MemoryError saving session

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

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

> open "F:\\\Study\\\Documents\\\Work Progress\\\PR-DUB\\\电镜密度\\\job151_map
> and model-003 colored-.cxs"

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  
Opened run_class001.mrc 0 as #3.1, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 1 as #3.2, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 2 as #3.3, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 3 as #3.4, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 4 as #3.5, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 5 as #3.6, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 6 as #3.7, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 7 as #3.8, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 8 as #3.9, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 9 as #3.10, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 10 as #3.11, grid size 256,256,256, pixel 1.1, shown
at level 0.00661, step 1, values float32  
Opened run_class001.mrc 11 as #3.12, grid size 256,256,256, pixel 1.1, shown
at level 0.00661, step 1, values float32  
Opened run_class001.mrc 12 as #3.13, grid size 256,256,256, pixel 1.1, shown
at level 0.00661, step 1, values float32  
Opened run_class001.mrc 13 as #3.14, grid size 256,256,256, pixel 1.1, shown
at level 0.00661, step 1, values float32  
Log from Mon Jul 3 12:00:20 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"

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/N

903 atoms, 922 bonds, 109 residues, 1 model selected  

> select #2/K

520 atoms, 523 bonds, 73 residues, 1 model selected  

> hide sel cartoons

Drag select of 18 residues, 1 run_class001.mrc  

> select clear

Drag select of 18 residues, 1 run_class001.mrc  

> hide #!1 models

> show #!1 models

> select clear

Drag select of 14 residues  
Drag select of 13 residues  

> hide sel cartoons

> select #2/I

3398 atoms, 3805 bonds, 167 residues, 1 model selected  

> color sel dark gray

> select #2/J

3449 atoms, 3875 bonds, 167 residues, 1 model selected  

> color sel dark gray

> select clear

> lighting soft

> lighting simple

> lighting soft

> hide #!1 models

> select clear

Drag select of 1633 residues, 2 pseudobonds  

> show #!1 models

> ui tool show "Color Zone"

> color zone #1 near sel distance 6.59

> color zone #1 near sel distance 13.09

> color zone #1 near sel distance 13

> color zone #1 near sel distance 3.27

> volume splitbyzone #1

Opened run_class001.mrc 0 as #3.1, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 1 as #3.2, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 2 as #3.3, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 3 as #3.4, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 4 as #3.5, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 5 as #3.6, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 6 as #3.7, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 7 as #3.8, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 8 as #3.9, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 9 as #3.10, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 10 as #3.11, grid size 256,256,256, pixel 1.1, shown
at level 0.00661, step 1, values float32  
Opened run_class001.mrc 11 as #3.12, grid size 256,256,256, pixel 1.1, shown
at level 0.00661, step 1, values float32  
Opened run_class001.mrc 12 as #3.13, grid size 256,256,256, pixel 1.1, shown
at level 0.00661, step 1, values float32  
Opened run_class001.mrc 13 as #3.14, grid size 256,256,256, pixel 1.1, shown
at level 0.00661, step 1, values float32  

> hide #!3.1 models

> select clear

> transparency
> #3.2.1#3.3.1#3.4.1#3.5.1#3.6.1#3.7.1#3.8.1#3.9.1#3.10.1#3.11.1#3.12.1#3.13.1#3.14.1
> 50

> select clear

> save "C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job151 Refine
> bin1 57.8Ww 3.43A, 3.34A/job151_map and model-003 colored.cxs" includeMaps
> true

Drag select of 7 residues  

> hide sel cartoons

Drag select of 2 residues  

> hide sel cartoons

> transparency
> #3.2.1#3.3.1#3.4.1#3.5.1#3.6.1#3.7.1#3.8.1#3.9.1#3.10.1#3.11.1#3.12.1#3.13.1#3.14.1
> 0

> transparency
> #3.2.1#3.3.1#3.4.1#3.5.1#3.6.1#3.7.1#3.8.1#3.9.1#3.10.1#3.11.1#3.12.1#3.13.1#3.14.1
> 50

> ui tool show "Side View"

> save "C:/Users/Lenovo/Desktop/20230617_H2AK119Ub-AT2-Ub-PR-DUB/job151 Refine
> bin1 57.8Ww 3.43A, 3.34A/job151_map and model-003 colored-.cxs" includeMaps
> true

——— End of log from Mon Jul 3 12:00:20 2023 ———

opened ChimeraX session  

> select add #1

44 atoms, 2 residues, 3 models selected  

> view

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!2 models

> hide #!3 models

> select clear

> show #!8 models

> hide #!8 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #2 /g

838 atoms, 848 bonds, 109 residues, 1 model selected  

> color sel forest green

> ui tool show "Color Actions"

> color sel medium aquamarine

> color sel medium sea green

> select #2 /c

858 atoms, 868 bonds, 111 residues, 1 model selected  

> color sel medium sea green

> select #2 /d,h

1474 atoms, 1496 bonds, 188 residues, 1 model selected  

> color sel peach puff

> color sel navajo white

> color sel moccasin

> select #2 /a,e

1597 atoms, 1621 bonds, 194 residues, 1 model selected  

> color sel royal blue

> color sel cornflower blue

> select #2 /b,f

1294 atoms, 1308 bonds, 162 residues, 1 model selected  

> color sel salmon

> select clear

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> ui tool show "Color Zone"

> color zone #3.2 near #2 distance 6.59

> hide #!3 models

> hide #10 models

> show #10 models

Drag select of 1624 residues, 2 pseudobonds  

> show #!3 models

> color zone #3.2 near sel distance 6.59

[Repeated 3 time(s)]

> color single #3.2

> color zone #3.2 near sel distance 6.59

[Repeated 2 time(s)]

> transparency (#10#!2 & sel) 0

> select clear

> select add #3

29 models selected  

> color #3 #ffaaffff models

> hide #!3 models

Drag select of 1624 residues, 2 pseudobonds  

> show #!3 models

> color zone #3.2 near sel distance 6.59

[Repeated 4 time(s)]

> color zone #3.2 near sel distance 51.05

> color zone #1 near sel distance 3.96

> color zone #1 near sel distance 6.92

> show #!1 models

> hide #!3 models

> color zone #1 near sel distance 3.31

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> color zone #1 near sel distance 6.01

> volume splitbyzone #1

Opened run_class001.mrc 0 as #4.1, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 1 as #4.2, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 2 as #4.3, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 3 as #4.4, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 4 as #4.5, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 5 as #4.6, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 6 as #4.7, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 7 as #4.8, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 8 as #4.9, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  
Opened run_class001.mrc 9 as #4.10, grid size 256,256,256, pixel 1.1, shown at
level 0.00661, step 1, values float32  

> hide #!4.6 models

> show #!4.6 models

> hide #!4.8 models

> show #!4.8 models

> hide #!2 models

> show #!2 models

> hide #!4 models

> show #!4 models

> 2021年12月24日

Unknown command: 2021年12月24日  

> 11:31

Unknown command: 11:31  

> volume all level 0.008 step 1

> hide #!4.1 models

> show #!4.1 models

> hide #!4.1 models

> hide #!4.2 models

> show #!4.2 models

> select clear

> graphics silhouettes true width 4

> graphics silhouettes true width 3

> hide #!2 models

> hide #10 models

> lighting soft

[Repeated 1 time(s)]

> lighting simple

> lighting soft

> lighting soft intensity 0.4

> save "F:/Study/Documents/Work Progress/PR-DUB/电镜密度/20231009-TZB-Color.cxs"
> includeMaps true

Traceback (most recent call last):  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
630, in save  
fserialize(stream, data)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\serialize.py",
line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\commands\run.py",
line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
630, in save  
fserialize(stream, data)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\serialize.py",
line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  

> save "F:/Study/Documents/Work Progress/PR-DUB/电镜密度/1.cxs" includeMaps true

Traceback (most recent call last):  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
630, in save  
fserialize(stream, data)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\serialize.py",
line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\commands\run.py",
line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
630, in save  
fserialize(stream, data)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\serialize.py",
line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> save "F:/Study/Documents/Work Progress/PR-DUB/电镜密度/1.cxs"

Traceback (most recent call last):  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
630, in save  
fserialize(stream, data)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\serialize.py",
line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\commands\run.py",
line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\save_command\cmd.py",
line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "E:\ChimeraX.1.6.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\session.py", line
630, in save  
fserialize(stream, data)  
File "E:\ChimeraX.1.6.1\bin\lib\site-packages\chimerax\core\serialize.py",
line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 304, in msgpack._cmsgpack.Packer.pack  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 537.42
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: ROG Strix G614JV_G614JV
OS: Microsoft Windows 11 家庭中文版 (Build 22621)
Memory: 16,780,587,008
MaxProcessMemory: 137,438,953,344
CPU: 20 13th Gen Intel(R) Core(TM) i7-13650HX
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    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: 2023.5.7
    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
    comtypes: 1.1.14
    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: 2022.9.26
    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: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    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
    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
    pywin32: 305
    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
    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
    WMI: 1.5.1
    zipp: 3.15.0