0,0,1,56.058 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.63535,0.17203,-0.75282,346.94,-0.61256,-0.70587,0.35568,321.57,-0.4702,0.68713,0.55386,63.797 > view matrix models > #3,-0.54923,0.82372,-0.14079,169.11,0.10116,0.23278,0.96725,25.979,0.82952,0.51701,-0.21118,21.764 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.54923,0.82372,-0.14079,171.23,0.10116,0.23278,0.96725,-7.7473,0.82952,0.51701,-0.21118,32.289 > view matrix models > #3,-0.54923,0.82372,-0.14079,169.56,0.10116,0.23278,0.96725,1.4665,0.82952,0.51701,-0.21118,34.665 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.042524,-0.096128,-0.99446,343.7,-0.66599,-0.73923,0.099935,338.32,-0.74474,0.66655,-0.032585,181.39 Fit map run_it051_class004.mrc in map run_class001.mrc using 45707 points correlation = 0.9642, correlation about mean = 0.7507, overlap = 8.193 steps = 128, shift = 8.6, angle = 19.4 degrees Position of run_it051_class004.mrc (#3) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation 0.99999852 -0.00051399 -0.00164086 0.66727054 0.00050899 0.99999521 -0.00304965 0.37791816 0.00164242 0.00304880 0.99999400 -0.29730557 Axis 0.87105144 -0.46895615 0.14611476 Axis point 0.00000000 115.14777973 179.18622894 Rotation angle (degrees) 0.20057144 Shift along axis 0.36055919 > select clear > graphics silhouettes false > graphics silhouettes true > lighting soft > hide #!1 models > transparency #3.1 50 > select clear > transparency #3.1 50 > select clear > transparency #3.1 50 > select clear > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select #3 2 models selected > transparency sel 0 > volume #3 level 0.01069 > select clear > volume #3 level 0.009991 > volume #3 level 0.009405 > hide #!1 models > transparency #3.1 50 > select clear > select #2/N:351 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > cofr sel > volume #3 level 0.008234 > volume #3 level 0.004721 > volume #3 level 0.003316 > volume #3 level 0.004253 > volume #3 level 0.006243 > volume #3 level 0.005541 > select #2/L:91 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > style sel stick Changed 6 atom styles > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > volume #3 level 0.0135 > volume #3 level 0.008351 > volume #3 level 0.006829 > volume #3 level 0.005072 > volume #3 level 0.006 > volume #3 level 0.0056 > volume #3 level 0.008528 > select #10/A:74 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > hide sel atoms > volume #3 level 0.005834 > volume #3 level 0.009816 > hide #!3 models > show #!1 models > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job151 Refine > bin1 57.8Ww 3.43A, 3.34A/job151_map and model-002.cxs"" includeMaps true ——— End of log from Sat Jul 1 11:38:15 2023 ——— opened ChimeraX session > hide #!1 models > color sel bynucleotide Alignment identifier is 10/A [Repeated 1 time(s)]Destroying pre-existing alignment with identifier 10/A Alignment identifier is 10/A Destroying pre-existing alignment with identifier 10/A Alignment identifier is 10/A > select add #2 17376 atoms, 18370 bonds, 434 pseudobonds, 1658 residues, 5 models selected Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 2/I Alignment identifier is 2/J Alignment identifier is 2/K Alignment identifier is 2/L Alignment identifier is 5 Alignment identifier is 2/N > select #2/L:82-83 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/L:82-106 183 atoms, 186 bonds, 25 residues, 1 model selected > color sel blue > select #2/L:123 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/L:123-138 112 atoms, 114 bonds, 16 residues, 1 model selected > color sel blue > select #2/N:312 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/N:312-326 130 atoms, 134 bonds, 15 residues, 1 model selected > color sel blue > save /Users/zhangtianyi/T/LiuLab/课题/ASXL/质谱送样-zty/PR-DUB-Ub-HDXlow- > blueed.tif width 649 height 787 supersample 3 > save /Users/zhangtianyi/T/LiuLab/课题/ASXL/质谱送样-zty/PR-DUB-Ub-HDXlow- > blueed.cxs ——— End of log from Wed Jul 10 17:09:03 2024 ——— opened ChimeraX session 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. > open /Users/zhangtianyi/T/LiuLab/课题/ASXL/质谱送样-zty/PR-DUB-Ub-HDXlow- > blueed.cxs Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.008, step 2, values float32 Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at level 0.008, step 1, values float32 Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown at level 0.00982, step 1, values float32 Log from Wed Jul 10 17:09:03 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open > ""/Users/zhangtianyi/T/LiuLab/课题/ASXL/sturctures/job151_map_and_model-002 > interaction analysis.cxs"" Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.008, step 2, values float32 Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at level 0.008, step 1, values float32 Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown at level 0.00982, step 1, values float32 Log from Sat Jul 1 11:38:15 2023UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:\\\Users\\\Lenovo\\\Desktop\\\20230617_H2AK119Ub-AT2-Ub-PR- > DUB\\\job151 Refine bin1 57.8Ww 3.43A, 3.34A\\\job151_map and model.cxs"" Updating list of available bundles failed: Internal Server Error Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.147, step 2, values float32 Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at level 0.00661, step 1, values float32 Log from Thu Jun 29 10:10:27 2023UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. > open ""C:\\\Users\\\Lenovo\\\Desktop\\\20230617_H2AK119Ub-AT2-Ub-PR- > DUB\\\xuruiming_map and model.cxs"" Opened run_it011_half1_class001.mrc as #1, grid size 128,128,128, pixel 2.2, shown at level 0.0245, step 1, values float32 Opened emdb 34431 as #3, grid size 352,352,352, pixel 1, shown at level 9.44, step 2, values float32 Opened emdb 34432 as #4, grid size 104,112,143, pixel 1.04,1.04,1.04, shown at level 0.0819, step 1, values float32 Opened emdb 35179 as #5, grid size 352,352,352, pixel 1, shown at level 0.271, step 2, values float32 Opened emdb 35180 as #6, grid size 352,352,352, pixel 1, shown at level 0.222, step 2, values float32 Opened emdb 35181 as #7, grid size 352,352,352, pixel 1, shown at level 0.00557, step 2, values float32 Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.14, step 2, values float32 Log from Wed Jun 28 16:03:29 2023UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:\\\Users\\\Lenovo\\\Desktop\\\20230617_H2AK119Ub-AT2-Ub-PR- > DUB\\\job149 Refine bin2\\\run_it011_half1_class001.mrc"" Opened run_it011_half1_class001.mrc as #1, grid size 128,128,128, pixel 2.2, shown at level 0.0284, step 1, values float32 > volume #1 level 0.0258 > volume #1 level 0.02467 > graphics silhouettes true > lighting soft > lighting simple > lighting soft > lighting full > lighting shadows false > set bgColor white > volume #1 level 0.02317 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job139 Refine > bin2 89W/job139_run_class001.mrc"" Opened job139_run_class001.mrc as #2, grid size 128,128,128, pixel 2.2, shown at level 0.0272, step 1, values float32 > ui tool show ""Command Line Interface"" > volume all level 0.034 > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > ui tool show ""Fit in Map"" Fit map run_it011_half1_class001.mrc in map job139_run_class001.mrc using 17425 points correlation = 0.9972, correlation about mean = 0.9785, overlap = 74.41 steps = 80, shift = 0.498, angle = 0.827 degrees Position of run_it011_half1_class001.mrc (#1) relative to job139_run_class001.mrc (#2) coordinates: Matrix rotation and translation 0.99989599 0.01380768 -0.00416533 -1.49573984 -0.01380653 0.99990464 0.00030410 1.81571435 0.00416913 -0.00024656 0.99999128 -0.08487031 Axis -0.01908692 -0.28889124 -0.95717164 Axis point 122.07421022 109.81952662 0.00000000 Rotation angle (degrees) 0.82651459 Shift along axis -0.41475944 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > lighting soft > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > volume #1 level 0.02741 > volume all level 0.03 > volume all level 0.026 > open emdb-34431 'emdb-34431' has no suffix > open emd-34431 'emd-34431' has no suffix > open emdb:34431 Opened emdb 34431 as #3, grid size 352,352,352, pixel 1, shown at level 1.98, step 2, values float32 > open emdb:34432 Summary of feedback from opening 34432 fetched from emdb --- note | Fetching compressed map 34432 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-34432/map/emd_34432.map.gz Opened emdb 34432 as #4, grid size 104,112,143, pixel 1.04,1.04,1.04, shown at level 0.515, step 1, values float32 > open emdb:35179 Summary of feedback from opening 35179 fetched from emdb --- note | Fetching compressed map 35179 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35179/map/emd_35179.map.gz Opened emdb 35179 as #5, grid size 352,352,352, pixel 1, shown at level 0.152, step 2, values float32 > hide #!1 models > show #!2 models > hide #!2 models > volume all level 0.026 > hide #!3 models > volume all level 0.26 > show #!3 models > volume all level 0.26 > volume all level 0.26 > volume #3 level 10.22 > select #4 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,64.535,0,1,0,-30.598,0,0,1,-35.187 > volume #4 level 0.1143 > view matrix models #4,1,0,0,51.454,0,1,0,57.822,0,0,1,9.7514 > view matrix models #4,1,0,0,42.295,0,1,0,38.932,0,0,1,29.293 Fit map emdb 34432 in map emdb 34431 using 83018 points correlation = 0.4644, correlation about mean = 0.04404, overlap = 1.204e+05 steps = 84, shift = 3.53, angle = 3.55 degrees Position of emdb 34432 (#4) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99890937 0.03123120 -0.03470859 45.72282835 -0.03261495 0.99866550 -0.04004359 48.84191918 0.03341167 0.04113194 0.99859492 21.64673436 Axis 0.65613302 -0.55060868 -0.51606157 Axis point 0.00000000 -386.78737202 1121.73286361 Rotation angle (degrees) 3.54652680 Shift along axis -8.06357459 Fit map emdb 34432 in map emdb 35179 using 83018 points correlation = 0.341, correlation about mean = 0.07392, overlap = 5453 steps = 100, shift = 0.913, angle = 1.96 degrees Position of emdb 34432 (#4) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99895234 0.03147412 -0.03322041 44.67487050 -0.03386640 0.99667610 -0.07409328 53.99915515 0.03077796 0.07514071 0.99669784 17.51778732 Axis 0.85261312 -0.36563957 -0.37330762 Axis point 0.00000000 -256.69518956 798.57926733 Rotation angle (degrees) 5.02070032 Shift along axis 11.80662940 Fit map emdb 34432 in map emdb 35179 using 83018 points correlation = 0.341, correlation about mean = 0.07394, overlap = 5452 steps = 44, shift = 0.0146, angle = 0.0403 degrees Position of emdb 34432 (#4) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99896681 0.03149240 -0.03276494 44.60844069 -0.03386663 0.99663623 -0.07462758 54.07082246 0.03030453 0.07566012 0.99667306 17.50011789 Axis 0.85584426 -0.35916209 -0.37220047 Axis point 0.00000000 -256.57318302 795.03454053 Rotation angle (degrees) 5.03710382 Shift along axis 12.24413623 Fit map emdb 34432 in map emdb 35179 using 83018 points correlation = 0.341, correlation about mean = 0.07394, overlap = 5452 steps = 44, shift = 0.00596, angle = 0.0177 degrees Position of emdb 34432 (#4) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99896062 0.03148124 -0.03296380 44.63846152 -0.03386334 0.99665396 -0.07439188 54.03788776 0.03051155 0.07543082 0.99668412 17.50755650 Axis 0.85444513 -0.36200262 -0.37266288 Axis point 0.00000000 -256.63943020 796.59903642 Rotation angle (degrees) 5.02972229 Shift along axis 12.05484243 Fit map emdb 34432 in map emdb 34431 using 83018 points correlation = 0.4644, correlation about mean = 0.0441, overlap = 1.204e+05 steps = 64, shift = 0.919, angle = 1.97 degrees Position of emdb 34432 (#4) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99892127 0.03122111 -0.03437357 45.68426787 -0.03259126 0.99866604 -0.04004939 48.83024008 0.03307733 0.04112646 0.99860628 21.67062546 Axis 0.65818149 -0.54689834 -0.51739669 Axis point 0.00000000 -390.05511420 1125.06043205 Rotation angle (degrees) 3.53548883 Shift along axis -7.84894767 Fit map emdb 35179 in map emdb 34431 using 14429 points correlation = 0.8366, correlation about mean = 0.5508, overlap = 1.227e+05 steps = 52, shift = 0.454, angle = 0.791 degrees Position of emdb 35179 (#5) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99999272 0.00214134 0.00315901 -0.47875128 -0.00218307 0.99990963 0.01326523 -1.99764456 -0.00313032 -0.01327203 0.99990702 2.89389585 Axis -0.96103935 0.22776623 -0.15660754 Axis point 0.00000000 211.74601648 144.34107449 Rotation angle (degrees) 0.79108162 Shift along axis -0.44810305 > select #5 2 models selected > view matrix models > #5,0.99999,0.0021413,0.003159,1.2511,-0.0021831,0.99991,0.013265,-5.7327,-0.0031303,-0.013272,0.99991,-7.6705 Fit map emdb 35179 in map emdb 34431 using 14429 points correlation = 0.4433, correlation about mean = 0.04557, overlap = 4.107e+04 steps = 112, shift = 1.17, angle = 3.83 degrees Position of emdb 35179 (#5) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99773017 0.06338782 -0.02272660 -4.62359927 -0.06321197 0.99796498 0.00837475 5.72175057 0.02321121 -0.00691915 0.99970664 -12.16494231 Axis -0.11283492 -0.33891882 -0.93402479 Axis point 141.89552302 60.31997900 0.00000000 Rotation angle (degrees) 3.88597703 Shift along axis 9.94485223 > select clear > hide #!3 models > hide #!5 models > volume #4 level 0.03876 > volume #4 level 0.08193 > show #!3 models > hide #!4 models > volume #3 level 4.363 > volume #3 level 8.661 > show #!5 models > hide #!3 models > select #5 2 models selected > view sel > volume #5 level 0.3157 > open emdb:35180 Summary of feedback from opening 35180 fetched from emdb --- note | Fetching compressed map 35180 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35180/map/emd_35180.map.gz Opened emdb 35180 as #6, grid size 352,352,352, pixel 1, shown at level 0.128, step 2, values float32 > volume #6 level 0.2169 Fit map emdb 35180 in map emdb 34431 using 16962 points correlation = 0.8659, correlation about mean = 0.5218, overlap = 1.141e+05 steps = 48, shift = 0.0239, angle = 0.0661 degrees Position of emdb 35180 (#6) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99999971 -0.00075739 -0.00000082 0.13211717 0.00075739 0.99999933 0.00087070 -0.26277045 0.00000016 -0.00087070 0.99999962 0.15962417 Axis -0.75449292 -0.00042428 0.65630805 Axis point 0.00000000 179.28267107 301.92626454 Rotation angle (degrees) 0.06612062 Shift along axis 0.00519265 Fit map emdb 35180 in map emdb 34431 using 16962 points correlation = 0.866, correlation about mean = 0.522, overlap = 1.141e+05 steps = 28, shift = 0.00571, angle = 0.00356 degrees Position of emdb 35180 (#6) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99999972 -0.00074902 -0.00004045 0.13504859 0.00074905 0.99999938 0.00082350 -0.25553678 0.00003983 -0.00082353 0.99999966 0.14874632 Axis -0.73928609 -0.03603432 0.67242666 Axis point 0.00000000 172.82599236 310.02542270 Rotation angle (degrees) 0.06382356 Shift along axis 0.00938954 > select #6 2 models selected > view matrix models > #6,1,-0.00074902,-4.0448e-05,1.5687,0.00074905,1,0.0008235,-5.4821,3.9831e-05,-0.00082353,1,-6.6841 Fit map emdb 35180 in map emdb 34431 using 16962 points correlation = 0.4546, correlation about mean = 0.01254, overlap = 3.337e+04 steps = 136, shift = 2.43, angle = 5.15 degrees Position of emdb 35180 (#6) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99603630 0.07637558 -0.04559006 -2.54488492 -0.07661283 0.99705486 -0.00347703 10.51923386 0.04519023 0.00695603 0.99895418 -17.89003642 Axis 0.05854684 -0.50942829 -0.85851912 Axis point 200.83602946 51.29508390 0.00000000 Rotation angle (degrees) 5.11184277 Shift along axis 9.85114802 > surface dust #6 size 10 > select clear > surface dust #5 size 10 > surface dust #6 size 10 > select clear > volume #6 level 0.1575 > show #!1 models > volume #1 level 0.02912 > hide #!1 models > show #!1 models > hide #!1 models > volume #6 level 0.1971 > select #1 2 models selected > ~select #1 Nothing selected > select #1 2 models selected > show #!1 models > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.3119,-0.84096,-0.44216,361.9,-0.58855,-0.19432,0.78476,149.8,-0.74587,0.505,-0.43434,221.31 > ui mousemode right ""translate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.3119,-0.84096,-0.44216,371.72,-0.58855,-0.19432,0.78476,164.27,-0.74587,0.505,-0.43434,266.26 > view matrix models > #1,-0.3119,-0.84096,-0.44216,400.86,-0.58855,-0.19432,0.78476,174.21,-0.74587,0.505,-0.43434,259.27 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.432, correlation about mean = -0.04102, overlap = 4048 steps = 176, shift = 7.2, angle = 16.4 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.41318297 -0.66529648 -0.62182025 411.95520538 -0.68732521 -0.22010093 0.69219913 209.11148816 -0.59738086 0.71339762 -0.36633309 204.01510017 Axis 0.54160944 -0.62441265 -0.56282151 Axis point 295.16780503 0.00000000 11.08768828 Rotation angle (degrees) 178.87865551 Shift along axis -22.27712010 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.41318,-0.6653,-0.62182,411.87,-0.68733,-0.2201,0.6922,199.3,-0.59738,0.7134,-0.36633,194.99 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.5482, correlation about mean = 0.08959, overlap = 6083 steps = 208, shift = 15.5, angle = 25.8 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.31694377 -0.32364929 -0.89151432 395.98909173 -0.79495142 -0.42202924 0.43582515 285.38972157 -0.51729961 0.84684263 -0.12352593 141.68444046 Axis 0.56399218 -0.51349195 -0.64671388 Axis point 300.29452266 27.46076670 0.00000000 Rotation angle (degrees) 158.63042959 Shift along axis -14.83986794 > view matrix models > #1,-0.31694,-0.32365,-0.89151,393.73,-0.79495,-0.42203,0.43583,283.47,-0.5173,0.84684,-0.12353,142.06 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.5482, correlation about mean = 0.08953, overlap = 6083 steps = 76, shift = 2.99, angle = 0.0146 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.31679506 -0.32384501 -0.89149610 395.98156900 -0.79492845 -0.42209014 0.43580807 285.40112818 -0.51742598 0.84673746 -0.12371755 141.73337945 Axis 0.56407668 -0.51348051 -0.64664926 Axis point 300.31774210 27.46109397 0.00000000 Rotation angle (degrees) 158.63859217 Shift along axis -14.83573259 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.19243,-0.42355,-0.8852,391.99,-0.42557,-0.7768,0.4642,280.65,-0.88423,0.46604,-0.030769,235.27 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.7122, correlation about mean = 0.235, overlap = 1.022e+04 steps = 112, shift = 1.88, angle = 13.5 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.20178070 -0.29779480 -0.93306099 380.47497501 -0.60749948 -0.70920833 0.35772605 311.11430563 -0.76826359 0.63901627 -0.03780564 194.14708143 Axis 0.62555392 -0.36648861 -0.68874407 Axis point 303.82924212 71.94693846 0.00000000 Rotation angle (degrees) 167.00694694 Shift along axis -9.72988983 > view matrix models > #1,-0.16656,-0.30219,-0.93858,376.9,-0.60955,-0.71665,0.33891,314.94,-0.77505,0.62856,-0.064835,200.15 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.16656,-0.30219,-0.93858,376.2,-0.60955,-0.71665,0.33891,311.95,-0.77505,0.62856,-0.064835,196.38 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.7121, correlation about mean = 0.2346, overlap = 1.022e+04 steps = 64, shift = 5.09, angle = 2.06 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.20176299 -0.29769584 -0.93309640 380.45281193 -0.60751348 -0.70924027 0.35763895 311.14795448 -0.76825717 0.63902694 -0.03775580 194.13599866 Axis 0.62555670 -0.36645589 -0.68875896 Axis point 303.82251702 71.96317881 0.00000000 Rotation angle (degrees) 167.00241071 Shift along axis -9.74010388 > hide #!6 models Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.7121, correlation about mean = 0.2346, overlap = 1.022e+04 steps = 64, shift = 5.09, angle = 2.06 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.20176299 -0.29769584 -0.93309640 380.45281193 -0.60751348 -0.70924027 0.35763895 311.14795448 -0.76825717 0.63902694 -0.03775580 194.13599866 Axis 0.62555670 -0.36645589 -0.68875896 Axis point 303.82251702 71.96317881 0.00000000 Rotation angle (degrees) 167.00241071 Shift along axis -9.74010388 > view matrix models > #1,-0.16656,-0.30219,-0.93858,378.11,-0.60955,-0.71665,0.33891,308.63,-0.77505,0.62856,-0.064835,192.89 Fit map run_it011_half1_class001.mrc in map emdb 34431 using 20495 points correlation = 0.7121, correlation about mean = 0.2348, overlap = 1.022e+04 steps = 84, shift = 9.91, angle = 2.06 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation -0.20180659 -0.29771230 -0.93308172 380.46420720 -0.60745123 -0.70927184 0.35768208 311.13089585 -0.76829494 0.63898423 -0.03770997 194.14017512 Axis 0.62554266 -0.36644285 -0.68877864 Axis point 303.81627391 71.96638447 0.00000000 Rotation angle (degrees) 167.00614810 Shift along axis -9.73470558 > show #!3 models > hide #!5 models > hide #!3 models > show #!5 models Fit map run_it011_half1_class001.mrc in map emdb 35179 using 20495 points correlation = 0.5641, correlation about mean = 0.3443, overlap = 396.5 steps = 124, shift = 10.3, angle = 4.26 degrees Position of run_it011_half1_class001.mrc (#1) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation -0.19831167 -0.30563080 -0.93126919 380.58367178 -0.59680949 -0.71603997 0.36208451 310.04870405 -0.77749014 0.62759587 -0.04040428 197.62893854 Axis 0.62768588 -0.36354354 -0.68836511 Axis point 304.20513642 72.78850850 0.00000000 Rotation angle (degrees) 167.78971868 Shift along axis -9.87007366 > transparency #1.1 60 > close #2 > show #!3 models Fit map emdb 34431 in map emdb 35179 using 12029 points correlation = 0.3497, correlation about mean = 0.01267, overlap = 3.078e+04 steps = 96, shift = 0.776, angle = 1.66 degrees Position of emdb 34431 (#3) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99625963 -0.06990513 0.05079393 1.50664356 0.07004571 0.99754329 -0.00099064 -7.95886029 -0.05059989 0.00454483 0.99870866 17.42013605 Axis 0.03201378 0.58639926 0.80938929 Axis point 193.23518824 6.87152612 0.00000000 Rotation angle (degrees) 4.95967493 Shift along axis 9.48083508 > select #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.99959,-0.0066177,0.027919,-4.062,0.0065039,0.99997,0.0041645,-7.2656,-0.027945,-0.0039812,0.9996,0.47012 Fit map emdb 34431 in map emdb 35179 using 12029 points correlation = 0.7124, correlation about mean = 0.1294, overlap = 1.149e+05 steps = 112, shift = 4.05, angle = 5 degrees Position of emdb 34431 (#3) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99999218 -0.00227110 -0.00323698 0.51422483 0.00222815 0.99991028 -0.01320851 2.01866916 0.00326669 0.01320119 0.99990752 -2.86268567 Axis 0.95797217 -0.23591082 0.16320358 Axis point 0.00000000 212.28134970 143.33731474 Rotation angle (degrees) 0.78979960 Shift along axis -0.45081335 > hide #!3 models > show #!4 models Fit map emdb 34432 in map emdb 35179 using 99027 points correlation = 0.7726, correlation about mean = 0.5611, overlap = 2.08e+04 steps = 52, shift = 0.211, angle = 1.42 degrees Position of emdb 34432 (#4) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99852213 -0.05371313 -0.00827333 51.26289725 0.05334807 0.99779961 -0.03936905 41.61501505 0.01036976 0.03886950 0.99919049 34.37988091 Axis 0.58427765 -0.13922477 0.79952242 Axis point -897.63552058 417.29504737 0.00000000 Rotation angle (degrees) 3.83900892 Shift along axis 51.64540936 > hide #!4 models > show #!4 models > hide #!4 models Fit map emdb 35180 in map emdb 35179 using 19722 points correlation = 0.9292, correlation about mean = 0.8881, overlap = 5539 steps = 64, shift = 0.721, angle = 1.42 degrees Position of emdb 35180 (#6) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99999156 -0.00263646 -0.00315049 0.55269862 0.00259706 0.99991921 -0.01244286 1.82961033 0.00318304 0.01243457 0.99991762 -2.72705004 Axis 0.94955487 -0.24174675 0.19975998 Axis point 0.00000000 212.79164492 136.67877369 Rotation angle (degrees) 0.75056863 Shift along axis -0.46224015 > show #!6 models > hide #!6 models > show #!3 models > hide #!5 models > open 7XD1 7xd1 title: cryo-EM structure of unmodified nucleosome [more info...] Chain information for #2 --- Chain | Description A E | Histone H3 B F | Histone H4 C G | Histone H2A type 1-B/E D H | Histone H2B type 1-K I | DNA (147-mer) J | DNA (147-mer) > select #2 12048 atoms, 12861 bonds, 367 pseudobonds, 1054 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,39.425,0,1,0,35.345,0,0,1,9.204 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.28926,0.44394,-0.84808,200.55,-0.58378,-0.62032,-0.52383,407.67,-0.75864,0.64662,0.079727,160.31 > view matrix models > #2,0.048879,0.13582,-0.98953,295.06,-0.74597,-0.65384,-0.12659,376.27,-0.66419,0.74434,0.06936,135.91 > close #2 > open 8h1t 8h1t title: Cryo-EM structure of BAP1-ASXL1 bound to chromatosome [more info...] Chain information for #2 --- Chain | Description A E | Histone H3.1 B F | Histone H4 C G | Histone H2A type 1-D D H | Histone H2B type 2-E I | DNA (187-mer) J | DNA (187-mer) K | Histone H1.4 L | Ubiquitin carboxyl-terminal hydrolase BAP1 M | Ubiquitin N | Polycomb group protein ASXL1 Fit molecule 8h1t (#2) to map emdb 35179 (#5) using 17365 atoms average map value = 0.1604, steps = 128 shifted from previous position = 2.03 rotated from previous position = 2 degrees atoms outside contour = 14706, contour level = 0.31574 Position of 8h1t (#2) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99939008 -0.02855745 0.02009832 1.18268568 0.02874245 0.99954654 -0.00897655 0.21120242 -0.01983286 0.00954875 0.99975771 11.97689886 Axis 0.25638336 0.55263300 0.79300967 Axis point 182.52799773 -51.52365080 0.00000000 Rotation angle (degrees) 2.07043952 Shift along axis 9.91773502 Fit molecule 8h1t (#2) to map emdb 35179 (#5) using 17365 atoms average map value = 0.1604, steps = 44 shifted from previous position = 0.00155 rotated from previous position = 0.00382 degrees atoms outside contour = 14707, contour level = 0.31574 Position of 8h1t (#2) relative to emdb 35179 (#5) coordinates: Matrix rotation and translation 0.99939193 -0.02850881 0.02007543 1.17883432 0.02869282 0.99954831 -0.00893804 0.21332593 -0.01981155 0.00950863 0.99975852 11.98113743 Axis 0.25572879 0.55295861 0.79299405 Axis point 182.93641222 -51.53965694 0.00000000 Rotation angle (degrees) 2.06692781 Shift along axis 9.92039298 Fit molecule 8h1t (#2) to map run_it011_half1_class001.mrc (#1) using 17365 atoms average map value = 0.05027, steps = 96 shifted from previous position = 10.7 rotated from previous position = 2.21 degrees atoms outside contour = 4557, contour level = 0.02912 Position of 8h1t (#2) relative to run_it011_half1_class001.mrc (#1) coordinates: Matrix rotation and translation -0.20207793 -0.60739316 -0.76826952 415.09666474 -0.30219656 -0.70750415 0.63883888 210.30924230 -0.93158024 0.36126365 -0.04058115 250.74357678 Axis -0.62560219 0.36807154 0.68785553 Axis point 304.10787251 71.45893239 0.00000000 Rotation angle (degrees) 167.18249364 Shift along axis -9.80117958 > select clear > hide atoms > show cartoons > select clear > hide #!1 models > select #5 2 models selected > volume #5 level 0.2711 > hide #!5 models > show #!6 models > volume #6 level 0.3258 > select clear > transparency #6.1 50 > show #!5 models > hide #!5 models > volume #6 level 0.2664 > volume #6 level 0.2218 > transparency #5.1 50 > select clear > lighting shadows true intensity 0.5 > lighting flat > lighting full > lighting soft > lighting simple > lighting shadows true > lighting soft > lighting full > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting soft > volume #1 level 0.03573 > transparency #4.1 50 > volume #3 level 5.925 > volume #3 level 9.442 > open emdb:35181 Summary of feedback from opening 35181 fetched from emdb --- note | Fetching compressed map 35181 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35181/map/emd_35181.map.gz Opened emdb 35181 as #7, grid size 352,352,352, pixel 1, shown at level 6.52e-06, step 2, values float32 > volume #7 level 0.007306 Fit map emdb 35181 in map run_it011_half1_class001.mrc using 4083 points correlation = 0.9093, correlation about mean = 0.3586, overlap = 2.248 steps = 68, shift = 10, angle = 3.45 degrees Position of emdb 35181 (#7) relative to run_it011_half1_class001.mrc (#1) coordinates: Matrix rotation and translation -0.23841936 -0.54780454 -0.80191420 417.02093533 -0.34619902 -0.72353752 0.59719318 227.06691731 -0.90736015 0.42000433 -0.01714404 231.26374693 Axis -0.61444130 0.36565700 0.69911147 Axis point 298.15032473 74.30215138 0.00000000 Rotation angle (degrees) 171.70979887 Shift along axis -11.52713835 Fit map emdb 35181 in map emdb 35180 using 4083 points correlation = 0.9073, correlation about mean = 0.5724, overlap = 17.33 steps = 84, shift = 1.3, angle = 1.74 degrees Position of emdb 35181 (#7) relative to emdb 35180 (#6) coordinates: Matrix rotation and translation 0.99718736 -0.07337531 0.01527862 10.74241755 0.07273164 0.99658427 0.03911391 -18.50292298 -0.01809643 -0.03789266 0.99911794 8.76555365 Axis -0.45702121 0.19807540 0.86712038 Axis point 257.87475932 130.45408627 0.00000000 Rotation angle (degrees) 4.83280414 Shift along axis -0.97369621 Fit map emdb 35181 in map emdb 34431 using 4083 points correlation = 0.9745, correlation about mean = 0.8424, overlap = 1313 steps = 48, shift = 0.157, angle = 0.0606 degrees Position of emdb 35181 (#7) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99715241 -0.07391523 0.01495331 10.95867242 0.07325251 0.99647639 0.04085177 -18.86344708 -0.01792019 -0.03964007 0.99905332 9.17345895 Axis -0.47089821 0.19231851 0.86096949 Axis point 261.54982201 132.51289479 0.00000000 Rotation angle (degrees) 4.90283886 Shift along axis -0.89014094 > surface dust #7 size 10 > volume #7 level 0.005574 > transparency #7.1 50 > volume #!7 style mesh > volume #!7 style surface > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting full > lighting shadows false > open emdb:35182 Summary of feedback from opening 35182 fetched from emdb --- note | Fetching compressed map 35182 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-35182/map/emd_35182.map.gz Opened emdb 35182 as #8, grid size 352,352,352, pixel 1, shown at level 0.0644, step 2, values float32 > volume #8 level 0.1449 Fit map emdb 35182 in map emdb 34431 using 24046 points correlation = 0.4763, correlation about mean = -0.0003831, overlap = 3.117e+04 steps = 76, shift = 1.36, angle = 2.22 degrees Position of emdb 35182 (#8) relative to emdb 34431 (#3) coordinates: Matrix rotation and translation 0.99572611 -0.06863698 0.06179381 1.64201538 0.06920377 0.99757745 -0.00707662 -6.61213603 -0.06115839 0.01132274 0.99806385 18.46918095 Axis 0.09912224 0.66237632 0.74258494 Axis point 186.40569216 -1.40044242 0.00000000 Rotation angle (degrees) 5.32536780 Shift along axis 9.49797358 Fit map emdb 35182 in map emdb 35180 using 24046 points correlation = 0.522, correlation about mean = 0.0978, overlap = 1120 steps = 56, shift = 1.14, angle = 1.27 degrees Position of emdb 35182 (#8) relative to emdb 35180 (#6) coordinates: Matrix rotation and translation 0.99619357 -0.07481814 0.04472832 4.53077775 0.07465857 0.99719544 0.00522997 -9.78343870 -0.04499417 -0.00187071 0.99898550 17.63317633 Axis -0.04069583 0.51422317 0.85669037 Axis point 201.26003236 55.69790579 0.00000000 Rotation angle (degrees) 5.00489231 Shift along axis 9.89091767 Fit map emdb 35182 in map emdb 35181 using 24046 points correlation = 0.3573, correlation about mean = -0.056, overlap = 16.2 steps = 316, shift = 9.92, angle = 4.98 degrees Position of emdb 35182 (#8) relative to emdb 35181 (#7) coordinates: Matrix rotation and translation 0.99721407 0.07252112 -0.01745822 -9.22927511 -0.07313472 0.99661547 -0.03753556 19.45060867 0.01467701 0.03870779 0.99914278 -8.01226063 Axis 0.45514287 -0.19183472 -0.86950814 Axis point 257.35740018 131.09208266 0.00000000 Rotation angle (degrees) 4.80458616 Shift along axis -0.96521509 > hide #!7 models > transparency #8.1 50 > volume #8 level 0.1159 > surface dust #8 size 10 > volume #8 level 0.1405 > volume #1 level 0.03184 > volume #1 level 0.02057 > volume #1 level 0.02523 > volume #1 level 0.02484 > lighting flat > lighting full > lighting simple > volume #1 level 0.02445 > show #!8 models > hide #!1 models > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/xuruiming_map > and model.cxs"" includeMaps true ——— End of log from Wed Jun 28 16:03:29 2023 ——— opened ChimeraX session > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job149 Refine > bin2/job149_run_class001_4.46A.mrc"" Opened job149_run_class001_4.46A.mrc as #9, grid size 128,128,128, pixel 2.2, shown at level 0.0276, step 1, values float32 > select #9 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #9,1,0,0,45.835,0,1,0,26.249,0,0,1,37.401 > ui mousemode right ""rotate selected models"" > view matrix models > #9,-0.17169,-0.11728,-0.97815,354.61,-0.71105,-0.67246,0.20544,337.48,-0.68186,0.73078,0.032062,155.29 > ui tool show ""Fit in Map"" Fit map job149_run_class001_4.46A.mrc in map run_it011_half1_class001.mrc using 20966 points correlation = 0.9966, correlation about mean = 0.9805, overlap = 82.65 steps = 100, shift = 6.36, angle = 16.2 degrees Position of job149_run_class001_4.46A.mrc (#9) relative to run_it011_half1_class001.mrc (#1) coordinates: Matrix rotation and translation 0.99999989 0.00020928 0.00041884 -0.06994052 -0.00020930 0.99999998 0.00004826 0.03452944 -0.00041883 -0.00004834 0.99999991 0.09029170 Axis -0.10261362 0.88981477 -0.44463481 Axis point 213.16237377 0.00000000 167.59255835 Rotation angle (degrees) 0.02696899 Shift along axis -0.00224518 Fit map job149_run_class001_4.46A.mrc in map emdb 35182 using 20966 points correlation = 0.9308, correlation about mean = 0.7175, overlap = 355.2 steps = 48, shift = 0.147, angle = 0.181 degrees Position of job149_run_class001_4.46A.mrc (#9) relative to emdb 35182 (#8) coordinates: Matrix rotation and translation -0.20298928 -0.30337753 -0.93099808 381.28750314 -0.60618210 -0.70775669 0.36279983 309.94973019 -0.76898544 0.63799885 -0.04023501 194.86601834 Axis 0.62533410 -0.36814095 -0.68806214 Axis point 303.99138854 71.48857777 0.00000000 Rotation angle (degrees) 167.28852422 Shift along axis -9.75304006 > hide #!8 models > transparency sel 50 > select clear > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job149 Refine > bin2/job149_map and model.cxs"" includeMaps true > select /L 2433 atoms, 2487 bonds, 2 pseudobonds, 301 residues, 2 models selected Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 2433 atoms average map value = 0.03568, steps = 64 shifted from previous position = 2.35 rotated from previous position = 1.97 degrees atoms outside contour = 748, contour level = 0.027568 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.20794411 -0.61149238 -0.76343717 414.87568309 -0.26697774 -0.71538055 0.64571942 203.42240837 -0.94100060 0.33809428 -0.01449568 250.07835222 Axis -0.62168400 0.35884046 0.69623453 Axis point 300.38077372 74.09859277 0.00000000 Rotation angle (degrees) 165.67553333 Shift along axis -10.81220027 > volume #9 level 0.03066 Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 2433 atoms average map value = 0.03568, steps = 64 shifted from previous position = 2.35 rotated from previous position = 1.97 degrees atoms outside contour = 943, contour level = 0.03066 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.20794411 -0.61149238 -0.76343717 414.87568309 -0.26697774 -0.71538055 0.64571942 203.42240837 -0.94100060 0.33809428 -0.01449568 250.07835222 Axis -0.62168400 0.35884046 0.69623453 Axis point 300.38077372 74.09859277 0.00000000 Rotation angle (degrees) 165.67553333 Shift along axis -10.81220027 Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 2433 atoms average map value = 0.03568, steps = 64 shifted from previous position = 2.35 rotated from previous position = 1.97 degrees atoms outside contour = 943, contour level = 0.03066 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.20794411 -0.61149238 -0.76343717 414.87568309 -0.26697774 -0.71538055 0.64571942 203.42240837 -0.94100060 0.33809428 -0.01449568 250.07835222 Axis -0.62168400 0.35884046 0.69623453 Axis point 300.38077372 74.09859277 0.00000000 Rotation angle (degrees) 165.67553333 Shift along axis -10.81220027 > select /N 903 atoms, 922 bonds, 109 residues, 1 model selected Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 903 atoms average map value = 0.03434, steps = 52 shifted from previous position = 0.869 rotated from previous position = 4.69 degrees atoms outside contour = 365, contour level = 0.03066 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.24163876 -0.58278597 -0.77586805 418.23265163 -0.33389716 -0.70080060 0.63038973 216.87762884 -0.91111108 0.41138673 -0.02524999 233.48173602 Axis -0.61165760 0.37772280 0.69512623 Axis point 297.47750506 71.69030385 0.00000000 Rotation angle (degrees) 169.68707388 Shift along axis -11.59627505 Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 903 atoms average map value = 0.03434, steps = 52 shifted from previous position = 0.869 rotated from previous position = 4.69 degrees atoms outside contour = 365, contour level = 0.03066 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.24163876 -0.58278597 -0.77586805 418.23265163 -0.33389716 -0.70080060 0.63038973 216.87762884 -0.91111108 0.41138673 -0.02524999 233.48173602 Axis -0.61165760 0.37772280 0.69512623 Axis point 297.47750506 71.69030385 0.00000000 Rotation angle (degrees) 169.68707388 Shift along axis -11.59627505 > volume #9 level 0.02315 Fit molecule 8h1t (#2) to map job149_run_class001_4.46A.mrc (#9) using 17365 atoms average map value = 0.05218, steps = 68 shifted from previous position = 2.31 rotated from previous position = 3.26 degrees atoms outside contour = 3341, contour level = 0.02315 Position of 8h1t (#2) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.20213510 -0.60700163 -0.76856388 415.10301458 -0.30219766 -0.70781072 0.63849867 210.40308740 -0.93156748 0.36132120 -0.04036108 250.71966046 Axis -0.62559675 0.36790337 0.68795045 Axis point 304.10399410 71.49954857 0.00000000 Rotation angle (degrees) 167.20105962 Shift along axis -9.79638843 > ui tool show ""Command Line Interface"" > open 1ubq 1ubq title: Structure of ubiquitin refined At 1.8 angstroms resolution [more info...] Chain information for #10 --- Chain | Description A | ubiquitin > select #10 660 atoms, 608 bonds, 134 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #10,1,0,0,174.52,0,1,0,181.95,0,0,1,110.84 > view matrix models #10,1,0,0,185.05,0,1,0,89.206,0,0,1,127.17 > view matrix models #10,1,0,0,196.16,0,1,0,101.46,0,0,1,174.23 > ui mousemode right ""rotate selected models"" > view matrix models > #10,-0.82351,-0.0038313,-0.56729,261.61,-0.56355,-0.10936,0.81881,138.19,-0.065176,0.99399,0.087899,161.77 > view matrix models > #10,-0.76264,0.12736,0.63416,234.39,0.63668,-0.025136,0.77072,100.07,0.1141,0.99154,-0.061916,159.07 Fit molecule 1ubq (#10) to map job149_run_class001_4.46A.mrc (#9) using 660 atoms average map value = 0.03339, steps = 116 shifted from previous position = 15.3 rotated from previous position = 43.1 degrees atoms outside contour = 193, contour level = 0.02315 Position of 1ubq (#10) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation 0.36567514 -0.66574960 -0.65042998 142.72529105 -0.35843437 0.54420056 -0.75853184 170.72600300 0.85895663 0.51051270 -0.03962692 52.18360007 Axis 0.63586180 -0.75628653 0.15398200 Axis point 107.91005288 0.00000000 143.84367550 Rotation angle (degrees) 93.71971072 Shift along axis -30.32888044 > volume #9 level 0.03331 > view matrix models > #10,-0.89195,0.43544,-0.12175,242.23,0.020557,0.30806,0.95115,105.27,0.45167,0.84587,-0.28372,157.27 > ui mousemode right ""translate selected models"" > view matrix models > #10,-0.89195,0.43544,-0.12175,242.21,0.020557,0.30806,0.95115,109.67,0.45167,0.84587,-0.28372,155.88 Fit molecule 1ubq (#10) to map job149_run_class001_4.46A.mrc (#9) using 660 atoms average map value = 0.03427, steps = 92 shifted from previous position = 3.06 rotated from previous position = 39.7 degrees atoms outside contour = 288, contour level = 0.033311 Position of 1ubq (#10) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation -0.13258148 -0.93511642 0.32860222 157.62955614 0.68580230 -0.32590484 -0.65073900 166.84812706 0.71560978 0.13908022 0.68451394 49.29275993 Axis 0.42827873 -0.20985448 0.87894165 Axis point -2.31223012 136.64161231 0.00000000 Rotation angle (degrees) 112.76710095 Shift along axis 75.82101791 > select clear > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job149 Refine > bin2/job149_map and model.cxs"" includeMaps true > close #1,3-7 > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job149 Refine > bin2/job149_map and model.cxs"" includeMaps true > volume #9 level 0.02475 > volume #8 level 0.1448 > volume #8 level 0.09928 > volume #8 level 0.1708 > volume #8 level 0.147 > select ::name=""CYS"" 48 atoms, 40 bonds, 8 residues, 1 model selected > select clear > volume #9 level 0.02989 > volume #9 level 0.02175 > volume #9 level 0.05772 > volume #9 level 0.04402 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job151 Refine > bin1 57.8Ww 3.43W/run_class001.mrc"" Opened run_class001.mrc as #1, grid size 256,256,256, pixel 1.1, shown at level 0.00696, step 1, values float32 > select #1 2 models selected > view matrix models #1,1,0,0,8.7638,0,1,0,1.6233,0,0,1,22.107 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.03523,-0.50961,-0.85969,339.24,-0.659,-0.63485,0.40334,273.55,-0.75132,0.58074,-0.31347,217.31 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.03523,-0.50961,-0.85969,368.01,-0.659,-0.63485,0.40334,264.77,-0.75132,0.58074,-0.31347,230.22 > view matrix models > #1,-0.03523,-0.50961,-0.85969,378.65,-0.659,-0.63485,0.40334,299.13,-0.75132,0.58074,-0.31347,237.58 > view matrix models > #1,-0.03523,-0.50961,-0.85969,381.77,-0.659,-0.63485,0.40334,297.49,-0.75132,0.58074,-0.31347,234.6 Fit map run_class001.mrc in map job149_run_class001_4.46A.mrc using 167671 points correlation = 0.9884, correlation about mean = 0.937, overlap = 162.2 steps = 100, shift = 5.97, angle = 15.1 degrees Position of run_class001.mrc (#1) relative to job149_run_class001_4.46A.mrc (#9) coordinates: Matrix rotation and translation 0.99989284 -0.01348029 -0.00570862 2.81034906 0.01349390 0.99990619 0.00235266 -2.30743279 0.00567637 -0.00242944 0.99998094 -0.93663428 Axis -0.16119593 -0.38376750 0.90925155 Axis point 184.32278969 202.00113952 0.00000000 Rotation angle (degrees) 0.84991014 Shift along axis -0.41913528 > hide #!9 models > transparency sel 50 > select clear > close #9 > show #!8 models > hide #!1 models > show #!1 models Fit map run_class001.mrc in map emdb 35182 using 167671 points correlation = 0.9392, correlation about mean = 0.7508, overlap = 746.6 steps = 48, shift = 0.0393, angle = 0.0285 degrees Position of run_class001.mrc (#1) relative to emdb 35182 (#8) coordinates: Matrix rotation and translation -0.21231165 -0.29847789 -0.93050240 382.32214675 -0.61322651 -0.70068711 0.36467906 309.49276413 -0.76083967 0.64803436 -0.03427052 191.37941737 Axis 0.62108509 -0.37188290 -0.68989595 Axis point 302.93039272 70.63664063 0.00000000 Rotation angle (degrees) 166.81399207 Shift along axis -9.67236664 Fit map run_class001.mrc in map emdb 35182 using 167671 points correlation = 0.9392, correlation about mean = 0.7507, overlap = 746.6 steps = 48, shift = 0.0228, angle = 0.0172 degrees Position of run_class001.mrc (#1) relative to emdb 35182 (#8) coordinates: Matrix rotation and translation -0.21221175 -0.29829448 -0.93058400 382.27801023 -0.61342455 -0.70062361 0.36446795 309.55502898 -0.76070789 0.64818745 -0.03430060 191.33446074 Axis 0.62110914 -0.37188703 -0.68987207 Axis point 302.93309814 70.63807057 -0.00000000 Rotation angle (degrees) 166.79725799 Shift along axis -9.67943583 Fit molecule 8h1t (#2) to map emdb 35182 (#8) using 17365 atoms average map value = 0.3408, steps = 44 shifted from previous position = 0.057 rotated from previous position = 0.047 degrees atoms outside contour = 2653, contour level = 0.14697 Position of 8h1t (#2) relative to emdb 35182 (#8) coordinates: Matrix rotation and translation 0.99999864 0.00149315 0.00069727 -0.37820928 -0.00149268 0.99999866 -0.00066961 0.35972914 -0.00069827 0.00066857 0.99999953 0.00332282 Axis 0.37619080 0.39231738 -0.83938522 Axis point 241.80430793 252.52367144 0.00000000 Rotation angle (degrees) 0.10190529 Shift along axis -0.00393999 Fit molecule 1ubq (#10) to map run_class001.mrc (#1) using 660 atoms average map value = 0.009062, steps = 80 shifted from previous position = 0.291 rotated from previous position = 1.61 degrees atoms outside contour = 209, contour level = 0.0069642 Position of 1ubq (#10) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.11608350 -0.94174178 0.31566918 157.53510623 0.70546341 -0.30189800 -0.64123237 165.89216253 0.69917521 0.14825657 0.69940975 49.66349923 Axis 0.42298845 -0.20547295 0.88253138 Axis point -3.76561599 137.43736452 0.00000000 Rotation angle (degrees) 111.05634547 Shift along axis 76.37877478 > hide #!1 models > show #!1 models > volume #1 level 0.009643 > volume #1 level 0.01034 > hide #!8 models > volume #1 level 0.008478 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.01526, steps = 40 shifted from previous position = 0.0317 rotated from previous position = 0.0681 degrees atoms outside contour = 4776, contour level = 0.0084782 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.21145685 -0.61351649 -0.76084396 416.48603296 -0.29827318 -0.70080529 0.64800081 206.94115048 -0.93076265 0.36396356 -0.03480543 249.69291717 Axis -0.62140839 0.37174315 0.68968010 Axis point 303.05533602 70.63883455 0.00000000 Rotation angle (degrees) 166.78868456 Shift along axis -9.67072658 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.01526, steps = 44 shifted from previous position = 0.0124 rotated from previous position = 0.0115 degrees atoms outside contour = 4773, contour level = 0.0084782 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.21143857 -0.61367434 -0.76072173 416.48544831 -0.29822791 -0.70069461 0.64814132 206.89677658 -0.93078131 0.36391053 -0.03486095 249.70691032 Axis -0.62140666 0.37179700 0.68965263 Axis point 303.05602496 70.62591450 -0.00000000 Rotation angle (degrees) 166.77948178 Shift along axis -9.67220051 > select #2/L 2433 atoms, 2487 bonds, 2 pseudobonds, 301 residues, 2 models selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 2433 atoms average map value = 0.009533, steps = 68 shifted from previous position = 2.2 rotated from previous position = 2.15 degrees atoms outside contour = 1032, contour level = 0.0084782 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.21986908 -0.61430897 -0.75781401 416.58755140 -0.26308600 -0.71070142 0.65244865 200.88172401 -0.93938455 0.34282355 -0.00535482 247.90702448 Axis -0.61655174 0.36155864 0.69938494 Axis point 298.88551366 73.75135875 0.00000000 Rotation angle (degrees) 165.45773086 Shift along axis -10.83481508 > select clear > select #2/N 903 atoms, 922 bonds, 109 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 903 atoms average map value = 0.009329, steps = 68 shifted from previous position = 0.812 rotated from previous position = 3.38 degrees atoms outside contour = 389, contour level = 0.0084782 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.24506651 -0.59430236 -0.76599420 419.01621102 -0.31120687 -0.70005479 0.64270799 210.42817241 -0.91820078 0.39588887 -0.01339100 236.25229875 Axis -0.60905023 0.37558458 0.69856570 Axis point 296.77188620 71.91015579 0.00000000 Rotation angle (degrees) 168.30942308 Shift along axis -11.13059129 > select clear > volume #1 level 0.002306 > volume #1 level 0.008245 > volume #1 level 0.006848 > volume #1 level 0.007081 > volume #1 level 0.007896 > volume #1 level 0.006615 > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job151 Refine > bin1 57.8Ww 3.43W/job151_map and model.cxs"" includeMaps true ——— End of log from Thu Jun 29 10:10:27 2023 ——— opened ChimeraX session > select #2/K 520 atoms, 523 bonds, 73 residues, 1 model selected > hide sel cartoons > select clear > lighting soft > lighting simple > select #1 2 models selected > transparency #1.1 40 > select clear > volume #1 level 0.007896 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class006.mrc"" Opened run_it021_class006.mrc as #3, grid size 256,256,256, pixel 1.1, shown at level 4.31e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class001.mrc"" Opened run_it021_class001.mrc as #4, grid size 256,256,256, pixel 1.1, shown at level 4.04e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class002.mrc"" Opened run_it021_class002.mrc as #5, grid size 256,256,256, pixel 1.1, shown at level 4.76e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class003.mrc"" Opened run_it021_class003.mrc as #6, grid size 256,256,256, pixel 1.1, shown at level 2.76e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class004.mrc"" Opened run_it021_class004.mrc as #7, grid size 256,256,256, pixel 1.1, shown at level 1.85e-06, step 1, values float32 > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job157 3D > bin1 no alignment mask UPD T=20/run_it021_class005.mrc"" Opened run_it021_class005.mrc as #9, grid size 256,256,256, pixel 1.1, shown at level 2.1e-06, step 1, values float32 > ui tool show ""Command Line Interface"" > volume all level 0.008 > close #3-7,9 > volume #1 level 0.01027 > volume #1 level 0.009071 > select #2/L 2433 atoms, 2487 bonds, 2 pseudobonds, 301 residues, 2 models selected > ui tool show ""Fit in Map"" Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 2433 atoms average map value = 0.009533, steps = 72 shifted from previous position = 1.32 rotated from previous position = 3.38 degrees atoms outside contour = 1167, contour level = 0.0090706 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.22006435 -0.61436338 -0.75771322 416.60394012 -0.26306176 -0.71060204 0.65256666 200.84393052 -0.93934562 0.34293203 -0.00523734 247.86391439 Axis -0.61646851 0.36162188 0.69942562 Axis point 298.85499338 73.74213259 0.00000000 Rotation angle (degrees) 165.45526674 Shift along axis -10.83127884 > select clear > select #2/L:126 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #10/A:11 15 atoms, 13 bonds, 2 residues, 2 models selected > select add #2/L:118 26 atoms, 24 bonds, 3 residues, 2 models selected > select add #2/L:114 37 atoms, 34 bonds, 4 residues, 2 models selected > cofr sel > volume #1 level 0.01081 > select #10/A:8 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/A:9 15 atoms, 13 bonds, 2 residues, 1 model selected Fit molecule 1ubq (#10) to map run_class001.mrc (#1) using 660 atoms average map value = 0.009062, steps = 44 shifted from previous position = 0.0103 rotated from previous position = 0.0333 degrees atoms outside contour = 430, contour level = 0.01081 Position of 1ubq (#10) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.11634722 -0.94156449 0.31610067 157.52391787 0.70524706 -0.30241731 -0.64122566 165.90768674 0.69934962 0.14832426 0.69922100 49.66305610 Axis 0.42310599 -0.20537641 0.88249751 Axis point -3.74330323 137.40539977 0.00000000 Rotation angle (degrees) 111.08617962 Shift along axis 76.40331190 Fit molecule 1ubq (#10) to map run_class001.mrc (#1) using 660 atoms average map value = 0.009062, steps = 40 shifted from previous position = 0.0219 rotated from previous position = 0.0604 degrees atoms outside contour = 430, contour level = 0.01081 Position of 1ubq (#10) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.11655578 -0.94186914 0.31511468 157.56738459 0.70527226 -0.30188253 -0.64144989 165.91215464 0.69928948 0.14747696 0.69946034 49.68385481 Axis 0.42272272 -0.20584851 0.88257118 Axis point -3.73963179 137.47920654 0.00000000 Rotation angle (degrees) 111.06881635 Shift along axis 76.30408258 > select clear > select #10/A:8 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #10/A:9 15 atoms, 13 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > select #2/L:115 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > select add #2/L:114 19 atoms, 17 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 19 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:115 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > ~label sel residues > select clear > select #2/L:111 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #2/L:118 18 atoms, 17 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 18 atom styles > volume #1 level 0.01068 > volume #1 level 0.01054 > volume #1 level 0.00974 > volume #1 level 0.009204 > volume #1 level 0.009071 > volume #1 level 0.009204 > volume #1 level 0.009338 > volume #1 level 0.009606 > volume #1 level 0.009071 > select #10/A:69 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > color sel byhetero > hide sel atoms > select #10/A:7 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/L:118 11 atoms, 11 bonds, 1 residue, 1 model selected > color sel byhetero > select #10/A:7 7 atoms, 6 bonds, 1 residue, 1 model selected > select #10/A:8 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > color sel byhetero > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:118 11 atoms, 11 bonds, 1 residue, 1 model selected > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:9 7 atoms, 6 bonds, 1 residue, 1 model selected > select #10/A:7 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > select #10/A:9 7 atoms, 6 bonds, 1 residue, 1 model selected > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:47 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #10/A:46 9 atoms, 7 bonds, 2 residues, 1 model selected > show sel atoms > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:48 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > volume #1 level 0.007465 > volume #1 level 0.008134 > select #10/A:68 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #2/L:117 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 8 atom styles > color sel byhetero > volume #1 level 0.0085 > select #2/L:117 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #2/L:117 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #10/A:68 10 atoms, 10 bonds, 1 residue, 1 model selected > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > volume #1 level 0.0084 > volume #1 level 0.0083 > volume #1 level 0.0082 > select #2/L:122 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:121 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > show sel atoms > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:123 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 6 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > color sel byhetero > color sel byhetero > select clear > volume #1 level 0.008 > volume #1 level 0.007866 > select #2/L:123 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > volume #1 level 0.008535 > volume #1 level 0.01215 > volume #1 level 0.009472 > select #10/A:71 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #10/A:72 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #10/A:70 18 atoms, 16 bonds, 2 residues, 1 model selected > show sel atoms > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:71 8 atoms, 7 bonds, 1 residue, 1 model selected > cofr sel > select #2/L:129 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #2/L:130 17 atoms, 16 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 17 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > color sel byhetero > select #10/A:71 8 atoms, 7 bonds, 1 residue, 1 model selected > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #10/A:70 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select #2/L:130 5 atoms, 4 bonds, 1 residue, 1 model selected > volume #1 level 0.01081 > select #10/A:35 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > show sel atoms > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select clear > volume #1 level 0.009472 > ui tool show ""Side View"" > select #2/L:126 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 6 atom styles > color sel byhetero > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select clear > select #2/N:345 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > select add #2/N:331 19 atoms, 18 bonds, 2 residues, 1 model selected > select add #2/N:335 26 atoms, 24 bonds, 3 residues, 1 model selected > select add #2/N:338 37 atoms, 34 bonds, 4 residues, 1 model selected > select add #2/N:342 46 atoms, 42 bonds, 5 residues, 1 model selected > select add #2/N:349 55 atoms, 50 bonds, 6 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 55 atoms average map value = 0.01109, steps = 132 shifted from previous position = 6.72 rotated from previous position = 14.5 degrees atoms outside contour = 16, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.22679911 -0.46135157 -0.85773941 416.21434935 -0.45848542 -0.72642649 0.51195279 269.58911283 -0.85927485 0.50937146 -0.04677008 207.75394959 Axis -0.62177001 0.36984489 0.69037440 Axis point 301.45461119 79.45150457 0.00000000 Rotation angle (degrees) 179.88106587 Shift along axis -15.65543721 > select add #2/N:324 63 atoms, 57 bonds, 7 residues, 1 model selected > select add #2/N:334 72 atoms, 65 bonds, 8 residues, 1 model selected > select add #2/N:336 83 atoms, 75 bonds, 9 residues, 1 model selected > select add #2/N:339 92 atoms, 83 bonds, 10 residues, 1 model selected > select add #2/N:340 101 atoms, 91 bonds, 11 residues, 1 model selected > select add #2/N:341 109 atoms, 98 bonds, 12 residues, 1 model selected > select add #2/N:343 118 atoms, 106 bonds, 13 residues, 1 model selected > select add #2/N:344 127 atoms, 114 bonds, 14 residues, 1 model selected > select add #2/N:346 136 atoms, 122 bonds, 15 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 136 atoms average map value = 0.009299, steps = 112 shifted from previous position = 3.31 rotated from previous position = 31.3 degrees atoms outside contour = 72, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.54854460 -0.68144385 -0.48449263 434.37846586 -0.26493939 -0.40793243 0.87372664 103.58900598 -0.79303590 0.60763922 0.04322781 157.52609050 Axis -0.45668726 0.52955445 0.71484882 Axis point 255.01502382 37.21410113 0.00000000 Rotation angle (degrees) 163.06279391 Shift along axis -30.91175146 > select subtract #2/N:324 128 atoms, 115 bonds, 14 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 128 atoms average map value = 0.009396, steps = 164 shifted from previous position = 0.48 rotated from previous position = 26.3 degrees atoms outside contour = 65, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.58314546 -0.80979090 -0.06465348 373.75155416 0.08263785 -0.13830574 0.98693591 -31.07419828 -0.80815367 0.57018438 0.14757174 144.42595520 Axis -0.33770775 0.60248314 0.72316495 Axis point 222.19196350 10.26599477 0.00000000 Rotation angle (degrees) 141.90043719 Shift along axis -40.49668693 > select add #2/N:332 137 atoms, 123 bonds, 15 residues, 1 model selected > select add #2/N:333 145 atoms, 130 bonds, 16 residues, 1 model selected > select add #2/N:337 153 atoms, 137 bonds, 17 residues, 1 model selected > select add #2/N:347 160 atoms, 143 bonds, 18 residues, 1 model selected > select add #2/N:348 169 atoms, 151 bonds, 19 residues, 1 model selected > select add #2/N:330 176 atoms, 157 bonds, 20 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 176 atoms average map value = 0.009365, steps = 268 shifted from previous position = 5.34 rotated from previous position = 11 degrees atoms outside contour = 97, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.53769066 -0.83474919 0.11866990 332.11649342 0.20514812 0.00699217 0.97870596 -74.88971818 -0.81780376 0.55058597 0.16748760 140.53317326 Axis -0.29254363 0.63991266 0.71058427 Axis point 209.05625591 -3.08645029 0.00000000 Rotation angle (degrees) 132.96922611 Shift along axis -45.22078002 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.79044,-0.3104,-0.52808,209.19,-0.16217,0.7253,-0.66906,207.84,0.59069,0.61449,0.52297,-121.67 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 176 atoms average map value = 0.009364, steps = 184 shifted from previous position = 6.68 rotated from previous position = 0.618 degrees atoms outside contour = 97, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.53955657 -0.83493074 0.10848677 334.63450154 0.19710722 0.00000955 0.98038193 -72.54681288 -0.81855205 0.55035504 0.16456571 141.33905594 Axis -0.29608297 0.63828660 0.71058081 Axis point 210.04307592 -2.45330610 0.00000000 Rotation angle (degrees) 133.43179879 Shift along axis -44.95241310 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.00913, steps = 344 shifted from previous position = 39.6 rotated from previous position = 27.8 degrees atoms outside contour = 10500, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.42319264 -0.90134436 -0.09212134 391.69050858 -0.26615742 0.02648366 0.96356569 20.28057429 -0.86606478 0.43229269 -0.25110718 266.35591441 Axis -0.46872332 0.68282284 0.56040290 Axis point 266.02012591 0.00000000 37.92016898 Rotation angle (degrees) 145.47794330 Shift along axis -20.47980838 > select clear > undo > undo > undo > select clear Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.00913, steps = 348 shifted from previous position = 39.9 rotated from previous position = 28.2 degrees atoms outside contour = 10507, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.42309183 -0.90136967 -0.09233647 391.72527440 -0.26619746 0.02624242 0.96356123 20.34755272 -0.86610173 0.43225462 -0.25104528 266.34013870 Axis -0.46880019 0.68273440 0.56044635 Axis point 266.05958798 0.00000000 37.87485409 Rotation angle (degrees) 145.48191253 Shift along axis -20.47954876 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.00913, steps = 40 shifted from previous position = 0.0192 rotated from previous position = 0.0135 degrees atoms outside contour = 10503, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.42320873 -0.90133480 -0.09214096 391.69900415 -0.26614795 0.02646294 0.96356887 20.28617899 -0.86605983 0.43231389 -0.25108776 266.34317035 Axis -0.46871788 0.68281639 0.56041532 Axis point 266.02258135 0.00000000 37.91101818 Rotation angle (degrees) 145.47882181 Shift along axis -20.48179714 > select #2 17365 atoms, 18360 bonds, 434 pseudobonds, 1657 residues, 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.99418,-0.057605,-0.091013,24.765,-0.024208,0.70385,-0.70994,174.14,0.10496,0.70801,0.69836,-100.68 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.00913, steps = 96 shifted from previous position = 0.979 rotated from previous position = 7.99 degrees atoms outside contour = 10497, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.42318072 -0.90135053 -0.09211574 391.69024564 -0.26616934 0.02649190 0.96356217 20.28315134 -0.86606695 0.43227932 -0.25112275 266.35812727 Axis -0.46872924 0.68282566 0.56039452 Axis point 266.02177032 0.00000000 37.92034576 Rotation angle (degrees) 145.47771035 Shift along axis -20.48118161 > select clear > view > select #2 17365 atoms, 18360 bonds, 434 pseudobonds, 1657 residues, 4 models selected > view matrix models > #2,0.92475,0.059199,-0.37594,69.837,-0.1112,0.98675,-0.11816,30.193,0.36397,0.15107,0.91908,-90.907 Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 17365 atoms average map value = 0.01526, steps = 160 shifted from previous position = 9.71 rotated from previous position = 21.8 degrees atoms outside contour = 5484, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.21139736 -0.61362839 -0.76077024 416.48922441 -0.29826333 -0.70073363 0.64808283 206.91982160 -0.93077931 0.36391287 -0.03488961 249.70846855 Axis -0.62142677 0.37177819 0.68964465 Axis point 303.06569089 70.63125323 0.00000000 Rotation angle (degrees) 166.78279792 Shift along axis -9.67916697 > select clear > select #2/K 520 atoms, 523 bonds, 73 residues, 1 model selected > select #2/N 903 atoms, 922 bonds, 109 residues, 1 model selected Fit molecule 8h1t (#2) to map run_class001.mrc (#1) using 903 atoms average map value = 0.009329, steps = 56 shifted from previous position = 1.84 rotated from previous position = 2.36 degrees atoms outside contour = 474, contour level = 0.009472 Position of 8h1t (#2) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation -0.24500346 -0.59414162 -0.76613905 419.01021599 -0.31141625 -0.70012214 0.64253318 210.50677733 -0.91814662 0.39601101 -0.01349301 236.24865723 Axis -0.60909025 0.37556999 0.69853866 Axis point 296.79220093 71.91220442 0.00000000 Rotation angle (degrees) 168.32446430 Shift along axis -11.12618967 > cofr sel > select clear > select #2/N:334 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > select #2/N:345 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > volume #1 level 0.008 > select #2/L:3 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/L:4 13 atoms, 11 bonds, 2 residues, 1 model selected > show sel atoms > style sel stick Changed 13 atom styles > color sel byhetero > open ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job162 3D > bin1 no alignment mask UPD T=6/run_it051_class004.mrc"" Opened run_it051_class004.mrc as #3, grid size 256,256,256, pixel 1.1, shown at level 0.000119, step 1, values float32 > volume all level 0.008 > select #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,87.213,0,1,0,38.442,0,0,1,56.058 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.63535,0.17203,-0.75282,346.94,-0.61256,-0.70587,0.35568,321.57,-0.4702,0.68713,0.55386,63.797 > view matrix models > #3,-0.54923,0.82372,-0.14079,169.11,0.10116,0.23278,0.96725,25.979,0.82952,0.51701,-0.21118,21.764 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.54923,0.82372,-0.14079,171.23,0.10116,0.23278,0.96725,-7.7473,0.82952,0.51701,-0.21118,32.289 > view matrix models > #3,-0.54923,0.82372,-0.14079,169.56,0.10116,0.23278,0.96725,1.4665,0.82952,0.51701,-0.21118,34.665 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.042524,-0.096128,-0.99446,343.7,-0.66599,-0.73923,0.099935,338.32,-0.74474,0.66655,-0.032585,181.39 Fit map run_it051_class004.mrc in map run_class001.mrc using 45707 points correlation = 0.9642, correlation about mean = 0.7507, overlap = 8.193 steps = 128, shift = 8.6, angle = 19.4 degrees Position of run_it051_class004.mrc (#3) relative to run_class001.mrc (#1) coordinates: Matrix rotation and translation 0.99999852 -0.00051399 -0.00164086 0.66727054 0.00050899 0.99999521 -0.00304965 0.37791816 0.00164242 0.00304880 0.99999400 -0.29730557 Axis 0.87105144 -0.46895615 0.14611476 Axis point 0.00000000 115.14777973 179.18622894 Rotation angle (degrees) 0.20057144 Shift along axis 0.36055919 > select clear > graphics silhouettes false > graphics silhouettes true > lighting soft > hide #!1 models > transparency #3.1 50 > select clear > transparency #3.1 50 > select clear > transparency #3.1 50 > select clear > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > select #3 2 models selected > transparency sel 0 > volume #3 level 0.01069 > select clear > volume #3 level 0.009991 > volume #3 level 0.009405 > hide #!1 models > transparency #3.1 50 > select clear > select #2/N:351 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 9 atom styles > color sel byhetero > cofr sel > volume #3 level 0.008234 > volume #3 level 0.004721 > volume #3 level 0.003316 > volume #3 level 0.004253 > volume #3 level 0.006243 > volume #3 level 0.005541 > select #2/L:91 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > style sel stick Changed 6 atom styles > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > volume #3 level 0.0135 > volume #3 level 0.008351 > volume #3 level 0.006829 > volume #3 level 0.005072 > volume #3 level 0.006 > volume #3 level 0.0056 > volume #3 level 0.008528 > select #10/A:74 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > hide sel atoms > volume #3 level 0.005834 > volume #3 level 0.009816 > hide #!3 models > show #!1 models > save ""C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job151 Refine > bin1 57.8Ww 3.43A, 3.34A/job151_map and model-002.cxs"" includeMaps true ——— End of log from Sat Jul 1 11:38:15 2023 ——— opened ChimeraX session > hide #!1 models > color sel bynucleotide Alignment identifier is 10/A [Repeated 1 time(s)]Destroying pre-existing alignment with identifier 10/A Alignment identifier is 10/A Destroying pre-existing alignment with identifier 10/A Alignment identifier is 10/A > select add #2 17376 atoms, 18370 bonds, 434 pseudobonds, 1658 residues, 5 models selected Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 2/I Alignment identifier is 2/J Alignment identifier is 2/K Alignment identifier is 2/L Alignment identifier is 5 Alignment identifier is 2/N > select #2/L:82-83 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2/L:82-106 183 atoms, 186 bonds, 25 residues, 1 model selected > color sel blue > select #2/L:123 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/L:123-138 112 atoms, 114 bonds, 16 residues, 1 model selected > color sel blue > select #2/N:312 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/N:312-326 130 atoms, 134 bonds, 15 residues, 1 model selected > color sel blue > save /Users/zhangtianyi/T/LiuLab/课题/ASXL/质谱送样-zty/PR-DUB-Ub-HDXlow- > blueed.tif width 649 height 787 supersample 3 > save /Users/zhangtianyi/T/LiuLab/课题/ASXL/质谱送样-zty/PR-DUB-Ub-HDXlow- > blueed.cxs ——— End of log from Wed Jul 10 17:09:03 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 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: MacBookPro17,1 Model Number: MYD92CH/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 28天13小时3分钟 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-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 closed normal Window Toolkit duplicate all ChimeraX