Restore new session in old ChimeraX

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-14.0-arm64-arm-64bit
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 "/Users/ankitachadda/Desktop/second conformation aligned with one
> closed and one open form of UvrD1 and DNA.cxs"

Opened cryosparc_P43_J1166_002_volume_map_sharp (1).mrc as #1, grid size
200,200,200, pixel 1.62, shown at level 0.61, step 1, values float32  
Log from Thu Aug 31 14:17:49 2023UCSF ChimeraX version: 1.7.dev202308180104
(2023-08-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/ankitachadda/Desktop/second conformation phosphate3.cxs"

Opened cryosparc_P43_J1166_002_volume_map_sharp (1).mrc as #1, grid size
200,200,200, pixel 1.62, shown at level 0.61, step 1, values float32  
Log from Thu Aug 31 13:47:34 2023UCSF ChimeraX version: 1.7.dev202308180104
(2023-08-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/ankitachadda/Desktop/second conformation phosphate2.cxs"

Opened cryosparc_P43_J1166_002_volume_map_sharp (1).mrc as #1, grid size
200,200,200, pixel 1.62, shown at level 0.61, step 1, values float32  
Log from Thu Aug 31 13:44:31 2023UCSF ChimeraX version: 1.7.dev202308180104
(2023-08-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/ankitachadda/Desktop/second conformation phosphate.cxs"

Opened cryosparc_P43_J1166_002_volume_map_sharp (1).mrc as #1, grid size
200,200,200, pixel 1.62, shown at level 0.718, step 1, values float32  
Log from Thu Aug 31 11:03:35 2023UCSF ChimeraX version: 1.7.dev202308180104
(2023-08-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/ankitachadda/Downloads/cryosparc_P43_J1166_002_volume_map_sharp
> (1).mrc"

Opened cryosparc_P43_J1166_002_volume_map_sharp (1).mrc as #1, grid size
200,200,200, pixel 1.62, shown at level 0.188, step 1, values float32  

> volume #1 level 0.5219

> volume #1 level 0.689

[Repeated 1 time(s)]

> volume #1 level 0.4335

> volume #1 level 0.7185

> save "/Users/ankitachadda/Desktop/second conformation phosphate.cxs"

——— End of log from Thu Aug 31 11:03:35 2023 ———

opened ChimeraX session  

> open "/Users/ankitachadda/Desktop/closed UvrD1.pdb"

closed UvrD1.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for closed UvrD1.pdb #2  
---  
Chain | Description  
C | No description available  
  

> select add #2

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> select ::name="CYS"

18 atoms, 15 bonds, 3 residues, 1 model selected  

> color sel red

> select add #2

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #2

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,16.105,0,1,0,41.994,0,0,1,56.596

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.99344,0.098183,0.05861,1.2457,-0.097979,0.99517,-0.0063417,43.057,-0.058949,0.00055754,0.99826,56.71

> view matrix models
> #2,0.06045,0.89031,0.45132,-109.42,-0.97206,0.15525,-0.17607,127,-0.22682,-0.42807,0.87482,104.53

> view matrix models
> #2,-0.96059,0.15852,0.22834,-27.013,-0.24291,-0.87806,-0.41232,235.74,0.13513,-0.45154,0.88196,105.79

> view matrix models
> #2,-0.74881,-0.66252,0.01885,61.752,0.61939,-0.70962,-0.33586,214.27,0.23589,-0.23982,0.94172,82.344

> view matrix models
> #2,-0.92981,0.20977,0.3024,-40.256,-0.33264,-0.83058,-0.44664,236.42,0.15748,-0.51588,0.84206,115.74

> view matrix models
> #2,-0.67493,0.46344,0.57419,-93.65,-0.73277,-0.51245,-0.44771,212.14,0.086758,-0.72292,0.68546,151.18

> view matrix models
> #2,-0.80154,0.54988,0.23489,-57.18,-0.59727,-0.75492,-0.27086,208.09,0.028381,-0.3574,0.93352,92.024

> view matrix models
> #2,-0.8425,0.4924,0.2185,-50.808,-0.53692,-0.80048,-0.26637,211.02,0.043745,-0.34174,0.93878,90.192

> view matrix models
> #2,-0.84548,0.52471,0.099183,-38.082,-0.53336,-0.82068,-0.20498,204.74,-0.026158,-0.22621,0.97373,76.963

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.84548,0.52471,0.099183,35.517,-0.53336,-0.82068,-0.20498,301.24,-0.026158,-0.22621,0.97373,108.48

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.84499,0.52942,0.075599,38.16,-0.53344,-0.82439,-0.18925,299.52,-0.037871,-0.20024,0.97901,105.83

> view matrix models
> #2,-0.72866,0.65334,-0.20542,64.661,-0.65898,-0.75053,-0.049561,276.06,-0.18656,0.099256,0.97742,83.291

> view matrix models
> #2,-0.57727,0.70333,-0.41483,87.673,-0.7746,-0.63243,0.0056752,260.01,-0.25836,0.3246,0.90988,74.805

> view matrix models
> #2,-0.19296,0.50532,-0.84108,157.2,-0.96433,-0.25596,0.067456,223.56,-0.1812,0.82409,0.53669,84.661

> view matrix models
> #2,0.11162,-0.037159,-0.99306,217.75,-0.99059,0.075452,-0.11416,221.63,0.07917,0.99646,-0.028388,143.77

> view matrix models
> #2,0.56075,-0.59061,-0.58029,207.51,-0.70826,0.020856,-0.70564,301.23,0.42886,0.80669,-0.40661,206.53

> view matrix models
> #2,0.36651,-0.63949,-0.67581,223.13,-0.73157,0.25071,-0.63399,274.77,0.57486,0.72677,-0.37594,208.82

> view matrix models
> #2,0.23419,-0.9048,-0.35564,202.29,-0.52718,0.18917,-0.82843,304.34,0.81685,0.3815,-0.43269,242.33

> view matrix models
> #2,0.071785,-0.88792,-0.45437,213.39,-0.50088,0.36185,-0.78625,285.99,0.86253,0.28402,-0.41877,247.96

> view matrix models
> #2,0.073206,-0.87988,-0.46953,214.71,-0.50548,0.3731,-0.778,284.09,0.85973,0.29429,-0.41745,247.02

> view matrix models
> #2,0.11301,-0.90724,-0.40516,208.64,-0.48208,0.30649,-0.82077,294.57,0.86881,0.28807,-0.40272,245.63

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.11301,-0.90724,-0.40516,202.35,-0.48208,0.30649,-0.82077,287.4,0.86881,0.28807,-0.40272,222.54

> view matrix models
> #2,0.11301,-0.90724,-0.40516,222.38,-0.48208,0.30649,-0.82077,239.21,0.86881,0.28807,-0.40272,196.93

> view matrix models
> #2,0.11301,-0.90724,-0.40516,230.38,-0.48208,0.30649,-0.82077,220.91,0.86881,0.28807,-0.40272,205.7

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.44398,-0.88305,-0.15199,196.74,-0.49255,-0.09882,-0.86465,257.03,0.74851,0.45875,-0.47882,202.37

> view matrix models
> #2,0.58448,-0.80837,-0.070155,180.86,-0.45568,-0.25547,-0.8527,267.37,0.67138,0.53035,-0.51767,201.83

> view matrix models
> #2,0.39046,-0.9104,0.13677,162.04,-0.46653,-0.32375,-0.82313,268.74,0.79366,0.25759,-0.55114,226.78

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.39046,-0.9104,0.13677,171.55,-0.46653,-0.32375,-0.82313,292.04,0.79366,0.25759,-0.55114,252.61

> view matrix models
> #2,0.39046,-0.9104,0.13677,170.42,-0.46653,-0.32375,-0.82313,294.43,0.79366,0.25759,-0.55114,234.73

> view matrix models
> #2,0.39046,-0.9104,0.13677,175.05,-0.46653,-0.32375,-0.82313,294.42,0.79366,0.25759,-0.55114,221.69

> view matrix models
> #2,0.39046,-0.9104,0.13677,196.28,-0.46653,-0.32375,-0.82313,301.75,0.79366,0.25759,-0.55114,245.88

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule closed UvrD1.pdb (#2) to map
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) using 5285 atoms  
average map value = 0.5368, steps = 116  
shifted from previous position = 24.2  
rotated from previous position = 23.5 degrees  
atoms outside contour = 3368, contour level = 0.71848  
  
Position of closed UvrD1.pdb (#2) relative to
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.27865761 -0.88082738 0.38274414 181.86686007  
-0.65541964 -0.46571343 -0.59458903 273.56885430  
0.70197937 -0.08517127 -0.70708615 279.66907820  
Axis 0.79342570 -0.49721361 0.35107589  
Axis point 0.00000000 168.59487994 133.52216240  
Rotation angle (degrees) 161.27512260  
Shift along axis 106.46075509  
  

> view matrix models
> #2,0.27866,-0.88083,0.38274,179.89,-0.65542,-0.46571,-0.59459,275.31,0.70198,-0.085171,-0.70709,281.66

> volume #1 level 0.7185

> volume #1 level 0.5834

> open "/Users/ankitachadda/Desktop/closed UvrD1.pdb"

closed UvrD1.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for closed UvrD1.pdb #3  
---  
Chain | Description  
C | No description available  
  

> select add #3

10570 atoms, 10742 bonds, 1348 residues, 2 models selected  

> select ::name="CYS"

36 atoms, 30 bonds, 6 residues, 2 models selected  

> color sel red

> select clear

> select add #3

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> view matrix models #3,1,0,0,40.868,0,1,0,31.936,0,0,1,-7.05

> view matrix models #3,1,0,0,137.82,0,1,0,107.37,0,0,1,-14.798

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.88026,0.24551,0.40603,67.571,-0.40941,0.82553,0.38844,70.702,-0.23982,-0.50817,0.8272,45.22

> view matrix models
> #3,0.13279,-0.24065,0.96148,32.811,-0.89332,0.39116,0.22128,124.17,-0.42935,-0.8883,-0.16303,199.53

> view matrix models
> #3,-0.55581,-0.69981,0.44872,131.85,-0.80757,0.32644,-0.49119,219.7,0.19726,-0.63538,-0.74658,255.32

> view matrix models
> #3,-0.60816,-0.75953,0.23077,164,-0.72433,0.41201,-0.55281,221.17,0.32479,-0.50335,-0.80072,252.38

> view matrix models
> #3,-0.079368,-0.8976,-0.4336,259.43,-0.14108,0.44071,-0.88649,262.06,0.98681,-0.0091853,-0.16162,134.62

> view matrix models
> #3,-0.89414,-0.22648,0.3863,103.73,-0.3969,0.0014055,-0.91786,298.89,0.20733,-0.97402,-0.091147,197.56

> view matrix models
> #3,-0.83352,-0.048952,0.55031,69.561,-0.55051,-0.01052,-0.83476,289.06,0.046653,-0.99875,-0.01818,189.97

> view matrix models
> #3,-0.86758,0.34657,0.35665,64.317,-0.43582,-0.18448,-0.88092,308.17,-0.23951,-0.91971,0.31109,141.85

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.86758,0.34657,0.35665,71.787,-0.43582,-0.18448,-0.88092,297.9,-0.23951,-0.91971,0.31109,173.32

> view matrix models
> #3,-0.86758,0.34657,0.35665,92.896,-0.43582,-0.18448,-0.88092,290.2,-0.23951,-0.91971,0.31109,164.06

> fitmap #3 inMap #1

Fit molecule closed UvrD1.pdb (#3) to map
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) using 5285 atoms  
average map value = 0.8569, steps = 120  
shifted from previous position = 6.95  
rotated from previous position = 44.3 degrees  
atoms outside contour = 1698, contour level = 0.58342  
  
Position of closed UvrD1.pdb (#3) relative to
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.60129319 0.79423015 -0.08743553 117.49940028  
-0.50784481 -0.46435554 -0.72558086 290.23973797  
-0.61687936 -0.39188315 0.68255948 83.78826684  
Axis 0.23098582 0.36648145 -0.90129734  
Axis point 133.20824423 137.49280482 0.00000000  
Rotation angle (degrees) 133.75250420  
Shift along axis 57.99003453  
  

> select subtract #3

Nothing selected  

> fitmap #2 inMap #1

Fit molecule closed UvrD1.pdb (#2) to map
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) using 5285 atoms  
average map value = 0.5368, steps = 88  
shifted from previous position = 3.3  
rotated from previous position = 0.00349 degrees  
atoms outside contour = 2837, contour level = 0.58342  
  
Position of closed UvrD1.pdb (#2) relative to
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.27866993 -0.88083158 0.38272551 181.86943645  
-0.65546064 -0.46570425 -0.59455101 273.56439013  
0.70193620 -0.08517802 -0.70712820 279.67553368  
Axis 0.79343092 -0.49722234 0.35105173  
Axis point 0.00000000 168.59575879 133.52379490  
Rotation angle (degrees) 161.27695689  
Shift along axis 106.45908583  
  

> volume #1 level 0.5564

> volume #1 level 0.6464

> hide #2 models

> open "/Users/ankitachadda/Desktop/UvrD1 open form predicted structure.pdb"

UvrD1 open form predicted structure.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for UvrD1 open form predicted structure.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select add #4

5257 atoms, 5341 bonds, 670 residues, 1 model selected  

> select ::name="CYS"

54 atoms, 45 bonds, 9 residues, 3 models selected  

> color (#3-4 & sel) red

> select clear

> select add #4

5257 atoms, 5341 bonds, 670 residues, 1 model selected  

> view matrix models #4,1,0,0,-54.753,0,1,0,73.954,0,0,1,70.976

> view matrix models #4,1,0,0,-86.295,0,1,0,122.15,0,0,1,179.43

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.22051,-0.09347,0.9709,-42.414,0.030047,0.99558,0.089022,117.26,-0.97492,0.0095423,0.22234,284.69

> view matrix models
> #4,-0.018082,-0.055275,0.99831,-22.821,0.010279,0.99841,0.055467,119.83,-0.99978,0.011265,-0.017485,293.1

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.018082,-0.055275,0.99831,2.0068,0.010279,0.99841,0.055467,144.55,-0.99978,0.011265,-0.017485,337.78

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.085949,0.29987,0.9501,4.4696,-0.076488,0.94883,-0.30639,162.24,-0.99336,-0.099005,-0.058614,339.76

> view matrix models
> #4,0.073074,0.35522,0.93192,-9.6656,-0.23622,0.914,-0.32987,177.25,-0.96895,-0.19603,0.1507,333.45

> view matrix models
> #4,0.169,0.575,0.80051,-17.521,0.20028,0.77521,-0.59911,148.05,-0.96505,0.26158,0.015845,330.56

> view matrix models
> #4,0.28765,0.45057,0.84513,-27.386,0.22377,0.82638,-0.51674,143.17,-0.93123,0.33775,0.13688,323.43

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.28765,0.45057,0.84513,-25.351,0.22377,0.82638,-0.51674,160.29,-0.93123,0.33775,0.13688,320.41

> view matrix models
> #4,0.28765,0.45057,0.84513,30.503,0.22377,0.82638,-0.51674,189.52,-0.93123,0.33775,0.13688,347.9

> view matrix models
> #4,0.28765,0.45057,0.84513,91.81,0.22377,0.82638,-0.51674,197.89,-0.93123,0.33775,0.13688,339.74

> view matrix models
> #4,0.28765,0.45057,0.84513,99.578,0.22377,0.82638,-0.51674,150.03,-0.93123,0.33775,0.13688,264.99

> view matrix models
> #4,0.28765,0.45057,0.84513,99.858,0.22377,0.82638,-0.51674,147.88,-0.93123,0.33775,0.13688,264.16

> fitmap #4 inMap #1

Fit molecule UvrD1 open form predicted structure.pdb (#4) to map
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) using 5257 atoms  
average map value = 0.6273, steps = 260  
shifted from previous position = 8.32  
rotated from previous position = 82.6 degrees  
atoms outside contour = 2701, contour level = 0.64645  
  
Position of UvrD1 open form predicted structure.pdb (#4) relative to
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.70295040 -0.65480989 0.27764136 105.28237475  
0.70900515 0.67606000 -0.20063539 99.82945336  
-0.05632419 0.33788589 0.93950024 163.52696353  
Axis 0.35809786 0.22207544 0.90688942  
Axis point -44.85499591 67.28763423 0.00000000  
Rotation angle (degrees) 48.75689544  
Shift along axis 208.17193594  
  

> view matrix models
> #4,0.70295,-0.65481,0.27764,104.61,0.70901,0.67606,-0.20064,100.94,-0.056324,0.33789,0.9395,164.16

> view matrix models
> #4,0.70295,-0.65481,0.27764,104.02,0.70901,0.67606,-0.20064,99.709,-0.056324,0.33789,0.9395,165.95

> fitmap #4 inMap #1

Fit molecule UvrD1 open form predicted structure.pdb (#4) to map
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) using 5257 atoms  
average map value = 0.6273, steps = 72  
shifted from previous position = 2.74  
rotated from previous position = 0.0394 degrees  
atoms outside contour = 2700, contour level = 0.64645  
  
Position of UvrD1 open form predicted structure.pdb (#4) relative to
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.70280727 -0.65491487 0.27775610 105.27033615  
0.70910554 0.67615275 -0.19996696 99.79545803  
-0.05684422 0.33749663 0.93960883 163.55985508  
Axis 0.35740666 0.22250509 0.90705676  
Axis point -44.63621865 67.38026488 0.00000000  
Rotation angle (degrees) 48.75467818  
Shift along axis 208.18738866  
  

> select subtract #4

Nothing selected  

> volume #1 level 0.705

> select add #3

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #2

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #3

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #2

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> hide #4 models

> volume #1 level 0.6099

> select add #3

10570 atoms, 10742 bonds, 1348 residues, 2 models selected  

> select subtract #3

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> show #2 models

> fitmap #2 inMap #1

Fit molecule closed UvrD1.pdb (#2) to map
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) using 5285 atoms  
average map value = 0.5368, steps = 48  
shifted from previous position = 0.0232  
rotated from previous position = 0.0246 degrees  
atoms outside contour = 2951, contour level = 0.60985  
  
Position of closed UvrD1.pdb (#2) relative to
cryosparc_P43_J1166_002_volume_map_sharp (1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.27835749 -0.88099204 0.38258351 181.91640707  
-0.65570275 -0.46536654 -0.59454848 273.55517512  
0.70183404 -0.08536404 -0.70720716 279.70457267  
Axis 0.79333302 -0.49740716 0.35101118  
Axis point 0.00000000 168.63307307 133.52260921  
Rotation angle (degrees) 161.28174943  
Shift along axis 106.43142071  
  

> save "/Users/ankitachadda/Desktop/first monomer and second aligned with
> closed .png" width 1440 height 723 supersample 3

> open model

'model' has no suffix  

> open model panel

'model' has no suffix  

> panel

Unknown command: modeller panel  

> panel

Unknown command: modeller panel  

> panel

Unknown command: modeller panel  

> save "/Users/ankitachadda/Desktop/second conformation phosphate2.cxs"

——— End of log from Thu Aug 31 13:44:31 2023 ———

opened ChimeraX session  

> select subtract #2

Nothing selected  

> hide #2 models

> show #4 models

> select add #4

5257 atoms, 5341 bonds, 670 residues, 1 model selected  

> select subtract #4

Nothing selected  

> save "/Users/ankitachadda/Desktop/second conformation aligned with one open
> and one closed conformation.png" width 1440 height 723 supersample 3

> save "/Users/ankitachadda/Desktop/second conformation phosphate3.cxs"

——— End of log from Thu Aug 31 13:47:34 2023 ———

opened ChimeraX session  

> open 4c30

4c30 title:  
Crystal structure of Deinococcus radiodurans UvrD in complex with DNA, form 2
[more info...]  
  
Chain information for 4c30 #5  
---  
Chain | Description | UniProt  
A D F I | DNA HELICASE II | Q9RTI9_DEIRA 1-665  
K X | DNA STRAND FOR25 |  
L Y | DNA STRAND REV25 |  
  
Non-standard residues in 4c30 #5  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
  
4c30 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  

> surface #1,3-5

> select add #5

22049 atoms, 22524 bonds, 122 pseudobonds, 2740 residues, 4 models selected  

> select subtract #5

8 models selected  

> select #5/A#5/D#5/F#5/I

20172 atoms, 20432 bonds, 36 pseudobonds, 2647 residues, 3 models selected  

> surface hidePatches (#!5 & sel)

> hide (#!5 & sel) target a

> select #5/K#5/X

942 atoms, 1050 bonds, 46 residues, 1 model selected  

> select clear

> select #5/K

471 atoms, 525 bonds, 23 residues, 1 model selected  

> hide (#!5 & sel) target a

> surface hidePatches (#!5 & sel)

> select #5/L

467 atoms, 521 bonds, 23 residues, 1 model selected  

> surface hidePatches (#!5 & sel)

> hide (#!5 & sel) target a

[Repeated 1 time(s)]

> select #2/C

5285 atoms, 5371 bonds, 674 residues, 1 model selected  

> select add #4

10542 atoms, 10712 bonds, 1344 residues, 2 models selected  

> surface hidePatches (#!4 & sel)

> select subtract #4

5285 atoms, 5371 bonds, 674 residues, 2 models selected  

> select add #3

10570 atoms, 10742 bonds, 1348 residues, 2 models selected  

> surface hidePatches (#!3 & sel)

> select subtract #2

5285 atoms, 5371 bonds, 674 residues, 2 models selected  

> select subtract #3

1 model selected  

> select #5/X

471 atoms, 525 bonds, 23 residues, 1 model selected  

> select #5/Y

468 atoms, 521 bonds, 24 residues, 1 model selected  

> surface hidePatches (#!5 & sel)

> cartoon (#!5 & sel)

> nucleotides (#!5 & sel) ladder

> select clear

> select #5/Y

468 atoms, 521 bonds, 24 residues, 1 model selected  

> select clear

> select #5/X

471 atoms, 525 bonds, 23 residues, 1 model selected  

> show (#!5 & sel) target ab

> surface hidePatches (#!5 & sel)

> nucleotides (#!5 & sel) ladder

> hide (#!5 & sel) target a

> show (#!5 & sel) target ab

> surface hidePatches (#!5 & sel)

> cartoon (#!5 & sel)

> select clear

> select add #5

22049 atoms, 22524 bonds, 122 pseudobonds, 2740 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,16.328,0,1,0,110.35,0,0,1,178.29

> view matrix models #5,1,0,0,42.897,0,1,0,154.43,0,0,1,237.22

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.88772,0.41816,-0.1926,44.33,-0.45959,0.82945,-0.31747,170.22,0.026998,0.37034,0.9285,234.4

> view matrix models
> #5,0.40251,0.65127,-0.6433,58.621,-0.91043,0.21158,-0.35545,185.54,-0.095389,0.72875,0.6781,237.29

> view matrix models
> #5,0.06262,0.55592,-0.82887,69.156,-0.93535,-0.25701,-0.24304,188.61,-0.34814,0.79051,0.50388,244.44

> view matrix models
> #5,0.086791,0.48057,-0.87265,70.095,-0.99461,-0.0080369,-0.10335,185.11,-0.056678,0.87692,0.47728,238.42

> view matrix models
> #5,0.64876,0.49226,-0.58034,54.526,-0.75486,0.51291,-0.40879,180.56,0.096434,0.70328,0.70434,233.46

> view matrix models
> #5,0.55723,0.45199,-0.69656,58.602,-0.65338,0.75636,-0.03188,170.1,0.51244,0.47288,0.71679,227.58

> view matrix models
> #5,0.61976,0.26134,-0.74,59.987,-0.28359,0.95379,0.099331,158.8,0.73176,0.1483,0.66523,227.37

> view matrix models
> #5,0.90446,-0.23852,-0.35364,52.635,0.10832,0.9303,-0.35043,158.91,0.41257,0.27864,0.86726,228.99

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.90446,-0.23852,-0.35364,113.24,0.10832,0.9303,-0.35043,155.64,0.41257,0.27864,0.86726,190.05

> view matrix models
> #5,0.90446,-0.23852,-0.35364,114,0.10832,0.9303,-0.35043,155.03,0.41257,0.27864,0.86726,188.57

> view matrix models
> #5,0.90446,-0.23852,-0.35364,108.44,0.10832,0.9303,-0.35043,166.12,0.41257,0.27864,0.86726,194.52

> view matrix models
> #5,0.90446,-0.23852,-0.35364,112.46,0.10832,0.9303,-0.35043,165.93,0.41257,0.27864,0.86726,193.13

> view matrix models
> #5,0.90446,-0.23852,-0.35364,110.18,0.10832,0.9303,-0.35043,172.75,0.41257,0.27864,0.86726,196.41

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.89993,0.27771,-0.33615,105.22,-0.31219,0.94859,-0.052087,175.73,0.30441,0.15182,0.94037,198.45

> view matrix models
> #5,0.79443,0.35046,-0.49604,109.21,-0.54597,0.76988,-0.33045,186.61,0.26608,0.53334,0.80296,197.74

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.79443,0.35046,-0.49604,107.83,-0.54597,0.76988,-0.33045,182.92,0.26608,0.53334,0.80296,197.13

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.69378,0.4207,-0.58453,110.59,-0.42091,0.89545,0.14489,171.43,0.58438,0.14551,0.79833,194.82

> view matrix models
> #5,0.66327,0.27177,-0.69729,114.42,0.059215,0.90976,0.4109,157.65,0.74603,-0.31383,0.58732,199.42

> view matrix models
> #5,0.65392,-0.04402,-0.75528,118.43,0.27464,0.94402,0.18277,156.9,0.70495,-0.32695,0.6294,199.65

> view matrix models
> #5,0.61149,-0.10349,-0.78445,120.26,0.42128,0.88179,0.21207,154.23,0.66977,-0.46015,0.5828,202.33

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.61149,-0.10349,-0.78445,121.6,0.42128,0.88179,0.21207,156.93,0.66977,-0.46015,0.5828,195.87

> view matrix models
> #5,0.61149,-0.10349,-0.78445,123.06,0.42128,0.88179,0.21207,155.78,0.66977,-0.46015,0.5828,193.44

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.69532,0.16471,-0.69957,117.57,0.22171,0.87675,0.42679,156.13,0.68364,-0.45186,0.57311,193.25

> ui mousemode right "rotate selected models"

> select subtract #5

8 models selected  

> ui tool show "Fit in Map"

> fitmap #5 inMap #1

Fit molecule 4c30 (#5) to map cryosparc_P43_J1166_002_volume_map_sharp (1).mrc
(#1) using 22049 atoms  
average map value = 0.1631, steps = 476  
shifted from previous position = 25  
rotated from previous position = 28.8 degrees  
atoms outside contour = 19590, contour level = 0.60985  
  
Position of 4c30 (#5) relative to cryosparc_P43_J1166_002_volume_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.31349830 0.18826051 -0.93073992 134.22673519  
0.09999540 0.96815606 0.22950982 155.41676439  
0.94430913 -0.16502065 0.28469009 186.59055286  
Axis -0.20568407 -0.97753598 -0.04601604  
Axis point -71.00478720 0.00000000 155.01469858  
Rotation angle (degrees) 73.55037541  
Shift along axis -188.11993755  
  

> ui mousemode right "translate selected models"

> select add #5

22049 atoms, 22524 bonds, 122 pseudobonds, 2740 residues, 4 models selected  

> view matrix models
> #5,0.3135,0.18826,-0.93074,135.13,0.099995,0.96816,0.22951,157.31,0.94431,-0.16502,0.28469,195.08

> view matrix models
> #5,0.3135,0.18826,-0.93074,130.85,0.099995,0.96816,0.22951,157.57,0.94431,-0.16502,0.28469,188.02

> view matrix models
> #5,0.3135,0.18826,-0.93074,132.5,0.099995,0.96816,0.22951,160.11,0.94431,-0.16502,0.28469,191.15

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.40501,0.053315,-0.91275,131.68,0.10094,0.98959,0.10259,161.97,0.90872,-0.13368,0.39542,189.75

> view matrix models
> #5,0.65506,0.24774,-0.71381,121.9,-0.034979,0.95365,0.29887,161.71,0.75477,-0.17081,0.63336,189.16

> select subtract #5

8 models selected  

> save "/Users/ankitachadda/Desktop/second conformation aligned with one
> closed and one open form of UvrD1 and DNA.cxs"

——— End of log from Thu Aug 31 14:17:49 2023 ———

opened ChimeraX session  

> open "/Users/ankitachadda/Desktop/second conformation aligned with one
> closed and one open form of UvrD1 and DNA.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/private/var/folders/c5/n9ghd9k10gbf_g_h55yd5k380000gn/T/AppTranslocation/2669BF73-6FC4-46D5-877E-4DEA709A3DAE/d/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 700, in restore  
self.reset()  
File
"/private/var/folders/c5/n9ghd9k10gbf_g_h55yd5k380000gn/T/AppTranslocation/2669BF73-6FC4-46D5-877E-4DEA709A3DAE/d/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset  
sm.reset_state(container, self)  
File
"/private/var/folders/c5/n9ghd9k10gbf_g_h55yd5k380000gn/T/AppTranslocation/2669BF73-6FC4-46D5-877E-4DEA709A3DAE/d/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 149, in reset_state  
self.clear()  
File
"/private/var/folders/c5/n9ghd9k10gbf_g_h55yd5k380000gn/T/AppTranslocation/2669BF73-6FC4-46D5-877E-4DEA709A3DAE/d/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/bond_rot/manager.py", line 45, in delete_all_rotations  
for rotater in self.bond_rotaters.values():  
AttributeError: 'list' object has no attribute 'values'  
  

Failed opening file /Users/ankitachadda/Desktop/second conformation aligned
with one closed and one open form of UvrD1 and DNA.cxs:  
'list' object has no attribute 'values'  




OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: MYD82LL/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.1.1
      OS Loader Version: 10151.1.1

Software:

    System Software Overview:

      System Version: macOS 14.0 (23A344)
      Kernel Version: Darwin 23.0.0
      Time since boot: 52 minutes, 16 seconds

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL 2208WFP:
          Resolution: 1680 x 1050 (Widescreen Super eXtended Graphics Array Plus)
          UI Looks like: 1680 x 1050 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
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    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0