![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 16 months ago
Closed 16 months ago
#15609 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
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
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{
"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"
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"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. Bytes before following region: 4337713128\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1028c4000-1028c8000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1333},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4337713128\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1028c4000-1028c8000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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"logWritingSignature" : "3d95b3cc1db0787918d90bd62950aef5c16d025b",
"trialInfo" : {
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{
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"factorPackIds" : {
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"factorPackIds" : {
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"experimentId" : "6639bc6ba73d460582162323",
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{
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"experimentId" : "662152ede2d11d1408c4db33",
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}
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}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open /Users/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
Change History (2)
comment:1 by , 16 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 16 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Tianyi,
--Eric