Unknown problem

[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/aligned UvrD dimer with first
> conformation.cxs"

Opened cryosparc_P43_J1034_003_volume_map_sharp (5).mrc as #1, grid size
200,200,200, pixel 1.62, shown at level 0.598, step 1, values float32  
Opened cryosparc_P43_J1057_003_volume_map_sharp (3).mrc as #4, grid size
200,200,200, pixel 1.62, shown at level 1.29, step 1, values float32  
Log from Wed Aug 23 09:45:24 2023UCSF ChimeraX version: 1.7.dev202308180104
(2023-08-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/ankitachadda/Desktop/aligned UvrD dimer with first
> conformation.cxs"

Opened cryosparc_P43_J1034_003_volume_map_sharp (5).mrc as #1, grid size
200,200,200, pixel 1.62, shown at level 0.598, step 1, values float32  
Log from Tue Aug 22 16:03:48 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_J1034_003_volume_map_sharp
> (5).mrc"

Opened cryosparc_P43_J1034_003_volume_map_sharp (5).mrc as #1, grid size
200,200,200, pixel 1.62, shown at level 0.106, step 1, values float32  

> volume #1 level 0.6254

> open 3lfu

3lfu title:  
Crystal Structure of E. coli UvrD [more info...]  
  
Chain information for 3lfu #2  
---  
Chain | Description | UniProt  
A | DNA helicase II | UVRD_ECOLI 1-647  
  
Non-standard residues in 3lfu #2  
---  
SO4 — sulfate ion  
  

> select add #2

5780 atoms, 5143 bonds, 4 pseudobonds, 1358 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-55.788,0,1,0,113.42,0,0,1,39.192

> view matrix models #2,1,0,0,64.769,0,1,0,29.049,0,0,1,95.891

> view matrix models #2,1,0,0,176.25,0,1,0,113.24,0,0,1,133.41

> view matrix models #2,1,0,0,136.92,0,1,0,173.54,0,0,1,139.71

> ui mousemode right "rotate selected models"

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule 3lfu (#2) to map cryosparc_P43_J1034_003_volume_map_sharp (5).mrc
(#1) using 5780 atoms  
average map value = 0.3941, steps = 120  
shifted from previous position = 13.2  
rotated from previous position = 31.4 degrees  
atoms outside contour = 4153, contour level = 0.62535  
  
Position of 3lfu (#2) relative to cryosparc_P43_J1034_003_volume_map_sharp
(5).mrc (#1) coordinates:  
Matrix rotation and translation  
0.85759559 0.39731839 0.32660053 132.37639049  
-0.36540385 0.91755685 -0.15674649 181.25942179  
-0.36195281 0.01508401 0.93207437 162.73325393  
Axis 0.16493393 0.66091765 -0.73210973  
Axis point 488.89928368 -148.60935367 0.00000000  
Rotation angle (degrees) 31.39311453  
Shift along axis 22.49231152  
  

> view matrix models
> #2,0.76127,0.49051,0.4241,133.79,-0.63882,0.67951,0.3608,185.61,-0.1112,-0.54559,0.83064,159.28

> view matrix models
> #2,0.51108,0.4892,0.70674,138.56,-0.75813,-0.13088,0.63884,191.07,0.40502,-0.8623,0.30399,150.7

> view matrix models
> #2,0.54816,0.33004,0.7685,137.67,-0.21994,-0.82963,0.51317,179.72,0.80693,-0.45032,-0.38218,143.14

> view matrix models
> #2,0.59465,0.081899,0.79981,137.33,-0.033906,-0.99136,0.12672,179.02,0.80327,-0.10247,-0.58673,143.42

> view matrix models
> #2,0.6758,0.035505,0.73623,135.75,0.34328,-0.89906,-0.27175,171.01,0.65227,0.43638,-0.61978,145.34

> view matrix models
> #2,0.62332,0.089468,0.77683,136.64,0.081488,-0.99546,0.049262,176.28,0.77771,0.032596,-0.62778,143.87

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.62332,0.089468,0.77683,136.21,0.081488,-0.99546,0.049262,178.23,0.77771,0.032596,-0.62778,136.13

> fitmap #2 inMap #1

Fit molecule 3lfu (#2) to map cryosparc_P43_J1034_003_volume_map_sharp (5).mrc
(#1) using 5780 atoms  
average map value = 0.3714, steps = 92  
shifted from previous position = 6.19  
rotated from previous position = 14.4 degrees  
atoms outside contour = 4313, contour level = 0.62535  
  
Position of 3lfu (#2) relative to cryosparc_P43_J1034_003_volume_map_sharp
(5).mrc (#1) coordinates:  
Matrix rotation and translation  
0.75444185 -0.04151153 0.65505289 138.86976343  
-0.08926968 -0.99521413 0.03974629 187.01451160  
0.65026796 -0.08846263 -0.75453691 143.43056302  
Axis -0.93652377 0.03495233 -0.34885751  
Axis point 0.00000000 97.61492048 42.31846030  
Rotation angle (degrees) 176.07507110  
Shift along axis -173.55507006  
  

> view matrix models
> #2,0.75444,-0.041512,0.65505,136.72,-0.08927,-0.99521,0.039746,194.45,0.65027,-0.088463,-0.75454,138.21

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.50888,0.6434,0.57191,141.27,0.25415,-0.74704,0.61428,176.11,0.82247,-0.16724,-0.54367,131.03

> view matrix models
> #2,0.1947,0.94322,0.26913,152.58,0.31898,-0.32035,0.89198,168.61,0.92755,-0.087823,-0.36324,125.35

> view matrix models
> #2,-0.10312,0.99066,-0.089194,165.44,0.23066,0.11105,0.96668,168.04,0.96756,0.079113,-0.23995,121.8

> view matrix models
> #2,-0.47617,0.56919,-0.67029,185.78,-0.17711,0.68455,0.70712,180.2,0.86133,0.45542,-0.22516,122.76

> view matrix models
> #2,-0.53058,-0.03261,-0.84701,192.9,-0.55961,0.76401,0.32113,195.81,0.63665,0.64438,-0.42362,130.79

> view matrix models
> #2,-0.66422,-0.55332,-0.50265,196.4,-0.70192,0.69294,0.16474,202.35,0.25715,0.46224,-0.84865,148.26

> view matrix models
> #2,-0.79939,-0.42854,-0.42109,199.01,-0.55246,0.79977,0.23486,196.31,0.23612,0.42039,-0.87608,149.46

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.79939,-0.42854,-0.42109,198.29,-0.55246,0.79977,0.23486,189.13,0.23612,0.42039,-0.87608,144.13

> fitmap #2 inMap #1

Fit molecule 3lfu (#2) to map cryosparc_P43_J1034_003_volume_map_sharp (5).mrc
(#1) using 5780 atoms  
average map value = 0.3764, steps = 92  
shifted from previous position = 3.52  
rotated from previous position = 22.7 degrees  
atoms outside contour = 4337, contour level = 0.62535  
  
Position of 3lfu (#2) relative to cryosparc_P43_J1034_003_volume_map_sharp
(5).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96810958 -0.15053614 -0.20025662 199.01714021  
-0.21669832 0.90429493 0.36782130 173.61182431  
0.12572065 0.39948660 -0.90807752 147.63579490  
Axis 0.09477005 -0.97560690 -0.19801466  
Axis point 103.11034510 0.00000000 65.51397457  
Rotation angle (degrees) 170.38285203  
Shift along axis -179.75008189  
  

> fitmap #2 inMap #1

Fit molecule 3lfu (#2) to map cryosparc_P43_J1034_003_volume_map_sharp (5).mrc
(#1) using 5780 atoms  
average map value = 0.3764, steps = 48  
shifted from previous position = 0.0145  
rotated from previous position = 0.014 degrees  
atoms outside contour = 4338, contour level = 0.62535  
  
Position of 3lfu (#2) relative to cryosparc_P43_J1034_003_volume_map_sharp
(5).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96805572 -0.15075378 -0.20035321 199.02364280  
-0.21693395 0.90426007 0.36776812 173.63294391  
0.12572898 0.39948344 -0.90807775 147.63736283  
Axis 0.09488836 -0.97559779 -0.19800291  
Axis point 103.12334599 0.00000000 65.51788364  
Rotation angle (degrees) 170.37963641  
Shift along axis -179.74351709  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.98675,-0.036238,-0.15813,198.48,-0.052167,0.99384,0.097775,170.88,0.15362,0.10473,-0.98257,149.29

> fitmap #2 inMap #1

Fit molecule 3lfu (#2) to map cryosparc_P43_J1034_003_volume_map_sharp (5).mrc
(#1) using 5780 atoms  
average map value = 0.3739, steps = 104  
shifted from previous position = 3.64  
rotated from previous position = 18.7 degrees  
atoms outside contour = 4348, contour level = 0.62535  
  
Position of 3lfu (#2) relative to cryosparc_P43_J1034_003_volume_map_sharp
(5).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99466512 -0.09035961 0.04976373 200.14666481  
-0.06855459 0.93948975 0.33564755 169.86985227  
-0.07708149 0.33044538 -0.94067226 151.61629055  
Axis -0.04038612 0.98474029 0.16927944  
Axis point 105.52611321 0.00000000 57.80943844  
Rotation angle (degrees) 176.30728539  
Shift along axis 184.86006078  
  

> view matrix models
> #2,-0.91891,-0.17058,-0.35567,202.61,-0.3093,0.87118,0.38129,177.28,0.24481,0.46038,-0.8533,139.88

> fitmap #2 inMap #1

Fit molecule 3lfu (#2) to map cryosparc_P43_J1034_003_volume_map_sharp (5).mrc
(#1) using 5780 atoms  
average map value = 0.3764, steps = 64  
shifted from previous position = 5.17  
rotated from previous position = 9.75 degrees  
atoms outside contour = 4337, contour level = 0.62535  
  
Position of 3lfu (#2) relative to cryosparc_P43_J1034_003_volume_map_sharp
(5).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96810674 -0.15063531 -0.20019575 199.01605023  
-0.21678012 0.90423360 0.36792386 173.60498084  
0.12560141 0.39958803 -0.90804939 147.64025221  
Axis 0.09481755 -0.97559127 -0.19806897  
Axis point 103.11652426 0.00000000 65.50714537  
Rotation angle (degrees) 170.38806046  
Shift along axis -179.74024139  
  

> view matrix models
> #2,-0.99134,-0.13105,-0.0089371,197.57,-0.12918,0.96036,0.24704,171.85,-0.023792,0.24606,-0.96896,153.85

> select clear

> save "/Users/ankitachadda/Desktop/aligned UvrD dimer with second
> conformation.cxs"

> open 3lfu

3lfu title:  
Crystal Structure of E. coli UvrD [more info...]  
  
Chain information for 3lfu #3  
---  
Chain | Description | UniProt  
A | DNA helicase II | UVRD_ECOLI 1-647  
  
Non-standard residues in 3lfu #3  
---  
SO4 — sulfate ion  
  

> select add #3

5780 atoms, 5143 bonds, 4 pseudobonds, 1358 residues, 2 models selected  

> view matrix models
> #3,0.9854,0.024607,-0.16846,2.1234,-0.10355,0.87204,-0.47835,9.1218,0.13513,0.48881,0.86186,-5.5833

> ui mousemode right "move picked models"

> view matrix models
> #3,0.9854,0.024607,-0.16846,58.021,-0.10355,0.87204,-0.47835,141.61,0.13513,0.48881,0.86186,102.42

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.95665,0.0046903,-0.29121,60.355,-0.16354,0.83602,-0.52376,144.18,0.241,0.54868,0.80054,99.428

> view matrix models
> #3,0.88958,-0.011437,-0.45664,64.319,-0.24637,0.8298,-0.50073,146.55,0.38465,0.55794,0.73536,95.596

> view matrix models
> #3,0.79267,0.043829,0.60807,55.566,0.25499,0.88215,-0.39598,129.48,-0.55377,0.46893,0.68807,125.89

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.79267,0.043829,0.60807,131.33,0.25499,0.88215,-0.39598,128.91,-0.55377,0.46893,0.68807,137.34

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.14134,0.48116,0.86517,146.32,0.28351,0.81766,-0.50105,129.53,-0.9485,0.3161,-0.020845,158.16

> view matrix models
> #3,-0.70897,0.58209,0.39816,177.27,0.3908,0.79423,-0.46526,125.93,-0.58706,-0.17425,-0.79057,158.04

> view matrix models
> #3,0.030967,0.9491,-0.31344,159.71,0.73824,-0.23313,-0.63297,122.9,-0.67382,-0.2118,-0.70789,160.07

> view matrix models
> #3,0.88619,-0.024949,-0.46264,140.34,-0.13909,-0.96682,-0.21428,150.04,-0.44195,0.25424,-0.86026,151.76

> view matrix models
> #3,0.819,-0.50708,0.26854,137.38,-0.47996,-0.86188,-0.16369,159.52,0.31446,0.0051754,-0.94926,130.58

> fitmap #3 inMap #1

Fit molecule 3lfu (#3) to map cryosparc_P43_J1034_003_volume_map_sharp (5).mrc
(#1) using 5780 atoms  
average map value = 0.2034, steps = 140  
shifted from previous position = 14.9  
rotated from previous position = 26.5 degrees  
atoms outside contour = 4901, contour level = 0.62535  
  
Position of 3lfu (#3) relative to cryosparc_P43_J1034_003_volume_map_sharp
(5).mrc (#1) coordinates:  
Matrix rotation and translation  
0.67801166 -0.46183921 0.57184328 138.31879100  
-0.26386941 -0.87903483 -0.39707770 148.95516123  
0.68605621 0.11833136 -0.71786110 102.76198869  
Axis 0.91415177 -0.20257299 0.35112778  
Axis point 0.00000000 85.37363282 38.64786803  
Rotation angle (degrees) 163.62602821  
Shift along axis 132.35266496  
  

> volume #1 level 0.2974

> volume #1 level 0.598

> fitmap #3 inMap #1

Fit molecule 3lfu (#3) to map cryosparc_P43_J1034_003_volume_map_sharp (5).mrc
(#1) using 5780 atoms  
average map value = 0.2034, steps = 44  
shifted from previous position = 0.0259  
rotated from previous position = 0.027 degrees  
atoms outside contour = 4826, contour level = 0.59802  
  
Position of 3lfu (#3) relative to cryosparc_P43_J1034_003_volume_map_sharp
(5).mrc (#1) coordinates:  
Matrix rotation and translation  
0.67777890 -0.46179219 0.57215708 138.34439986  
-0.26397541 -0.87911352 -0.39683297 148.97152617  
0.68624539 0.11792962 -0.71774638 102.76541931  
Axis 0.91409131 -0.20259268 0.35127379  
Axis point 0.00000000 85.39428910 38.61753418  
Rotation angle (degrees) 163.64603082  
Shift along axis 132.37767108  
  

> fitmap #2 inMap #1

Fit molecule 3lfu (#2) to map cryosparc_P43_J1034_003_volume_map_sharp (5).mrc
(#1) using 5780 atoms  
average map value = 0.3739, steps = 80  
shifted from previous position = 4.41  
rotated from previous position = 6.76 degrees  
atoms outside contour = 4182, contour level = 0.59802  
  
Position of 3lfu (#2) relative to cryosparc_P43_J1034_003_volume_map_sharp
(5).mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99462809 -0.09076355 0.04976885 200.14595375  
-0.06892228 0.93941000 0.33579543 169.86475700  
-0.07723134 0.33056138 -0.94061921 151.59906794  
Axis -0.04058316 0.98471998 0.16935043  
Axis point 105.54482615 0.00000000 57.78998143  
Rotation angle (degrees) 176.30269151  
Shift along axis 184.82003253  
  

> save "/Users/ankitachadda/Desktop/aligned UvrD dimer with first
> conformation.cxs"

——— End of log from Tue Aug 22 16:03:48 2023 ———

opened ChimeraX session  

> select subtract #3

Nothing selected  

> hide #!3 models

> hide #!2 models

> open "/Users/ankitachadda/Downloads/cryosparc_P43_J1057_003_volume_map_sharp
> (3).mrc"

Opened cryosparc_P43_J1057_003_volume_map_sharp (3).mrc as #4, grid size
200,200,200, pixel 1.62, shown at level 0.199, step 1, values float32  

> volume #4 level 1.288

> color #4 #ff85ffff models

> select add #4

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,-0.21341,0,1,0,7.2976,0,0,1,-3.4448

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.17688,-0.14993,-0.97275,328.61,-0.076596,0.98324,-0.16547,50.805,0.98125,0.10378,0.16243,-51.443

> view matrix models
> #4,-0.80284,-0.27052,-0.53129,444.87,-0.28782,0.95627,-0.05198,72.976,0.52212,0.11118,-0.84559,195.04

> view matrix models
> #4,-0.86005,-0.21876,-0.46094,434.98,-0.31337,0.93943,0.13886,48.342,0.40264,0.26387,-0.8765,196.94

> view matrix models
> #4,-0.60771,-0.14633,-0.78056,432.77,-0.32955,0.94072,0.080223,60.709,0.72255,0.30598,-0.61991,91.89

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.60771,-0.14633,-0.78056,421.32,-0.32955,0.94072,0.080223,65.455,0.72255,0.30598,-0.61991,66.866

> view matrix models
> #4,-0.60771,-0.14633,-0.78056,413.14,-0.32955,0.94072,0.080223,86.366,0.72255,0.30598,-0.61991,55.586

> view matrix models
> #4,-0.60771,-0.14633,-0.78056,412.71,-0.32955,0.94072,0.080223,73.316,0.72255,0.30598,-0.61991,49.668

> view matrix models
> #4,-0.60771,-0.14633,-0.78056,410.92,-0.32955,0.94072,0.080223,75.324,0.72255,0.30598,-0.61991,46.226

> view matrix models
> #4,-0.60771,-0.14633,-0.78056,410.91,-0.32955,0.94072,0.080223,75.334,0.72255,0.30598,-0.61991,46.207

> view matrix models
> #4,-0.60771,-0.14633,-0.78056,408.9,-0.32955,0.94072,0.080223,94.73,0.72255,0.30598,-0.61991,48.808

> view matrix models
> #4,-0.60771,-0.14633,-0.78056,410.37,-0.32955,0.94072,0.080223,88.167,0.72255,0.30598,-0.61991,49.784

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.60884,-0.25545,-0.75104,422.85,-0.20847,0.96498,-0.15922,103.08,0.76541,0.059633,-0.64077,84.602

> view matrix models
> #4,-0.99303,0.072654,-0.092783,328.61,-0.080613,-0.9931,0.085122,348.68,-0.085959,0.092008,0.99204,-43.748

> view matrix models
> #4,-0.6952,-0.66164,0.28094,330.26,0.68985,-0.50426,0.51945,65.188,-0.20202,0.55493,0.807,-65.689

> view matrix models
> #4,0.035447,-0.62379,0.78078,113.86,0.85241,0.4267,0.30221,-73.686,-0.52168,0.65483,0.54685,17.529

> view matrix models
> #4,0.90407,0.16046,0.39612,-97.06,0.0010445,0.92601,-0.37749,109.02,-0.42739,0.34169,0.83701,2.1801

> view matrix models
> #4,0.95323,-0.28796,0.091847,15.637,0.3011,0.87819,-0.37165,63.306,0.026361,0.38193,0.92382,-97.65

> view matrix models
> #4,0.81994,-0.4246,-0.38394,139.52,0.19282,0.83636,-0.51314,112.29,0.539,0.34672,0.76764,-155.44

> view matrix models
> #4,0.92964,-0.18076,-0.32107,71.536,0.021563,0.89659,-0.44234,120.86,0.36783,0.4043,0.8374,-146.29

> view matrix models
> #4,0.97531,-0.19624,0.1013,-4.233,0.1516,0.26141,-0.95325,283.27,0.16058,0.94507,0.2847,-103.46

> view matrix models
> #4,0.53342,-0.48372,0.69389,19.487,0.71055,-0.1888,-0.67784,211.02,0.45889,0.85462,0.24299,-134.25

> view matrix models
> #4,-0.23401,-0.25267,0.93883,76.046,0.75987,-0.64992,0.014488,159.93,0.6065,0.71678,0.34408,-155.06

> view matrix models
> #4,-0.2802,-0.30401,0.91053,96.888,0.79403,-0.60643,0.041873,142.57,0.53944,0.73473,0.41131,-157.39

> view matrix models
> #4,-0.31304,-0.531,0.78742,158.85,0.9125,-0.39805,0.094344,80.367,0.26333,0.74806,0.60915,-144.29

> view matrix models
> #4,-0.18143,-0.61276,0.76916,151.84,0.96182,-0.27355,0.0089461,66.363,0.20492,0.74141,0.639,-138.03

> view matrix models
> #4,-0.14924,-0.37974,0.91297,85.6,0.86096,-0.50399,-0.068895,133.19,0.4863,0.77575,0.40216,-153.07

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.14924,-0.37974,0.91297,88.479,0.86096,-0.50399,-0.068895,126.42,0.4863,0.77575,0.40216,-129.9

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.47186,-0.39206,0.7897,2.7135,0.25745,-0.79538,-0.54871,357.28,0.84325,0.46223,-0.27437,-30.161

> view matrix models
> #4,0.71173,-0.5621,0.42128,48.994,-0.39101,-0.81525,-0.42718,453.17,0.58357,0.13931,-0.80003,153.39

> view matrix models
> #4,0.5054,-0.82802,-0.24281,237.29,-0.85728,-0.51385,-0.032083,421.2,-0.098204,0.22437,-0.96954,286.96

> view matrix models
> #4,0.08686,-0.83355,-0.54557,361.44,-0.99545,-0.094128,-0.014672,376.25,-0.039123,0.54436,-0.83794,204.36

> view matrix models
> #4,0.13938,-0.84032,-0.52387,349.75,-0.93163,-0.29058,0.21822,357.35,-0.3356,0.45764,-0.82337,267.25

> view matrix models
> #4,0.40809,-0.72163,-0.55921,290.11,-0.91248,-0.3418,-0.22483,435.77,-0.028899,0.60202,-0.79796,186.84

> view matrix models
> #4,0.65348,-0.70995,-0.26255,196.17,-0.75054,-0.65275,-0.10299,436.29,-0.09826,0.26435,-0.95941,278.99

> view matrix models
> #4,0.8428,-0.5372,-0.033101,97.809,-0.51019,-0.81698,0.26879,358.45,-0.17144,-0.20965,-0.96263,366.96

> view matrix models
> #4,0.89461,-0.44482,0.042581,61.641,-0.36592,-0.67454,0.64117,248.94,-0.25649,-0.58918,-0.76622,408.9

> view matrix models
> #4,-0.17083,-0.89448,-0.41319,393.92,-0.95401,0.045323,0.29632,295.33,-0.24632,0.44481,-0.86109,259.99

> view matrix models
> #4,-0.31973,-0.81277,-0.48702,419.26,-0.87482,0.055787,0.48122,249.13,-0.36395,0.57991,-0.72886,237.21

> view matrix models
> #4,-0.77863,-0.59725,-0.19242,416.26,-0.52559,0.45326,0.71994,85.956,-0.34277,0.66169,-0.66683,210.32

> view matrix models
> #4,-0.78047,0.067509,-0.62154,383.21,-0.53432,0.44415,0.71919,89.036,0.32461,0.89341,-0.31057,-1.7198

> view matrix models
> #4,-0.28768,-0.57377,-0.76683,422.56,-0.95771,0.17729,0.22663,286.77,0.0059157,0.7996,-0.6005,116.81

> view matrix models
> #4,0.69777,-0.42033,-0.58004,195.63,-0.70227,-0.561,-0.43828,469.19,-0.14118,0.71316,-0.68663,170.38

> view matrix models
> #4,0.15414,-0.98772,-0.025669,287.54,-0.98501,-0.15158,-0.082365,394.74,0.077462,0.03798,-0.99627,290.17

> view matrix models
> #4,0.81842,-0.37767,-0.43308,143.45,-0.20023,-0.89387,0.40112,294.56,-0.53861,-0.24157,-0.80718,410.1

> view matrix models
> #4,0.97021,0.22257,-0.095705,-33.687,0.24228,-0.89183,0.38202,220.32,-0.00032615,-0.39383,-0.91918,358.94

> view matrix models
> #4,0.96194,0.15359,-0.226,0.29303,0.23281,-0.89368,0.38358,222,-0.14306,-0.4216,-0.89543,384.23

> view matrix models
> #4,0.87647,0.13915,-0.46092,56.532,0.17252,-0.98452,0.030824,305.49,-0.4495,-0.10653,-0.88691,386.56

> view matrix models
> #4,0.82819,-0.40616,0.38618,9.9701,-0.4453,-0.89528,0.013402,401.96,0.34029,-0.18306,-0.92233,266.91

> view matrix models
> #4,0.99294,0.031708,-0.11432,-4.4792,0.046153,-0.99095,0.12602,312.68,-0.10929,-0.1304,-0.98542,347.43

> view matrix models
> #4,0.96082,-0.038177,-0.27454,38.777,0.014072,-0.98247,0.18587,306.98,-0.27682,-0.18245,-0.94344,377.84

> view matrix models
> #4,0.73266,0.67972,0.03453,-85.992,0.43183,-0.50348,0.74835,65.174,0.52605,-0.53337,-0.6624,246.51

> view matrix models
> #4,0.58362,0.62376,-0.51992,41.009,0.75883,-0.191,0.62265,-20.125,0.28908,-0.75792,-0.5848,310.27

> view matrix models
> #4,0.0065479,0.47036,-0.88245,226.02,0.92063,0.34168,0.18895,-60.108,0.39039,-0.81365,-0.43079,275.78

> view matrix models
> #4,-0.32452,0.36207,-0.87384,299.32,0.86755,0.48204,-0.12245,-21.184,0.37689,-0.79784,-0.47054,282.26

> view matrix models
> #4,-0.40876,0.5007,-0.76303,273.73,0.44052,0.84047,0.31553,-76.108,0.79929,-0.20715,-0.56412,131.16

> view matrix models
> #4,0.40015,0.64266,-0.65336,92.19,0.89326,-0.11414,0.43481,-24.414,0.20486,-0.75761,-0.61973,330.7

> view matrix models
> #4,0.24806,0.53188,-0.80967,162.14,0.86151,-0.50334,-0.066706,125.86,-0.44302,-0.681,-0.58308,425.41

> view matrix models
> #4,0.1007,0.96691,-0.2344,23.588,0.87923,0.023782,0.47581,-50.519,0.46564,-0.254,-0.84774,243.84

> view matrix models
> #4,0.21478,0.92004,-0.32772,26.62,0.94558,-0.27986,-0.16599,92.511,-0.24443,-0.27424,-0.93008,384.44

> view matrix models
> #4,0.41746,0.52707,-0.74022,121.83,0.43337,-0.83147,-0.34764,298.87,-0.7987,-0.17566,-0.57552,406.5

> view matrix models
> #4,0.417,0.14281,-0.89762,208.64,-0.095516,-0.97522,-0.19954,389.04,-0.90387,0.16894,-0.39303,340.17

> view matrix models
> #4,0.77235,-0.082852,-0.62978,137.74,-0.16407,-0.98383,-0.07178,381.09,-0.61365,0.15877,-0.77345,354.48

> view matrix models
> #4,0.89371,-0.38261,-0.2343,98.047,-0.39647,-0.91795,-0.013287,401.47,-0.21,0.10477,-0.97207,325.7

> view matrix models
> #4,0.70272,-0.42207,-0.57275,193.83,-0.59481,-0.79022,-0.14745,438.21,-0.39037,0.4443,-0.80636,276.07

> view matrix models
> #4,0.72478,-0.12398,-0.67773,160.48,-0.33195,-0.92481,-0.18582,420,-0.60374,0.35965,-0.71144,310.79

> view matrix models
> #4,0.71559,0.3093,-0.62631,85.259,0.19954,-0.94978,-0.24106,340.53,-0.66941,0.047522,-0.74137,376.39

> view matrix models
> #4,0.66184,0.35078,-0.66251,94.11,0.23433,-0.93629,-0.26165,335.77,-0.71208,0.017924,-0.70187,381.92

> view matrix models
> #4,0.35738,0.51193,-0.78116,141.5,0.50192,-0.81062,-0.30161,275.99,-0.78763,-0.28429,-0.54665,416.88

> view matrix models
> #4,0.48986,0.73615,-0.46703,30.839,0.87041,-0.44318,0.21441,68.069,-0.049141,-0.51155,-0.85785,375.79

> view matrix models
> #4,-0.10303,0.91801,-0.38295,91.493,0.81248,0.29977,0.50002,-86.402,0.57381,-0.25962,-0.77675,214.07

> view matrix models
> #4,-0.26698,0.67125,-0.69148,210.25,0.89834,0.4331,0.073585,-51.443,0.34888,-0.60154,-0.71864,297.47

> view matrix models
> #4,-0.29254,0.81563,-0.49916,159.97,0.82131,0.48166,0.30569,-84.279,0.48976,-0.32054,-0.8108,243.98

> view matrix models
> #4,0.19552,0.90171,-0.38561,42.491,0.85035,0.039996,0.52469,-56.174,0.48854,-0.43049,-0.75895,252.89

> view matrix models
> #4,-0.24279,0.91183,-0.33109,108.19,0.9265,0.3191,0.19942,-59.318,0.28749,-0.25833,-0.92229,287.96

> select subtract #4

Nothing selected  

> hide #!4 models

> open "/Users/ankitachadda/Library/CloudStorage/Box-
> Box/backup/Desktop/structures/closed UvrD1.pdb"

closed UvrD1.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for closed UvrD1.pdb #5  
---  
Chain | Description  
C | No description available  
  

> select add #5

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

> color #5 #ff8ad8ff

> view matrix models
> #5,0.70829,-0.44934,0.54444,-35.637,0.62905,0.75174,-0.19793,44.564,-0.32034,0.48268,0.81511,-13.245

> view matrix models
> #5,0.070321,-0.48565,0.87132,-75.144,0.99749,0.027033,-0.065436,82.77,0.0082244,0.87374,0.48633,-0.58341

> view matrix models
> #5,-0.29145,-0.018365,0.95641,-121.59,0.87743,-0.40336,0.25964,73.773,0.38101,0.91485,0.13368,41.547

> select ::name="CYS"

90 atoms, 75 bonds, 15 residues, 3 models selected  

> color (#5 & sel) red

> select clear

> select add #5

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

> view matrix models
> #5,-0.40575,-0.5295,0.74498,-56.299,0.68178,-0.7182,-0.13914,147.98,0.60872,0.45146,0.65242,10.804

> view matrix models
> #5,-0.17578,-0.72504,0.6659,-31.253,0.93672,-0.33122,-0.11336,115.81,0.30275,0.60383,0.73738,-11.819

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.17578,-0.72504,0.6659,91.163,0.93672,-0.33122,-0.11336,152.15,0.30275,0.60383,0.73738,101.71

> view matrix models
> #5,-0.17578,-0.72504,0.6659,127.7,0.93672,-0.33122,-0.11336,167.65,0.30275,0.60383,0.73738,5.4678

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.15447,-0.5471,0.82269,94.378,0.94976,-0.31164,-0.028916,155.45,0.27221,0.77689,0.56775,13.945

> view matrix models
> #5,-0.7648,-0.51103,0.39234,145.69,0.50225,-0.091517,0.85986,25.401,-0.40351,0.85468,0.32666,37.985

> view matrix models
> #5,-0.87191,-0.30002,0.38698,130.34,0.41818,-0.045072,0.90725,15.784,-0.25475,0.95287,0.16476,51.321

> view matrix models
> #5,-0.89943,0.26184,0.34994,92.655,0.37819,0.064909,0.92345,5.3885,0.21908,0.96293,-0.15741,92.028

> view matrix models
> #5,-0.77548,0.51118,0.37057,71.368,0.43514,0.0074337,0.90033,12.723,0.45748,0.85944,-0.2282,109.09

> view matrix models
> #5,-0.49386,0.86923,0.023253,88.824,0.46976,0.2442,0.84834,1.5159,0.73173,0.42988,-0.52894,180

> view matrix models
> #5,-0.18746,0.77549,-0.60289,175.81,0.62216,0.56869,0.53805,16.654,0.76011,-0.27424,-0.58909,240.77

> view matrix models
> #5,0.29925,-0.26037,-0.91796,294.49,0.86094,0.48846,0.14211,73.289,0.41139,-0.83284,0.37033,160.56

> view matrix models
> #5,0.65552,-0.52543,-0.54242,267.14,0.69689,0.69759,0.16646,54.247,0.29092,-0.48712,0.82345,76.773

> view matrix models
> #5,0.38926,-0.63918,-0.66326,290.78,0.92097,0.2832,0.26759,72.883,0.016797,-0.71501,0.69891,109.49

> view matrix models
> #5,0.34973,-0.93376,-0.075979,238.31,0.91909,0.32625,0.221,75.556,-0.18157,-0.14712,0.97231,31.701

> view matrix models
> #5,-0.020672,-0.86712,0.49767,159.96,0.91773,0.18104,0.35355,69.658,-0.39666,0.46404,0.79204,8.2964

> view matrix models
> #5,0.64857,-0.7212,-0.24338,243.88,0.70696,0.68926,-0.1585,96.188,0.28206,-0.069263,0.95689,28.296

> view matrix models
> #5,0.24385,-0.045981,-0.96872,284.72,0.58667,0.80238,0.1096,53.453,0.77224,-0.59505,0.22264,161.8

> view matrix models
> #5,-0.091919,0.48571,-0.86927,231.62,0.53251,0.76163,0.36925,23.463,0.84142,-0.42896,-0.32865,219.42

> view matrix models
> #5,0.0052577,-0.13226,-0.9912,293.82,0.73269,0.67508,-0.086189,88.095,0.68054,-0.72579,0.10045,187.09

> view matrix models
> #5,0.0795,-0.56577,-0.82072,304.92,0.86827,0.44375,-0.22179,122.92,0.48968,-0.69498,0.52652,130.4

> view matrix models
> #5,0.041468,0.20742,-0.97737,266.49,0.70222,0.68982,0.17619,53.602,0.71075,-0.69363,-0.11705,212.34

> view matrix models
> #5,-0.1585,-0.13359,-0.97828,292.1,0.89501,0.39896,-0.19949,123.49,0.41694,-0.90719,0.056328,206.09

> view matrix models
> #5,-0.080097,-0.51781,-0.85174,305.07,0.89584,0.3373,-0.28931,139.56,0.4371,-0.78619,0.43686,148.62

> view matrix models
> #5,0.12278,-0.81881,-0.56078,291.01,0.88228,0.34879,-0.31612,142.09,0.45443,-0.45595,0.76525,82

> view matrix models
> #5,0.32057,-0.87304,-0.36748,270.74,0.80279,0.45632,-0.38379,142.49,0.50275,-0.17198,0.84715,50.231

> view matrix models
> #5,0.4573,-0.62509,-0.63257,285.89,0.36652,0.78055,-0.50636,133.15,0.81027,-0.00028771,0.58605,70.808

> view matrix models
> #5,-0.24846,-0.32002,-0.91425,297.92,0.29948,0.87222,-0.3867,110.95,0.92118,-0.36988,-0.12087,188.65

> view matrix models
> #5,-0.61762,0.19841,-0.76104,238.95,0.27016,0.9623,0.031632,50.958,0.73863,-0.18606,-0.64793,241.58

> view matrix models
> #5,-0.07469,0.14716,-0.98629,272.04,0.17602,0.97547,0.13221,37.078,0.98155,-0.16374,-0.09876,170.36

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.07469,0.14716,-0.98629,280.1,0.17602,0.97547,0.13221,94.937,0.98155,-0.16374,-0.09876,172.36

> view matrix models
> #5,-0.07469,0.14716,-0.98629,268.51,0.17602,0.97547,0.13221,94.124,0.98155,-0.16374,-0.09876,163.69

> view matrix models
> #5,-0.07469,0.14716,-0.98629,271.44,0.17602,0.97547,0.13221,94.875,0.98155,-0.16374,-0.09876,166.66

> view matrix models
> #5,-0.07469,0.14716,-0.98629,268.28,0.17602,0.97547,0.13221,90.304,0.98155,-0.16374,-0.09876,158.1

> ui tool show "Fit in Map"

> fitmap #5 inMap #1

Fit molecule closed UvrD1.pdb (#5) to map
cryosparc_P43_J1034_003_volume_map_sharp (5).mrc (#1) using 5285 atoms  
average map value = 0.3457, steps = 204  
shifted from previous position = 14.7  
rotated from previous position = 34.3 degrees  
atoms outside contour = 4003, contour level = 0.59802  
  
Position of closed UvrD1.pdb (#5) relative to
cryosparc_P43_J1034_003_volume_map_sharp (5).mrc (#1) coordinates:  
Matrix rotation and translation  
0.37803766 -0.21127716 -0.90135980 291.84128744  
0.14094550 0.97539642 -0.16951752 117.33602487  
0.91499830 -0.06295860 0.39851514 96.24325557  
Axis 0.05749810 -0.98008815 0.19005573  
Axis point 64.94612176 0.00000000 284.06296690  
Rotation angle (degrees) 67.91543743  
Shift along axis -79.92774673  
  

> view matrix models
> #5,0.37804,-0.21128,-0.90136,285.39,0.14095,0.9754,-0.16952,126.24,0.915,-0.062959,0.39852,100.62

> fitmap #5 inMap #1

Fit molecule closed UvrD1.pdb (#5) to map
cryosparc_P43_J1034_003_volume_map_sharp (5).mrc (#1) using 5285 atoms  
average map value = 0.3457, steps = 152  
shifted from previous position = 11.8  
rotated from previous position = 0.00782 degrees  
atoms outside contour = 4003, contour level = 0.59802  
  
Position of closed UvrD1.pdb (#5) relative to
cryosparc_P43_J1034_003_volume_map_sharp (5).mrc (#1) coordinates:  
Matrix rotation and translation  
0.37805787 -0.21117645 -0.90137493 291.83678936  
0.14082528 0.97542389 -0.16945939 117.32954349  
0.91500846 -0.06287092 0.39850566 96.23527627  
Axis 0.05751452 -0.98010999 0.18993810  
Axis point 64.95710984 0.00000000 284.04882876  
Rotation angle (degrees) 67.91425670  
Shift along axis -79.93225910  
  

> select subtract #5

Nothing selected  

> select add #5

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

> view matrix models
> #5,0.37806,-0.21118,-0.90137,292.72,0.14083,0.97542,-0.16946,126.99,0.91501,-0.062871,0.39851,94.338

> fitmap #5 inMap #1

Fit molecule closed UvrD1.pdb (#5) to map
cryosparc_P43_J1034_003_volume_map_sharp (5).mrc (#1) using 5285 atoms  
average map value = 0.3457, steps = 136  
shifted from previous position = 9.86  
rotated from previous position = 0.0427 degrees  
atoms outside contour = 3998, contour level = 0.59802  
  
Position of closed UvrD1.pdb (#5) relative to
cryosparc_P43_J1034_003_volume_map_sharp (5).mrc (#1) coordinates:  
Matrix rotation and translation  
0.37797273 -0.21054585 -0.90155813 291.81768556  
0.14027325 0.97557902 -0.16902365 117.28499063  
0.91512842 -0.06257816 0.39827621 96.22712843  
Axis 0.05743537 -0.98023936 0.18929335  
Axis point 64.99673877 0.00000000 283.93320054  
Rotation angle (degrees) 67.91918639  
Shift along axis -79.99155264  
  

> select subtract #5

Nothing selected  

> save "/Users/ankitachadda/Desktop/aligned UvrD dimer with first
> conformation.cxs"

——— End of log from Wed Aug 23 09:45:24 2023 ———

opened ChimeraX session  




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: 19 hours, 38 minutes

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
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Eric Pettersen]

Reported by Ankita Chadda