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Opened 3 years ago
Last modified 3 years ago
#7540 feedback defect
QObject::~QObject: Timers cannot be stopped from another thread
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19043
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x80000003
Thread 0x0000254c (most recent call first):
File "D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 55 in create_profile
File "D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 391 in create_chimerax_profile
File "D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\widgets\htmlview.py", line 367 in __init__
File "D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\file_history.py", line 103 in __init__
File "D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\file_history.py", line 26 in __init__
File "D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 481 in __init__
File "D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\ui\gui.py", line 220 in build
File "D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 688 in init
File "D:\Program Files\ChimeraX 1.3\bin\lib\site-packages\ChimeraX_main.py", line 1018 in
File "D:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 87 in _run_code
File "D:\Program Files\ChimeraX 1.3\bin\lib\runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
QObject::~QObject: Timers cannot be stopped from another thread
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open D:\\\SIMM_CHM\\\A2b\\\Figure\\\binding_pocket\\\bingding_pocket.cxs
Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level
0.0254, step 1, values float32
Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level
0.0117, step 1, values float32
Log from Thu Sep 1 15:18:30 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> D:\\\SIMM_CHM\\\A2b\\\Figure\\\overall_structure\\\overall_structures.cxs
Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level
0.0254, step 1, values float32
Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level
0.0117, step 1, values float32
Log from Wed Aug 31 21:51:59 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> D:\\\SIMM_CHM\\\A2b\\\Figure\\\overall_structure\\\overall_structures.cxs
Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level
0.0254, step 1, values float32
Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level
0.0117, step 1, values float32
Log from Wed Aug 31 20:59:20 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> D:\\\SIMM_CHM\\\Figure\\\BBBBBBBBBBBBBB0502\\\overall_structure\\\map_model_color.cxs
Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level
0.0254, step 1, values float32
Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level
0.0117, step 1, values float32
Log from Fri May 6 16:23:50 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
> open E:\\\copy-SIMM\\\Figure\\\BBBBBBBBBBBBBB0502\\\Two_models_color.cxs
Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level
0.0254, step 1, values float32
Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level
0.0145, step 1, values float32
Log from Mon May 2 23:27:06 2022UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open E:/copy-SIMM/A2b_A3/structure/20220428/A2B_ADN_0214-4.pdb
Chain information for A2B_ADN_0214-4.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> open E:/copy-SIMM/A2b_A3/structure/20220428/BAY-
> flip3-coot-0303-xyw_20220425_5.pdb
Chain information for BAY-flip3-coot-0303-xyw_20220425_5.pdb #2
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> open E:/copy-SIMM/Figure/ADN_map.mrc
Opened ADN_map.mrc as #3, grid size 200,200,200, pixel 1.04, shown at level
0.0168, step 1, values float32
> open E:/copy-SIMM/Figure/BAY_map.mrc
Opened BAY_map.mrc as #4, grid size 320,320,320, pixel 0.8, shown at level
0.00604, step 2, values float32
> hide atoms
> show cartoons
> volume #4 step 1
> volume #4 level 0.01393
> volume #3 level 0.02602
> volume #4 level 0.01316
> hide #!3 models
> hide #!4 models
> matchmaker #1 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker BAY-flip3-coot-0303-xyw_20220425_5.pdb, chain B (#2) with
A2B_ADN_0214-4.pdb, chain B (#1), sequence alignment score = 1718.9
RMSD between 334 pruned atom pairs is 0.464 angstroms; (across all 334 pairs:
0.464)
> matchmaker #1/R to #2/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker BAY-flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2) with
A2B_ADN_0214-4.pdb, chain R (#1), sequence alignment score = 1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> select #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,18.404,0,1,0,6.1272,0,0,1,27.911
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.60509,-0.78919,0.10505,131.86,0.77481,0.55337,-0.3057,11.967,0.18313,0.26637,0.94631,-13.298
> view matrix models
> #3,0.86712,-0.49654,0.039479,81.231,0.4684,0.78587,-0.40376,28.747,0.16946,0.36859,0.91401,-19.33
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.86712,-0.49654,0.039479,83.375,0.4684,0.78587,-0.40376,29.917,0.16946,0.36859,0.91401,-20.814
> view matrix models
> #3,0.86712,-0.49654,0.039479,82.364,0.4684,0.78587,-0.40376,36.972,0.16946,0.36859,0.91401,-23.857
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.64694,-0.7582,-0.081296,146.84,0.71302,0.63927,-0.28799,15.022,0.27032,0.12834,0.95418,-12.48
> view matrix models
> #3,0.96617,-0.23256,-0.11147,61.045,0.13854,0.8326,-0.53626,80.274,0.21752,0.50268,0.83666,-34.381
> ui mousemode right "move picked models"
> view matrix models
> #3,0.96617,-0.23256,-0.11147,60.964,0.13854,0.8326,-0.53626,76.336,0.21752,0.50268,0.83666,-32.798
> view matrix models
> #3,0.96617,-0.23256,-0.11147,63.017,0.13854,0.8326,-0.53626,79.357,0.21752,0.50268,0.83666,-33.397
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.96617,-0.23256,-0.11147,62.139,0.13854,0.8326,-0.53626,81.078,0.21752,0.50268,0.83666,-34.608
> view matrix models
> #3,0.96617,-0.23256,-0.11147,64.949,0.13854,0.8326,-0.53626,76.098,0.21752,0.50268,0.83666,-31.774
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.93244,-0.24643,-0.26424,87.409,0.041236,0.79912,-0.59976,96.818,0.35896,0.54834,0.75529,-41.604
> view matrix models
> #3,0.95571,0.15286,-0.25151,40.176,-0.20648,0.95719,-0.20285,58.902,0.20973,0.2458,0.94636,-15.659
> view matrix models
> #3,0.96671,0.13291,-0.21867,37.465,-0.22168,0.86184,-0.45617,99.919,0.12782,0.48946,0.86261,-24.302
> view matrix models
> #3,0.96199,0.0060174,-0.27301,57.987,-0.11613,0.91387,-0.38906,75.936,0.24715,0.40597,0.87983,-29.195
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.96199,0.0060174,-0.27301,58.11,-0.11613,0.91387,-0.38906,76.515,0.24715,0.40597,0.87983,-28.892
> view matrix models
> #3,0.96199,0.0060174,-0.27301,58.509,-0.11613,0.91387,-0.38906,78.784,0.24715,0.40597,0.87983,-27.548
> view matrix models
> #3,0.96199,0.0060174,-0.27301,56.87,-0.11613,0.91387,-0.38906,81.862,0.24715,0.40597,0.87983,-25.422
> view matrix models
> #3,0.96199,0.0060174,-0.27301,60.257,-0.11613,0.91387,-0.38906,80.148,0.24715,0.40597,0.87983,-26.709
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.96924,0.14576,-0.1983,35.742,-0.16598,0.98207,-0.089371,43.293,0.18172,0.11953,0.97606,-0.03727
> view matrix models
> #3,0.98583,-0.16046,-0.048919,50.211,0.16142,0.98675,0.016519,-2.2945,0.04562,-0.024181,0.99867,26.676
> ui mousemode right "move picked models"
> view matrix models
> #1,0.93925,-0.32783,-0.10169,71.622,0.29735,0.92513,-0.23603,18.467,0.17145,0.19146,0.96641,-7.8145
> undo
> view matrix models
> #3,0.98583,-0.16046,-0.048919,49.415,0.16142,0.98675,0.016519,7.9814,0.04562,-0.024181,0.99867,29.489
> view matrix models
> #1,0.93925,-0.32783,-0.10169,76.339,0.29735,0.92513,-0.23603,22.173,0.17145,0.19146,0.96641,-5.6807
> view matrix models
> #1,0.93925,-0.32783,-0.10169,77.348,0.29735,0.92513,-0.23603,22.064,0.17145,0.19146,0.96641,-5.1299
> view matrix models
> #3,0.98583,-0.16046,-0.048919,50.199,0.16142,0.98675,0.016519,1.6905,0.04562,-0.024181,0.99867,30.186
> view matrix models
> #3,0.98583,-0.16046,-0.048919,49.763,0.16142,0.98675,0.016519,5.0132,0.04562,-0.024181,0.99867,29.865
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.95007,-0.29291,-0.10756,74.504,0.29645,0.95488,0.018194,-5.2841,0.097377,-0.049171,0.99403,27.913
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.95007,-0.29291,-0.10756,71.517,0.29645,0.95488,0.018194,-5.2627,0.097377,-0.049171,0.99403,26.153
> view matrix models
> #3,0.95007,-0.29291,-0.10756,72.241,0.29645,0.95488,0.018194,-5.5304,0.097377,-0.049171,0.99403,25.712
> ~select #3
Nothing selected
> fitmap #1 inMap #3
Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms
average map value = 0.03367, steps = 116
shifted from previous position = 7.2
rotated from previous position = 14.8 degrees
atoms outside contour = 3217, contour level = 0.026017
Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999709 -0.00228215 -0.00078051 0.30319160
0.00228311 0.99999662 0.00123941 -0.37560316
0.00077768 -0.00124119 0.99999893 0.06737381
Axis -0.45731452 -0.28726029 0.84163231
Axis point 161.45288095 137.84719352 0.00000000
Rotation angle (degrees) 0.15539468
Shift along axis 0.02594593
> fitmap #1 inMap #3
Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms
average map value = 0.03367, steps = 40
shifted from previous position = 0.0144
rotated from previous position = 0.0159 degrees
atoms outside contour = 3219, contour level = 0.026017
Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999695 -0.00237768 -0.00066673 0.29531295
0.00237835 0.99999667 0.00100573 -0.34485141
0.00066433 -0.00100731 0.99999927 0.04530441
Axis -0.37744783 -0.24957591 0.89176510
Axis point 143.59895806 126.39953189 0.00000000
Rotation angle (degrees) 0.15278733
Shift along axis 0.01500226
> hide #!3 models
> show #!2 models
> matchmaker #3 to #4
No 'to' model specified
> show #!3 models
> show #!4 models
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain B (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain B (#2), sequence alignment score =
1718.9
RMSD between 334 pruned atom pairs is 0.464 angstroms; (across all 334 pairs:
0.464)
> hide #!1 models
> hide #!3 models
> select #4
2 models selected
> view matrix models #4,1,0,0,4.9796,0,1,0,-1.2895,0,0,1,0.21268
> view matrix models #4,1,0,0,2.5367,0,1,0,2.9519,0,0,1,0.95685
> view matrix models #4,1,0,0,2.1989,0,1,0,3.0664,0,0,1,4.7596
> view matrix models #4,1,0,0,6.2857,0,1,0,-0.1747,0,0,1,6.5534
> view matrix models #4,1,0,0,4.2705,0,1,0,-1.1232,0,0,1,4.8089
> view matrix models #4,1,0,0,3.7519,0,1,0,-1.1812,0,0,1,5.4671
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99966,-0.026166,-0.0014905,7.424,0.026177,0.99963,0.0080197,-5.563,0.0012801,-0.008056,0.99997,6.3629
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99966,-0.026166,-0.0014905,7.5705,0.026177,0.99963,0.0080197,-6.0153,0.0012801,-0.008056,0.99997,7.1986
> view matrix models
> #4,0.99966,-0.026166,-0.0014905,8.2247,0.026177,0.99963,0.0080197,-4.1145,0.0012801,-0.008056,0.99997,3.9471
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99818,0.00086579,-0.06025,13.25,-0.0037961,0.99881,-0.048539,7.8131,0.060136,0.04868,0.997,-10.432
> view matrix models
> #4,0.99474,0.070011,-0.0748,6.7268,-0.075812,0.99409,-0.077753,21.638,0.068914,0.083015,0.99416,-15.614
> view matrix models
> #4,0.99922,0.032396,-0.022564,3.6344,-0.033658,0.99775,-0.057963,13.046,0.020635,0.058678,0.99806,-6.9269
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99922,0.032396,-0.022564,3.8442,-0.033658,0.99775,-0.057963,9.2979,0.020635,0.058678,0.99806,-6.1139
> view matrix models
> #4,0.99922,0.032396,-0.022564,3.768,-0.033658,0.99775,-0.057963,8.8694,0.020635,0.058678,0.99806,-3.869
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99208,0.10035,-0.07549,3.331,-0.109,0.98665,-0.12101,28.765,0.062339,0.12828,0.98978,-17.016
> view matrix models
> #4,0.99297,0.10137,-0.061151,1.0434,-0.10812,0.98691,-0.11967,28.43,0.048218,0.12544,0.99093,-15.036
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99297,0.10137,-0.061151,2.9808,-0.10812,0.98691,-0.11967,28.844,0.048218,0.12544,0.99093,-19.04
> view matrix models
> #4,0.99297,0.10137,-0.061151,4.089,-0.10812,0.98691,-0.11967,28.474,0.048218,0.12544,0.99093,-17.374
> view matrix models
> #4,0.99297,0.10137,-0.061151,3.6163,-0.10812,0.98691,-0.11967,28.456,0.048218,0.12544,0.99093,-18.035
> view matrix models
> #4,0.99297,0.10137,-0.061151,1.0971,-0.10812,0.98691,-0.11967,37.742,0.048218,0.12544,0.99093,-18.238
> view matrix models
> #4,0.99297,0.10137,-0.061151,5.2958,-0.10812,0.98691,-0.11967,40.973,0.048218,0.12544,0.99093,-19.694
> view matrix models
> #4,0.99297,0.10137,-0.061151,5.4503,-0.10812,0.98691,-0.11967,40.694,0.048218,0.12544,0.99093,-19.649
> ui mousemode right "move picked models"
> view matrix models
> #4,0.99297,0.10137,-0.061151,5.808,-0.10812,0.98691,-0.11967,36.143,0.048218,0.12544,0.99093,-16.837
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.98523,0.12525,0.11675,-21.678,-0.1263,0.99199,0.0016041,20.487,-0.11562,-0.016326,0.99316,21.938
> view matrix models
> #4,0.99384,0.076454,0.080204,-11.183,-0.079182,0.99637,0.031402,9.7526,-0.077512,-0.03756,0.99628,19.479
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99384,0.076454,0.080204,-9.5305,-0.079182,0.99637,0.031402,7.9219,-0.077512,-0.03756,0.99628,16.536
> view matrix models
> #4,0.99384,0.076454,0.080204,-10.19,-0.079182,0.99637,0.031402,9.0183,-0.077512,-0.03756,0.99628,16.373
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.9753,0.1728,0.13757,-28.614,-0.17769,0.98379,0.023991,24.091,-0.1312,-0.047844,0.9902,25.326
> view matrix models
> #4,0.98165,0.16266,0.099519,-22.666,-0.17524,0.9753,0.1345,9.1519,-0.075183,-0.14947,0.9859,32.171
> view matrix models
> #4,0.99714,0.06153,0.043977,-3.4953,-0.068343,0.9821,0.17551,-11.008,-0.032391,-0.17801,0.9835,30.865
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99714,0.06153,0.043977,-3.659,-0.068343,0.9821,0.17551,-10.089,-0.032391,-0.17801,0.9835,30.602
> view matrix models
> #4,0.99714,0.06153,0.043977,-4.0148,-0.068343,0.9821,0.17551,-8.9965,-0.032391,-0.17801,0.9835,30.856
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99583,0.087037,0.027364,-4.8148,-0.090719,0.97652,0.19538,-8.2874,-0.0097164,-0.19704,0.98035,30.942
> view matrix models
> #4,0.98864,0.14917,0.018525,-10.765,-0.14998,0.97076,0.18742,1.0426,0.009974,-0.18807,0.9821,27.046
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.98864,0.14917,0.018525,-13.583,-0.14998,0.97076,0.18742,0.093376,0.009974,-0.18807,0.9821,26.869
> view matrix models
> #4,0.98864,0.14917,0.018525,-13.081,-0.14998,0.97076,0.18742,-1.1395,0.009974,-0.18807,0.9821,26.91
> view matrix models
> #4,0.98864,0.14917,0.018525,-12.618,-0.14998,0.97076,0.18742,-3.039,0.009974,-0.18807,0.9821,27.74
> view matrix models
> #4,0.98864,0.14917,0.018525,-12.792,-0.14998,0.97076,0.18742,-3.0558,0.009974,-0.18807,0.9821,27.678
> view matrix models
> #4,0.98864,0.14917,0.018525,-13.192,-0.14998,0.97076,0.18742,-2.9273,0.009974,-0.18807,0.9821,28.209
> view matrix models
> #4,0.98864,0.14917,0.018525,-13.577,-0.14998,0.97076,0.18742,-1.8298,0.009974,-0.18807,0.9821,28.639
> ui mousemode right "move picked models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99367,0.11161,-0.012524,-4.8826,-0.1071,0.97524,0.19348,-8.6643,0.033808,-0.19092,0.98102,26.17
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 68
shifted from previous position = 2.33
rotated from previous position = 5.31 degrees
atoms outside contour = 2558, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999993 0.00006391 -0.00036620 0.04851337
-0.00006383 0.99999997 0.00021578 -0.04489731
0.00036622 -0.00021575 0.99999991 -0.00205420
Axis -0.50198853 -0.85201313 -0.14859726
Axis point -0.11721179 0.00000000 151.94834913
Rotation angle (degrees) 0.02462684
Shift along axis 0.01420519
> show #!1 models
> hide #!4 models
> hide #!2 models
> show #!3 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!1 models
> show #!2 models
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain B (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain B (#2), sequence alignment score =
1718.9
RMSD between 334 pruned atom pairs is 0.464 angstroms; (across all 334 pairs:
0.464)
> hide #!1 models
> show #!4 models
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99367,0.11161,-0.012524,-4.9556,-0.1071,0.97524,0.19348,-8.0408,0.033808,-0.19092,0.98102,25.55
> hide #!2 models
> hide #!4 models
> show #!2 models
> show #!1 models
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!4 models
> view matrix models
> #4,0.99367,0.11161,-0.012524,-5.5714,-0.1071,0.97524,0.19348,-8.2228,0.033808,-0.19092,0.98102,25.402
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 84
shifted from previous position = 1.37
rotated from previous position = 5.67 degrees
atoms outside contour = 2558, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999989 0.00004416 -0.00046633 0.05954713
-0.00004411 0.99999999 0.00009869 -0.02024493
0.00046634 -0.00009867 0.99999988 -0.04016215
Axis -0.20613398 -0.97417062 -0.09219749
Axis point 83.95036136 0.00000000 132.60127722
Rotation angle (degrees) 0.02742747
Shift along axis 0.01115018
> show #!1 models
> hide #!4 models
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> hide #!2 models
> hide #!1 models
> show #!3 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!4 models
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99367,0.11161,-0.012524,-5.2364,-0.1071,0.97524,0.19348,-6.776,0.033808,-0.19092,0.98102,25.03
> view matrix models
> #4,0.99367,0.11161,-0.012524,-6.5132,-0.1071,0.97524,0.19348,-7.2757,0.033808,-0.19092,0.98102,24.99
> view matrix models
> #4,0.99367,0.11161,-0.012524,-6.0679,-0.1071,0.97524,0.19348,-8.599,0.033808,-0.19092,0.98102,26.139
> view matrix models
> #4,0.99367,0.11161,-0.012524,-5.6784,-0.1071,0.97524,0.19348,-7.8772,0.033808,-0.19092,0.98102,25.422
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 72
shifted from previous position = 1.07
rotated from previous position = 5.67 degrees
atoms outside contour = 2557, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999980 0.00013116 -0.00061743 0.07544382
-0.00013098 0.99999995 0.00028568 -0.04459578
0.00061746 -0.00028560 0.99999977 -0.01945038
Axis -0.41228191 -0.89119756 -0.18918387
Axis point 27.77483149 0.00000000 130.40786548
Rotation angle (degrees) 0.03969604
Shift along axis 0.01231923
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> hide #!4 models
> hide #!2 models
> show #!1 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!4 models
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99793,0.062884,0.013602,-3.572,-0.064334,0.97279,0.22259,-17.075,0.00076483,-0.223,0.97482,34.647
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 72
shifted from previous position = 1.61
rotated from previous position = 2.45 degrees
atoms outside contour = 2557, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999984 0.00011944 -0.00055356 0.06578881
-0.00011927 0.99999994 0.00030093 -0.04631770
0.00055359 -0.00030086 0.99999980 -0.00963222
Axis -0.46922004 -0.86324420 -0.18612364
Axis point 13.77843114 0.00000000 128.08886628
Rotation angle (degrees) 0.03674213
Shift along axis 0.01090684
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 72
shifted from previous position = 1.61
rotated from previous position = 2.45 degrees
atoms outside contour = 2557, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999983 0.00011684 -0.00056020 0.06743838
-0.00011668 0.99999995 0.00028937 -0.04511803
0.00056024 -0.00028930 0.99999980 -0.01202133
Axis -0.45121024 -0.87364474 -0.18208291
Axis point 17.87081160 0.00000000 129.37928445
Rotation angle (degrees) 0.03674062
Shift along axis 0.01117712
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 72
shifted from previous position = 1.61
rotated from previous position = 2.45 degrees
atoms outside contour = 2557, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999984 0.00011944 -0.00055356 0.06578881
-0.00011927 0.99999994 0.00030093 -0.04631770
0.00055359 -0.00030086 0.99999980 -0.00963222
Axis -0.46922004 -0.86324420 -0.18612364
Axis point 13.77843118 0.00000000 128.08886618
Rotation angle (degrees) 0.03674213
Shift along axis 0.01090684
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 72
shifted from previous position = 1.61
rotated from previous position = 2.45 degrees
atoms outside contour = 2557, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999983 0.00011684 -0.00056020 0.06743838
-0.00011668 0.99999995 0.00028937 -0.04511803
0.00056024 -0.00028930 0.99999980 -0.01202133
Axis -0.45121024 -0.87364474 -0.18208291
Axis point 17.87081164 0.00000000 129.37928432
Rotation angle (degrees) 0.03674062
Shift along axis 0.01117712
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> transparency #4 30
> color #4 #ffaa00 models transparency 0
> color #4 #55ff7f models transparency 0
> color #4 #ffaa7f models transparency 0
> color #4 #ffaaff models transparency 0
> transparency #4 30
> color #4 black models transparency 0
> color #4 #a3a3a3 models transparency 0
> color #4 #b3b3b3 models transparency 0
> color #4 #6c6c6c models transparency 0
> transparency #4 30
> show #!1 models
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 72
shifted from previous position = 1.61
rotated from previous position = 2.45 degrees
atoms outside contour = 2557, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999983 0.00011684 -0.00056020 0.06743838
-0.00011668 0.99999995 0.00028937 -0.04511803
0.00056024 -0.00028930 0.99999980 -0.01202133
Axis -0.45121024 -0.87364474 -0.18208291
Axis point 17.87081144 0.00000000 129.37928448
Rotation angle (degrees) 0.03674062
Shift along axis 0.01117712
> transparency #4 0
> view matrix models
> #4,0.99787,0.060745,0.023585,-4.7079,-0.06473,0.96569,0.2515,-20.217,-0.0074979,-0.25249,0.96757,40.568
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 56
shifted from previous position = 0.352
rotated from previous position = 1.8 degrees
atoms outside contour = 2553, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999981 0.00011957 -0.00060342 0.06888708
-0.00011940 0.99999995 0.00028442 -0.04034825
0.00060345 -0.00028435 0.99999978 -0.01623753
Axis -0.41962883 -0.89040876 -0.17630623
Axis point 24.06516585 0.00000000 121.02626303
Rotation angle (degrees) 0.03882965
Shift along axis 0.00988221
> show #!3 models
> hide #!2 models
> hide #!1 models
> ~select #4
Nothing selected
> color #4 #6c6624 models transparency 0
> color #4 #6c632f models transparency 0
> color #4 #686c3a models transparency 0
> color #4 #aaffff models transparency 0
> color #4 #55ff00 models transparency 0
> color #4 #ffaa7f models transparency 0
> select #4
2 models selected
> view matrix models
> #4,0.99904,0.037554,0.022484,-1.6696,-0.041911,0.96887,0.244,-22.43,-0.012621,-0.2447,0.96952,39.917
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99904,0.037554,0.022484,-3.0061,-0.041911,0.96887,0.244,-22.327,-0.012621,-0.2447,0.96952,39.137
> view matrix models
> #4,0.99904,0.037554,0.022484,-2.8992,-0.041911,0.96887,0.244,-22.413,-0.012621,-0.2447,0.96952,38.076
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99976,-0.0027219,0.021517,2.4066,-0.0038669,0.95383,0.30033,-33.253,-0.021341,-0.30034,0.95359,48.704
> view matrix models
> #4,0.99745,0.068166,0.021151,-6.5064,-0.071339,0.96117,0.26656,-20.926,-0.0021595,-0.26739,0.96359,40.569
> view matrix models
> #4,0.99835,0.052891,0.022207,-4.7759,-0.056812,0.96521,0.25523,-21.664,-0.0079348,-0.25607,0.96662,39.384
> view matrix models
> #4,0.99854,0.052535,0.012754,-3.4059,-0.053942,0.95257,0.29949,-26.679,0.0035847,-0.29974,0.95401,45.435
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.99854,0.052535,0.012754,-3.4063,-0.053942,0.95257,0.29949,-25.325,0.0035847,-0.29974,0.95401,45.718
> view matrix models
> #4,0.99854,0.052535,0.012754,-2.0528,-0.053942,0.95257,0.29949,-26.185,0.0035847,-0.29974,0.95401,46.254
> view matrix models
> #4,0.99854,0.052535,0.012754,-2.5455,-0.053942,0.95257,0.29949,-26.323,0.0035847,-0.29974,0.95401,45.775
> view matrix models
> #4,0.99854,0.052535,0.012754,-2.5979,-0.053942,0.95257,0.29949,-25.992,0.0035847,-0.29974,0.95401,45.283
> ~select #4
Nothing selected
> ui mousemode right "translate selected models"
> select #4
2 models selected
> ~select #4
Nothing selected
> select #4
2 models selected
> ~select #4
Nothing selected
> select #4
2 models selected
> ~select #4
Nothing selected
> select #4
2 models selected
> ~select #4
Nothing selected
> color #3 #b27079 models transparency 0
> color #3 #928fb2 models transparency 0
> color #3 #b29ca6 models transparency 0
> color #3 #b2afb0 models transparency 0
> color #3 #b2b2b2 models transparency 0
> color #3 #4d4db2 models transparency 0
> select #3
2 models selected
> view matrix models
> #3,0.95007,-0.29291,-0.10756,72.188,0.29645,0.95488,0.018194,-5.9105,0.097377,-0.049171,0.99403,25.012
> ~select #3
Nothing selected
> select #3
2 models selected
> view matrix models
> #3,0.95007,-0.29291,-0.10756,73.199,0.29645,0.95488,0.018194,-5.2449,0.097377,-0.049171,0.99403,25.678
> view matrix models
> #3,0.95007,-0.29291,-0.10756,73.575,0.29645,0.95488,0.018194,-5.1691,0.097377,-0.049171,0.99403,25.699
> view matrix models
> #3,0.95007,-0.29291,-0.10756,73.262,0.29645,0.95488,0.018194,-5.6719,0.097377,-0.049171,0.99403,25.164
> ~select #3
Nothing selected
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 76
shifted from previous position = 2.28
rotated from previous position = 2.94 degrees
atoms outside contour = 2555, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999992 0.00005428 -0.00039989 0.04757224
-0.00005422 0.99999999 0.00014220 -0.02474018
0.00039990 -0.00014218 0.99999991 -0.02756479
Axis -0.33231711 -0.93460773 -0.12678220
Axis point 65.53109402 0.00000000 127.93016806
Rotation angle (degrees) 0.02451563
Shift along axis 0.01080802
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> hide #!3 models
> hide #!4 models
> show #!1 models
> show #!3 models
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 60
shifted from previous position = 1.58
rotated from previous position = 3.08 degrees
atoms outside contour = 2553, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999982 0.00014338 -0.00057796 0.06595899
-0.00014322 0.99999995 0.00027420 -0.03836534
0.00057799 -0.00027411 0.99999979 -0.02323370
Axis -0.41820326 -0.88166049 -0.21858824
Axis point 35.95951023 0.00000000 122.30439953
Rotation angle (degrees) 0.03756041
Shift along axis 0.01131956
> fitmap #1 inMap #3
Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms
average map value = 0.03367, steps = 52
shifted from previous position = 1.16
rotated from previous position = 0.0173 degrees
atoms outside contour = 3225, contour level = 0.026017
Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999681 -0.00235604 -0.00090656 0.32127614
0.00235711 0.99999652 0.00118706 -0.35937366
0.00090376 -0.00118919 0.99999888 0.04156631
Axis -0.42584376 -0.32442464 0.84463350
Axis point 150.62003713 138.84957924 0.00000000
Rotation angle (degrees) 0.15985861
Shift along axis 0.01488453
> ui tool show "Fit in Map"
Fit map ADN_map.mrc in map BAY_map.mrc using 35267 points
correlation = 0.9582, correlation about mean = 0.8117, overlap = 38.83
steps = 60, shift = 0.911, angle = 3.49 degrees
Position of ADN_map.mrc (#3) relative to BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.93903847 -0.32930428 -0.09882019 71.32499165
0.30063328 0.92591232 -0.22870506 21.72211567
0.16681239 0.18505422 0.96846712 -5.88346381
Axis 0.51777433 -0.33241002 0.78829773
Axis point -53.85717924 187.14222038 0.00000000
Rotation angle (degrees) 23.55040054
Shift along axis 25.07167981
> show #!4 models
Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms
average map value = 0.03367, steps = 64
shifted from previous position = 1.13
rotated from previous position = 3.49 degrees
atoms outside contour = 3221, contour level = 0.026017
Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999700 -0.00230959 -0.00081123 0.30653114
0.00231059 0.99999657 0.00123363 -0.36880105
0.00080838 -0.00123551 0.99999891 0.06574383
Axis -0.45030817 -0.29537407 0.84260116
Axis point 156.45642258 137.64546674 0.00000000
Rotation angle (degrees) 0.15708298
Shift along axis 0.02629661
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 44
shifted from previous position = 0.00423
rotated from previous position = 0.00846 degrees
atoms outside contour = 2554, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999990 0.00010028 -0.00043705 0.05049934
-0.00010016 0.99999996 0.00026504 -0.04313308
0.00043707 -0.00026499 0.99999987 -0.00379762
Axis -0.50879702 -0.83910787 -0.19241510
Axis point 3.78327640 0.00000000 128.61928177
Rotation angle (degrees) 0.02984333
Shift along axis 0.01123011
> hide #!4 models
> hide #!3 models
> show #!2 models
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
> ui tool show "Fit in Map"
Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms
average map value = 0.03367, steps = 44
shifted from previous position = 0.00894
rotated from previous position = 0.0143 degrees
atoms outside contour = 3212, contour level = 0.026017
Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999717 -0.00230485 -0.00058894 0.28113638
0.00230551 0.99999671 0.00112094 -0.36282354
0.00058635 -0.00112230 0.99999920 0.07518789
Axis -0.42646211 -0.22343483 0.87647416
Axis point 154.92943648 126.79526989 0.00000000
Rotation angle (degrees) 0.15069141
Shift along axis 0.02707365
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 64
shifted from previous position = 0.444
rotated from previous position = 0.555 degrees
atoms outside contour = 2553, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999991 0.00005757 -0.00041763 0.04525609
-0.00005749 0.99999997 0.00020017 -0.03082159
0.00041765 -0.00020015 0.99999989 -0.01517344
Axis -0.42889261 -0.89490536 -0.12327016
Axis point 33.39712799 0.00000000 118.66932590
Rotation angle (degrees) 0.02673918
Shift along axis 0.01004283
> show #!4 models
> show #!3 models
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> show #!4 models
Fit map ADN_map.mrc in map BAY_map.mrc using 35267 points
correlation = 0.9582, correlation about mean = 0.8118, overlap = 38.83
steps = 44, shift = 0.0171, angle = 0.00476 degrees
Position of ADN_map.mrc (#3) relative to BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.93903876 -0.32931742 -0.09877373 71.31747725
0.30066588 0.92591737 -0.22864176 21.71270443
0.16675203 0.18500558 0.96848681 -5.85774252
Axis 0.51767144 -0.33230022 0.78841159
Axis point -53.84103831 187.09490016 0.00000000
Rotation angle (degrees) 23.54860667
Shift along axis 25.08557296
Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms
average map value = 0.03367, steps = 40
shifted from previous position = 0.0195
rotated from previous position = 0.0125 degrees
atoms outside contour = 3219, contour level = 0.026017
Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999686 -0.00235631 -0.00085286 0.31617862
0.00235727 0.99999658 0.00113243 -0.35726124
0.00085019 -0.00113443 0.99999900 0.03971978
Axis -0.41210954 -0.30961109 0.85691698
Axis point 149.87056576 136.49379601 0.00000000
Rotation angle (degrees) 0.15758144
Shift along axis 0.01434837
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 40
shifted from previous position = 0.0135
rotated from previous position = 0.00363 degrees
atoms outside contour = 2555, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999990 0.00008782 -0.00042449 0.05124927
-0.00008771 0.99999996 0.00025551 -0.04418421
0.00042451 -0.00025548 0.99999988 -0.00334207
Axis -0.50777304 -0.84364852 -0.17442394
Axis point 3.04860892 0.00000000 134.88997229
Rotation angle (degrees) 0.02882943
Shift along axis 0.01183589
> hide #!3 models
> hide #!4 models
> show #!1 models
> show #!2 models
> matchmaker #2/R to #1/R
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker A2B_ADN_0214-4.pdb, chain R (#1) with BAY-
flip3-coot-0303-xyw_20220425_5.pdb, chain R (#2), sequence alignment score =
1394.8
RMSD between 264 pruned atom pairs is 0.606 angstroms; (across all 277 pairs:
1.038)
Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms
average map value = 0.03367, steps = 28
shifted from previous position = 0.0182
rotated from previous position = 0.0122 degrees
atoms outside contour = 3215, contour level = 0.026017
Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999709 -0.00232241 -0.00064406 0.28952177
0.00232312 0.99999669 0.00110222 -0.36255840
0.00064150 -0.00110371 0.99999919 0.07019031
Axis -0.41614089 -0.24251744 0.87636297
Axis point 153.22672457 129.66122639 0.00000000
Rotation angle (degrees) 0.15186055
Shift along axis 0.02895708
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 52
shifted from previous position = 0.464
rotated from previous position = 0.556 degrees
atoms outside contour = 2560, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999995 0.00005233 -0.00029677 0.04136720
-0.00005229 0.99999998 0.00014790 -0.03572378
0.00029678 -0.00014788 0.99999994 -0.00828863
Axis -0.44056054 -0.88409476 -0.15582958
Axis point 20.26633348 0.00000000 161.13710112
Rotation angle (degrees) 0.01923305
Shift along axis 0.01465006
> hide #!1 models
> hide #!2 models
> show #!3 models
> show #!4 models
Fit map ADN_map.mrc in map BAY_map.mrc using 35267 points
correlation = 0.9582, correlation about mean = 0.8118, overlap = 38.83
steps = 44, shift = 0.000532, angle = 0.0147 degrees
Position of ADN_map.mrc (#3) relative to BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.93902032 -0.32929446 -0.09902518 71.34739775
0.30060466 0.92594979 -0.22859093 21.70907238
0.16696607 0.18488410 0.96847313 -5.86410526
Axis 0.51745627 -0.33288307 0.78830696
Axis point -53.85428275 187.24535269 0.00000000
Rotation angle (degrees) 23.54858400
Shift along axis 25.06986085
> hide #!4 models
> show #!1 models
> color #3 #aaaaff models transparency 0
Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms
average map value = 0.03367, steps = 40
shifted from previous position = 0.0191
rotated from previous position = 0.0206 degrees
atoms outside contour = 3220, contour level = 0.026017
Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999679 -0.00241404 -0.00077050 0.31124352
0.00241480 0.99999660 0.00098537 -0.34369906
0.00076812 -0.00098723 0.99999922 0.03234052
Axis -0.36271689 -0.28291654 0.88791592
Axis point 140.98416812 130.70537044 0.00000000
Rotation angle (degrees) 0.15579885
Shift along axis 0.01306053
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!4 models
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 40
shifted from previous position = 0.0149
rotated from previous position = 0.0065 degrees
atoms outside contour = 2552, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999991 0.00006413 -0.00040551 0.04664867
-0.00006406 0.99999998 0.00017830 -0.02856534
0.00040552 -0.00017827 0.99999990 -0.02176817
Axis -0.39832414 -0.90599702 -0.14320361
Axis point 50.03198808 0.00000000 125.25944365
Rotation angle (degrees) 0.02564479
Shift along axis 0.01041610
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!1 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> fitmap #1 inMap #3
Fit molecule A2B_ADN_0214-4.pdb (#1) to map ADN_map.mrc (#3) using 8174 atoms
average map value = 0.03367, steps = 40
shifted from previous position = 0.00222
rotated from previous position = 0.00825 degrees
atoms outside contour = 3220, contour level = 0.026017
Position of A2B_ADN_0214-4.pdb (#1) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.99999692 -0.00235038 -0.00079171 0.30792277
0.00235126 0.99999662 0.00111290 -0.35410831
0.00078909 -0.00111476 0.99999907 0.04248527
Axis -0.40968193 -0.29071987 0.86466333
Axis point 149.12240691 133.17343906 0.00000000
Rotation angle (degrees) 0.15577396
Shift along axis 0.01353138
> fitmap #2 inMap #4
Fit molecule BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) to map BAY_map.mrc
(#4) using 8228 atoms
average map value = 0.02292, steps = 40
shifted from previous position = 0.003
rotated from previous position = 0.0123 degrees
atoms outside contour = 2553, contour level = 0.013165
Position of BAY-flip3-coot-0303-xyw_20220425_5.pdb (#2) relative to
BAY_map.mrc (#4) coordinates:
Matrix rotation and translation
0.99999980 0.00010306 -0.00061327 0.07117225
-0.00010298 0.99999998 0.00014402 -0.01662992
0.00061329 -0.00014395 0.99999980 -0.05095063
Axis -0.22556685 -0.96076653 -0.16139168
Axis point 80.97290895 0.00000000 119.02440807
Rotation angle (degrees) 0.03657313
Shift along axis 0.00814638
> color #4 black models transparency 0
> color #4 #969696 models transparency 0
> volume #3 color black
> volume #3 color #969696
> volume #3 color #aaaaaa
> volume #4 color #aaaaaa
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 color #b4b4b4
> volume #4 color #b3b3b3
> volume #4 color #b5b5b5
> volume #4 color #b4b4b4
> hide #!4 models
> hide #!3 models
> color #1/R light sea green
> color #2/R dark orange
> color chainA medium purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color A medium purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
Drag select of 33 residues, 1 pseudobonds
> select up
681 atoms, 691 bonds, 1 pseudobond, 83 residues, 3 models selected
> select up
3937 atoms, 4015 bonds, 1 pseudobond, 471 residues, 3 models selected
> color sele medium purple
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel medium purple
> select clear
Drag select of 35 residues
> select up
466 atoms, 468 bonds, 66 residues, 2 models selected
> select up
1943 atoms, 1985 bonds, 256 residues, 2 models selected
> color sel violet
> select clear
Drag select of 25 residues
> select up
387 atoms, 387 bonds, 52 residues, 2 models selected
> select up
6024 atoms, 6127 bonds, 786 residues, 2 models selected
> select down
387 atoms, 387 bonds, 52 residues, 2 models selected
> select clear
Drag select of 34 residues
> select clear
Drag select of 6 residues
> select up
358 atoms, 356 bonds, 43 residues, 2 models selected
> select up
5156 atoms, 5247 bonds, 672 residues, 2 models selected
> select down
358 atoms, 356 bonds, 43 residues, 2 models selected
> select clear
Drag select of 11 residues
> select up
288 atoms, 297 bonds, 37 residues, 2 models selected
> select up
868 atoms, 880 bonds, 114 residues, 2 models selected
> color sel olive drab
> select clear
Drag select of 39 residues
> select up
1197 atoms, 1211 bonds, 157 residues, 2 models selected
> select up
5156 atoms, 5247 bonds, 672 residues, 2 models selected
> color sel burly wood
> select clear
> set bgColor white
> lighting full
> lighting shadows false
> hide #!2 models
> select clear
> hide #2.1 models
> hide #1.1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select ::name="ADN"
19 atoms, 21 bonds, 1 residue, 1 model selected
> color sel hotpink
> show sel atoms
> select clear
> select ::name="BAY"
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> show #!1 atoms
> show #!1 cartoons
> style #!1 stick
Changed 8174 atom styles
> hide #!1 atoms
> show #!1 cartoons
> show #!2 models
> select ::name="BAY"
27 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select ::name="ADN"
19 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!2 models
> show #!2 models
> show #!4 models
> show #!3 models
> volume #4 level 0.01552
> volume #3 level 0.02476
> hide #!4 models
> volume #4 level 0.01447
> hide #!4 models
> volume #3 level 0.02602
> hide #!1 models
> volume #3 level 0.02539
> hide #!2 models
> volume #3 level 0.02539
> save E:/copy-SIMM/Figure/BBBBBBBBBBBBBB0502/Two_models.cxs includeMaps true
——— End of log from Mon May 2 23:27:06 2022 ———
opened ChimeraX session
> show #!1 models
> select #1
8174 atoms, 8341 bonds, 2 pseudobonds, 1042 residues, 2 models selected
> color zone #3 near sel distance 5
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!4 models
> color zone #4 near sel distance 5
> ~select #1
Nothing selected
> select #2
8228 atoms, 8402 bonds, 4 pseudobonds, 1037 residues, 2 models selected
> color zone #4 near sel distance 5
> select clear
> select #2
8228 atoms, 8402 bonds, 4 pseudobonds, 1037 residues, 2 models selected
> ~select #2
Nothing selected
> select #2
8228 atoms, 8402 bonds, 4 pseudobonds, 1037 residues, 2 models selected
> ~select #2
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!3 models
> show #!1 models
> surface dust #3 size 10.4
> surface dust #4 size 8
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
19 atoms, 21 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> show #!2 models
> hide #!1 models
> select #2/R:184
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
53 atoms, 54 bonds, 6 residues, 1 model selected
> select clear
[Repeated 1 time(s)]
> select add #2/L:396@C7
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 2 bonds, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!4 models
> volume #4 level 0.01269
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> save E:/copy-
> SIMM/Figure/BBBBBBBBBBBBBB0502/overall_structure/map_model_color.cxs
> includeMaps true
> show #!1 models
> save E:/copy-SIMM/Figure/BBBBBBBBBBBBBB0502/overall_structure/ADN_model.png
> width 1340 height 819 supersample 3 transparentBackground true
> cartoon style width 1
> cartoon style width 1.3
> select clear
> show #!2 models
> hide #!2 models
> cartoon style width 1.5
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> graphics silhouettes false
> lighting simple
> lighting soft
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting shadows false
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
[Repeated 2 time(s)]
> lighting soft
> graphics silhouettes false
> lighting simple
> lighting full
> lighting simple
> lighting soft
> lighting flat
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting simple
> graphics silhouettes false
> select clear
> lighting soft
[Repeated 2 time(s)]
> lighting simple
> lighting flat
> lighting soft
> set bgColor white
> lighting simple
[Repeated 1 time(s)]
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting soft
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
[Repeated 1 time(s)]
> select clear
> lighting shadows true intensity 1
> lighting shadows true intensity 0.55
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting soft
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!1 models
> volume #4 level 0.01167
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!4 models
> hide #!1 models
> show #!2 models
> select clear
> lighting flat
[Repeated 1 time(s)]
> lighting simple
> lighting soft
> lighting flat
> graphics silhouettes false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
[Repeated 1 time(s)]
> show #!1 models
> hide #!2 models
> save E:/copy-
> SIMM/Figure/BBBBBBBBBBBBBB0502/overall_structure/map_model_color.cxs
> includeMaps true
——— End of log from Fri May 6 16:23:50 2022 ———
opened ChimeraX session
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!4 models
> show #!4 models
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
——— End of log from Wed Aug 31 20:59:20 2022 ———
opened ChimeraX session
> close #1
> close #2
> open D:/SIMM_CHM/A2b/Figure/A2B_ADN_0214-4-coot-21.pdb
Chain information for A2B_ADN_0214-4-coot-21.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> open D:/SIMM_CHM/A2b/Figure/BAY-flip3-coot-335.pdb
Chain information for BAY-flip3-coot-335.pdb #2
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> hide atoms
> show cartoons
> hide #!2 models
> hide #!4 models
> ui mousemode right "translate selected models"
> select #3
2 models selected
> ~select #3
Nothing selected
> select #1
8282 atoms, 8460 bonds, 2 pseudobonds, 1046 residues, 2 models selected
> view matrix models #1,1,0,0,24.439,0,1,0,16.022,0,0,1,26.024
> view matrix models #1,1,0,0,23.295,0,1,0,18.659,0,0,1,24.618
> view matrix models #1,1,0,0,29.011,0,1,0,21.855,0,0,1,27.724
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.96295,-0.26941,0.012165,60.467,0.26822,0.96143,0.060877,-8.4807,-0.028097,-0.055358,0.99807,36.797
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.96295,-0.26941,0.012165,57.465,0.26822,0.96143,0.060877,-8.1392,-0.028097,-0.055358,0.99807,38.939
> view matrix models
> #1,0.96295,-0.26941,0.012165,58.308,0.26822,0.96143,0.060877,-8.4703,-0.028097,-0.055358,0.99807,35.958
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.97609,-0.21736,-0.00060747,52.868,0.21707,0.9746,0.055054,-4.0053,-0.011375,-0.05387,0.99848,34.049
> ui mousemode right "move picked models"
> view matrix models
> #3,0.95557,-0.27781,-0.098538,70.481,0.2857,0.95517,0.07764,-10.749,0.072551,-0.10234,0.9921,33.166
> undo
> show #!4 models
> ui tool show "Fit in Map"
Fit map BAY_map.mrc in map ADN_map.mrc using 97041 points
correlation = 0.9635, correlation about mean = 0.8072, overlap = 89.63
steps = 48, shift = 0.0146, angle = 0.0167 degrees
Position of BAY_map.mrc (#4) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.93906585 0.30039962 0.16707905 -72.54473097
-0.32913845 0.92596648 0.18507828 4.44088943
-0.09911216 -0.22879283 0.96841655 17.75539475
Axis -0.51796032 0.33313869 -0.78786783
Axis point -54.01182656 187.31870099 0.00000000
Rotation angle (degrees) 23.54818099
Shift along axis 25.06581944
Fit map BAY_map.mrc in map ADN_map.mrc using 97041 points
correlation = 0.9635, correlation about mean = 0.8072, overlap = 89.62
steps = 44, shift = 0.00616, angle = 0.00177 degrees
Position of BAY_map.mrc (#4) relative to ADN_map.mrc (#3) coordinates:
Matrix rotation and translation
0.93906650 0.30040896 0.16705861 -72.54574878
-0.32914073 0.92596990 0.18505708 4.44933009
-0.09909844 -0.22876670 0.96842413 17.74930972
Axis -0.51791841 0.33310710 -0.78790874
Axis point -53.98555382 187.31792131 0.00000000
Rotation angle (degrees) 23.54734529
Shift along axis 25.07004625
> show #!2 models
> hide #!1 models
> hide #!2 models
> hide #!4 models
> show #!1 models
Fit molecule A2B_ADN_0214-4-coot-21.pdb (#1) to map ADN_map.mrc (#3) using
8282 atoms
average map value = 0.03341, steps = 92
shifted from previous position = 4.36
rotated from previous position = 6.94 degrees
atoms outside contour = 3187, contour level = 0.025387
Position of A2B_ADN_0214-4-coot-21.pdb (#1) relative to ADN_map.mrc (#3)
coordinates:
Matrix rotation and translation
0.99999899 -0.00140801 -0.00019955 0.18428754
0.00140821 0.99999849 0.00102027 -0.25071495
0.00019811 -0.00102055 0.99999946 0.09835392
Axis -0.58299173 -0.11359755 0.80449751
Axis point 178.16484102 130.82688931 0.00000000
Rotation angle (degrees) 0.10028468
Shift along axis 0.00016798
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!2 models
> show #!4 models
> hide #!3 models
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.95516,-0.27906,-0.099012,70.887,0.28706,0.95469,0.078557,-11.624,0.072603,-0.10346,0.99198,32.094
> view matrix models
> #1,0.95516,-0.27906,-0.099012,71.705,0.28706,0.95469,0.078557,-12.36,0.072603,-0.10346,0.99198,30.93
> ~select #1
Nothing selected
> select #2
8278 atoms, 8460 bonds, 5 pseudobonds, 1036 residues, 2 models selected
> view matrix models #2,1,0,0,1.868,0,1,0,-1.3351,0,0,1,-2.8944
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,6.3053,0,1,0,-0.80806,0,0,1,0.80714
Fit molecule BAY-flip3-coot-335.pdb (#2) to map BAY_map.mrc (#4) using 8278
atoms
average map value = 0.02305, steps = 176
shifted from previous position = 7.76
rotated from previous position = 17.7 degrees
atoms outside contour = 2165, contour level = 0.011674
Position of BAY-flip3-coot-335.pdb (#2) relative to BAY_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99999985 -0.00036405 -0.00040922 0.08893967
0.00036417 0.99999989 0.00029218 -0.08952954
0.00040911 -0.00029233 0.99999987 -0.00172172
Axis -0.47076111 -0.65908495 0.58650747
Axis point 27.40319730 0.00000000 235.88413693
Rotation angle (degrees) 0.03556970
Shift along axis 0.01612844
> hide #!4 models
> hide #!2 models
> ~select #2
Nothing selected
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
Fit molecule A2B_ADN_0214-4-coot-21.pdb (#1) to map ADN_map.mrc (#3) using
8282 atoms
average map value = 0.0334, steps = 64
shifted from previous position = 3.43
rotated from previous position = 0.00905 degrees
atoms outside contour = 3191, contour level = 0.025387
Position of A2B_ADN_0214-4-coot-21.pdb (#1) relative to ADN_map.mrc (#3)
coordinates:
Matrix rotation and translation
0.99999901 -0.00139621 -0.00015211 0.18029397
0.00139639 0.99999834 0.00117052 -0.27922772
0.00015047 -0.00117074 0.99999930 0.13637940
Axis -0.64026055 -0.08274599 0.76368811
Axis point 199.42334543 134.41071414 -0.00000000
Rotation angle (degrees) 0.10475769
Shift along axis 0.01182118
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!3 models
> show #!4 models
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
> hide #!4 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!1 models
Drag select of 41 residues
> select up
721 atoms, 742 bonds, 87 residues, 2 models selected
> select up
3937 atoms, 4015 bonds, 471 residues, 2 models selected
> color sel medium slate blue
[Repeated 1 time(s)]
> select clear
Drag select of 21 residues
> select up
343 atoms, 339 bonds, 48 residues, 2 models selected
> select up
1943 atoms, 1983 bonds, 256 residues, 2 models selected
> color sel orchid
> select clear
Drag select of 46 residues
> select up
1119 atoms, 1126 bonds, 146 residues, 2 models selected
> select up
5156 atoms, 5247 bonds, 672 residues, 2 models selected
> color sel burly wood
> select clear
Drag select of 6 residues
> select up
355 atoms, 362 bonds, 48 residues, 2 models selected
> select up
868 atoms, 880 bonds, 114 residues, 2 models selected
> color sel olive drab
> select clear
> hide #!2 models
Drag select of 95 residues
> select up
1663 atoms, 1698 bonds, 220 residues, 1 model selected
> select up
2297 atoms, 2363 bonds, 285 residues, 1 model selected
> color sel orange
> hide #!1 models
> show #!2 models
> select clear
Drag select of 108 residues
> select up
1715 atoms, 1751 bonds, 227 residues, 1 model selected
> select up
2332 atoms, 2403 bonds, 283 residues, 1 model selected
> color sel light sea green
> select clear
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show #!2 models
> cartoon style width 1。2
Invalid "width" argument: Expected a number
> cartoon style width 1.2
> cartoon style width 1.5
> hide #1.1 models
> hide #2.1 models
> select ::name="ADN"
19 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel hot pink
> hide #!2 models
> show #!2 models
> hide #!2 models
Drag select of 57 residues
> show #!3 models
> hide #!3 models
> select up
1183 atoms, 1201 bonds, 157 residues, 1 model selected
> select up
2297 atoms, 2363 bonds, 285 residues, 1 model selected
> color sel light sea green
> select clear
> select ::name="ADN"
19 atoms, 21 bonds, 1 residue, 1 model selected
> color sel hot pink
> select ::name="BAY"
27 atoms, 29 bonds, 1 residue, 1 model selected
> color #!1 cornflower blue
> undo
> select ::name="BAY"
27 atoms, 29 bonds, 1 residue, 1 model selected
> show #!1 atoms
> undo
> hide #!1 models
> show #!2 models
Drag select of 84 residues
> select up
1536 atoms, 1571 bonds, 202 residues, 1 model selected
> select up
2359 atoms, 2432 bonds, 284 residues, 1 model selected
> color sel orange
> select clear
> select ::name="BAY"
27 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel cornflower blue
> select clear
> show #!3 models
> hide #!2 models
> hide #!3 models
> show #!1 models
> hide #!1 models
> show #1.1 models
> hide #1.1 models
> show #!2 models
> hide #!1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!2 models
> show #!2 models
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
——— End of log from Wed Aug 31 21:51:59 2022 ———
opened ChimeraX session
> close #1
> close #2
> open D:/SIMM_CHM/A2b/Figure/BAY-flip3-coot-336.pdb
Chain information for BAY-flip3-coot-336.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> close #1
> open D:/SIMM_CHM/A2b/Figure/A2B_ADN_0214-4-coot-23.pdb
Chain information for A2B_ADN_0214-4-coot-23.pdb #1
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> open D:/SIMM_CHM/A2b/Figure/BAY-flip3-coot-336.pdb
Chain information for BAY-flip3-coot-336.pdb #2
---
Chain | Description
A | No description available
B | No description available
G | No description available
N | No description available
R | No description available
> hide #!2 models
> show #!3 models
> ui mousemode right "translate selected models"
> select #1
8226 atoms, 8396 bonds, 2 pseudobonds, 1044 residues, 2 models selected
> view matrix models #1,1,0,0,26.596,0,1,0,28.995,0,0,1,29.45
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98885,-0.094941,-0.11474,51.677,0.095143,0.99546,-0.0037279,20.323,0.11457,-0.0072301,0.99339,19.452
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.98885,-0.094941,-0.11474,52.198,0.095143,0.99546,-0.0037279,15.349,0.11457,-0.0072301,0.99339,21.816
> view matrix models
> #1,0.98885,-0.094941,-0.11474,53.162,0.095143,0.99546,-0.0037279,11.901,0.11457,-0.0072301,0.99339,22.049
> style sel stick
Changed 8226 atom styles
> view matrix models
> #1,0.98885,-0.094941,-0.11474,51.093,0.095143,0.99546,-0.0037279,10.74,0.11457,-0.0072301,0.99339,19.889
> view matrix models
> #1,0.98885,-0.094941,-0.11474,50.432,0.095143,0.99546,-0.0037279,11.847,0.11457,-0.0072301,0.99339,18.399
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.96121,-0.27476,-0.024003,61.96,0.2758,0.95807,0.077674,-11.984,0.0016545,-0.081281,0.99669,37.433
> hide sel atoms
> show sel cartoons
> view matrix models
> #1,0.9509,-0.30903,0.017236,61.791,0.30852,0.95084,0.026883,-8.4585,-0.024697,-0.020245,0.99949,33.171
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9509,-0.30903,0.017236,62.605,0.30852,0.95084,0.026883,-7.7482,-0.024697,-0.020245,0.99949,33.779
> ui tool show "Fit in Map"
Fit molecule A2B_ADN_0214-4-coot-23.pdb (#1) to map ADN_map.mrc (#3) using
8226 atoms
average map value = 0.03351, steps = 84
shifted from previous position = 3.65
rotated from previous position = 7.48 degrees
atoms outside contour = 3146, contour level = 0.025387
Position of A2B_ADN_0214-4-coot-23.pdb (#1) relative to ADN_map.mrc (#3)
coordinates:
Matrix rotation and translation
0.99999890 -0.00144806 -0.00031865 0.20289001
0.00144836 0.99999849 0.00096031 -0.24567261
0.00031726 -0.00096077 0.99999949 0.08440214
Axis -0.54370590 -0.17997726 0.81975123
Axis point 169.38393278 141.14420265 0.00000000
Rotation angle (degrees) 0.10122136
Shift along axis 0.00309175
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!4 models
> select #4
2 models selected
> select #2
8278 atoms, 8460 bonds, 5 pseudobonds, 1036 residues, 2 models selected
> view matrix models #2,1,0,0,5.2053,0,1,0,1.8057,0,0,1,3.025
Fit molecule BAY-flip3-coot-336.pdb (#2) to map BAY_map.mrc (#4) using 8278
atoms
average map value = 0.02305, steps = 168
shifted from previous position = 5.39
rotated from previous position = 17.7 degrees
atoms outside contour = 2177, contour level = 0.011674
Position of BAY-flip3-coot-336.pdb (#2) relative to BAY_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99999985 -0.00038910 -0.00038050 0.09345215
0.00038926 0.99999982 0.00044010 -0.12135381
0.00038033 -0.00044025 0.99999983 0.02834974
Axis -0.62886538 -0.54348927 0.55601056
Axis point 0.00000000 35.31714124 247.41581793
Rotation angle (degrees) 0.04010415
Shift along axis 0.02294843
> show sel cartoons
> hide sel atoms
Fit molecule BAY-flip3-coot-336.pdb (#2) to map BAY_map.mrc (#4) using 8278
atoms
average map value = 0.02305, steps = 48
shifted from previous position = 0.0178
rotated from previous position = 0.00748 degrees
atoms outside contour = 2168, contour level = 0.011674
Position of BAY-flip3-coot-336.pdb (#2) relative to BAY_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99999980 -0.00039610 -0.00048192 0.10143576
0.00039627 0.99999985 0.00035813 -0.09941606
0.00048178 -0.00035832 0.99999982 -0.00571011
Axis -0.49798142 -0.66984177 0.55075086
Axis point 26.72262678 0.00000000 223.83666993
Rotation angle (degrees) 0.04121582
Shift along axis 0.01293506
Fit molecule BAY-flip3-coot-336.pdb (#2) to map BAY_map.mrc (#4) using 8278
atoms
average map value = 0.02305, steps = 44
shifted from previous position = 0.0208
rotated from previous position = 0.00707 degrees
atoms outside contour = 2180, contour level = 0.011674
Position of BAY-flip3-coot-336.pdb (#2) relative to BAY_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99999984 -0.00038772 -0.00041279 0.09805148
0.00038791 0.99999982 0.00045997 -0.12464496
0.00041261 -0.00046013 0.99999981 0.03089738
Axis -0.63052298 -0.56562275 0.53151828
Axis point 0.00000000 38.05416083 240.13221743
Rotation angle (degrees) 0.04180510
Shift along axis 0.02510084
Fit molecule BAY-flip3-coot-336.pdb (#2) to map BAY_map.mrc (#4) using 8278
atoms
average map value = 0.02305, steps = 40
shifted from previous position = 0.00579
rotated from previous position = 0.0133 degrees
atoms outside contour = 2173, contour level = 0.011674
Position of BAY-flip3-coot-336.pdb (#2) relative to BAY_map.mrc (#4)
coordinates:
Matrix rotation and translation
0.99999988 -0.00044929 -0.00019795 0.07273846
0.00044937 0.99999982 0.00039775 -0.12146203
0.00019777 -0.00039784 0.99999990 0.04264992
Axis -0.62952725 -0.31312396 0.71108989
Axis point 254.64383753 193.45071166 0.00000000
Rotation angle (degrees) 0.03620477
Shift along axis 0.02256975
> select #4
2 models selected
> hide #!4 models
> hide #!2 models
> ~select #4
Nothing selected
> select #4
2 models selected
> ~select #4
Nothing selected
> show #!1 models
> show #!2 models
> select clear
Drag select of 49 residues, 1 pseudobonds
> select up
734 atoms, 748 bonds, 1 pseudobond, 89 residues, 3 models selected
> select up
3937 atoms, 4015 bonds, 1 pseudobond, 471 residues, 3 models selected
> color sel medium slate blue
> select clear
Drag select of 19 residues
> select up
359 atoms, 358 bonds, 50 residues, 2 models selected
> select up
1943 atoms, 1983 bonds, 256 residues, 2 models selected
> color sel orchid
> select clear
Drag select of 15 residues
> select up
479 atoms, 483 bonds, 66 residues, 2 models selected
> select up
5156 atoms, 5247 bonds, 672 residues, 2 models selected
> color sel burly wood
> select clear
Drag select of 4 residues
> select up
206 atoms, 207 bonds, 29 residues, 2 models selected
> select up
868 atoms, 880 bonds, 114 residues, 2 models selected
> color sel olive drab
> select clear
> hide #!2 models
Drag select of 90 residues
> select up
1663 atoms, 1698 bonds, 220 residues, 1 model selected
> select up
2241 atoms, 2299 bonds, 283 residues, 1 model selected
> color sel light sea green
> hide #!1 models
> show #!2 models
> select clear
Drag select of 59 residues
> select up
1257 atoms, 1277 bonds, 167 residues, 1 model selected
> select up
2332 atoms, 2403 bonds, 283 residues, 1 model selected
> color sel orange
> select clear
> cartoon style width 1.5
> select ::name="CLR"
252 atoms, 279 bonds, 9 residues, 2 models selected
> show sel & #!2 atoms
> color sel dark gray
> select clear
> show #!1 models
> hide #!1 models
> select ::name="ADN"
19 atoms, 21 bonds, 1 residue, 1 model selected
> color sel hot pink
> select ::name="BAY"
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel cornflowerblue
> select clear
> show #!2 atoms
> undo
> select clear
> select ::name="ADN"
19 atoms, 21 bonds, 1 residue, 1 model selected
> show #!2 atoms
> undo
> select clear
> show #!1 models
> select ::name="ADN"
19 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select ::name="BAY"
27 atoms, 29 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
> select clear
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> select ::name="CLR"
252 atoms, 279 bonds, 9 residues, 2 models selected
> show sel & #!1 atoms
> select clear
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
> ui tool show "Color Zone"
> color zone #3 near #1 distance 1.04
> color zone #3 near #1 distance 1.16
[Repeated 1 time(s)]
> color zone #3 near #1 distance 15.37
> hide #!3 models
> hide #!1 models
> show #!2 models
> show #!4 models
> color zone #4 near #2 distance 5
> color zone #4 near #2 distance 5.51
> select ::name="CLR"
252 atoms, 279 bonds, 9 residues, 2 models selected
> ui tool show "Color Actions"
> color sel blue
> color sel dark slate gray
> color zone #4 near #2 distance 5.51
> color sel medium purple
> color zone #4 near #2 distance 5.51
> color sel pale violet red
> color zone #4 near #2 distance 5.51
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
> hide #!2 models
> hide #!4 models
> show #!3 models
> show #!1 models
> color zone #3 near #2 distance 15.48
> color zone #3 near #1 distance 15.48
> select ::name="CLR"
252 atoms, 279 bonds, 9 residues, 2 models selected
> ui tool show "Color Actions"
> color sel dodger blue
> color zone #3 near #1 distance 15.48
> hide #!1 models
> hide #!3 models
> show #!2 models
> show #!4 models
> color zone #4 near #2 distance 5.51
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
> ui mousemode right "map eraser"
> volume erase #4 center 115.3,130.78,116.84 radius 7.3853
> volume erase #4 center 127.69,99.408,103.58 radius 7.3853
> volume erase #4 center 131.99,95.46,105.55 radius 7.3853
> volume erase #4 center 120.89,121.83,93.851 radius 7.3853
> volume erase #4 center 130.43,135.59,89.244 radius 7.3853
> volume erase #4 center 127.02,134.71,94.101 radius 7.3853
> volume erase #4 center 122.79,127.73,94.539 radius 7.3853
> volume erase #4 center 122.79,125.5,96.644 radius 7.3853
> volume erase #4 center 121.8,141.98,113.61 radius 7.3853
> select clear
> volume erase #4 center 120.23,142.41,116.66 radius 7.3853
> volume erase #4 center 118.51,136.95,116.21 radius 7.3853
> volume erase #4 center 113.97,130.1,121.42 radius 7.3853
> volume erase #4 center 114.9,116.89,124.37 radius 7.3853
> volume erase #4 center 117.51,114.96,121.9 radius 7.3853
> volume erase #4 center 132.17,109.78,146.56 radius 4.3003
> volume erase #4 center 145.09,113.41,132.56 radius 3.9264
> volume erase #4 center 142.6,110.01,129.63 radius 3.9264
> volume erase #4 center 137.36,112.96,138.18 radius 3.9264
> volume erase #4 center 133.68,109.88,133.04 radius 3.9264
> volume erase #4 center 131.88,110.03,136.94 radius 3.9264
> volume erase #4 center 157.25,126.21,130.87 radius 3.9264
> volume erase #4 center 159.18,131.28,133.04 radius 3.9264
> volume erase #4 center 158.36,122.01,137.45 radius 3.9264
> volume erase #4 center 157.07,140.51,126.71 radius 3.9264
> volume erase #4 center 157.22,138.66,128.19 radius 3.9264
> volume erase #4 center 156.11,140.63,131.98 radius 3.9264
> volume erase #4 center 156.12,139.28,129.55 radius 3.9264
> volume erase #4 center 155.2,140.25,131.33 radius 3.9264
> volume erase #4 center 130.25,151.86,131.27 radius 3.9264
> volume erase #4 center 134.19,148.41,125.19 radius 2.5241
> volume erase #4 center 129.15,149.64,127.52 radius 2.5241
> volume erase #4 center 132.31,149.48,130.45 radius 2.5241
> volume erase #4 center 134.24,98.808,102.04 radius 7.5723
> volume erase #4 center 159.19,117.25,116.43 radius 5.6091
> volume erase #4 center 157.38,113.82,118.32 radius 5.6091
> volume erase #4 center 154.12,120.73,139.44 radius 0.93485
> volume erase #4 center 147.04,117.73,139.32 radius 0.93485
> volume erase #4 center 146.14,117.45,139.42 radius 0.93485
> volume erase #4 center 146.48,118.3,139.42 radius 0.93485
> volume erase #4 center 145.64,117.96,138.86 radius 0.93485
> volume erase #4 center 145.18,118.09,139.05 radius 0.93485
> volume erase #4 center 137.89,101.42,110.17 radius 0.93485
> hide #!4 models
> hide #5 models
> hide #!2 models
> show #!1 models
> show #!3 models
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
> hide #!1 models
> hide #!3 models
> show #!4 models
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting soft
> hide #!4 models
> show #!4 models
> hide #!4 models
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
> show #5 models
> hide #5 models
> show #5 models
> close #5
> show #!1 models
> select add #1/R:401@N3
1 atom, 1 residue, 1 model selected
> select up
19 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> show #!2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
27 atoms, 29 bonds, 1 residue, 1 model selected
> color sel byhetero
> select clear
> select ::name="CLR"
252 atoms, 279 bonds, 9 residues, 2 models selected
> color sel byhetero
> select clear
> hide #!2 models
> select clear
> show #!2 models
> hide #!1 models
> select clear
> cartoon style width 2
> cartoon style width 2.2
> cartoon style width 2.5
> cartoon style width 2
> select clear
> show #!1 models
> hide #!2 models
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
> save D:/SIMM_CHM/A2b/Figure/overall_structure/ADN_model.png width 1342
> height 834 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save D:/SIMM_CHM/A2b/Figure/overall_structure/BAY_model.png width 1342
> height 834 supersample 3 transparentBackground true
> hide #!2 models
> show #!3 models
> close #5
> hide #!3 models
> show #!4 models
> close #5
> save D:/SIMM_CHM/A2b/Figure/overall_structure/BAY_map.png width 1342 height
> 834 supersample 3 transparentBackground true
> hide #!4 models
> show #!3 models
> close #5
> save D:/SIMM_CHM/A2b/Figure/overall_structure/ADN_map.png width 1342 height
> 834 supersample 3 transparentBackground true
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures.cxs
> includeMaps true
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> show #!1 models
Drag select of 3 atoms, 2 residues, 4 bonds
> select clear
Drag select of 2 atoms, 3 bonds
> select up
5 atoms, 3 bonds, 2 residues, 2 models selected
> select up
46 atoms, 50 bonds, 2 residues, 2 models selected
> size sel stickRadius 0.3
Changed 50 bond radii
> select clear
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #1.1 models
> save D:/SIMM_CHM/A2b/Figure/overall_structure/ADN_model2.png width 1342
> height 834 supersample 3 transparentBackground true
> hide #!1 models
> show #!2 models
> save D:/SIMM_CHM/A2b/Figure/overall_structure/BAY_model2.png width 1342
> height 834 supersample 3 transparentBackground true
> save D:/SIMM_CHM/A2b/Figure/overall_structure/overall_structures2.cxs
> includeMaps true
——— End of log from Thu Sep 1 15:18:30 2022 ———
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 512.15
OpenGL renderer: NVIDIA GeForce GTX 1650 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: IPASON
Model:
OS: Microsoft Windows 10 企业版 (Build 19043)
Memory: 17,130,639,360
MaxProcessMemory: 137,438,953,344
CPU: 6 AMD Ryzen 5 3500X 6-Core Processor
OSLanguage: zh-CN
Locale: ('zh_CN', 'cp936')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-Phenix: 0.3
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.1
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
MolecularDynamicsViewer: 1.2
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → QObject::~QObject: Timers cannot be stopped from another thread |
comment:2 by , 3 years ago
| Status: | accepted → feedback |
|---|
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Hi Jess,
--Eric
this ticket has some features in common with #7160