Permission Denied saving MRC file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open D:\PT-Fab.cxs format session

Opened cryosparc_P19_J504_007_volume_map_sharp.mrc as #1.1, grid size
256,256,256, pixel 1.16, shown at level 1.01, step 1, values float32  
Opened cryosparc_P19_J381_003_volume_map_sharp (1).mrc as #1.2, grid size
128,128,128, pixel 1.16, shown at level 0.36, step 1, values float32  
Opened Fab-PT.mrc as #5, grid size 256,256,256, pixel 1.16, shown at level
0.764, step 1, values float32  
Log from Fri Oct 14 22:31:01 2022UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/13146/Downloads/cryosparc_P19_J493_003_volume_map_sharp.mrc

Opened cryosparc_P19_J493_003_volume_map_sharp.mrc as #1, grid size 64,64,64,
pixel 2.32, shown at level 1.88, step 1, values float32  

> volume #1 level 1.322

> close

> open C:/Users/13146/Downloads/cryosparc_P19_J504_007_volume_map_sharp.mrc
> "C:/Users/13146/Downloads/cryosparc_P19_J381_003_volume_map_sharp (1).mrc"

Opened cryosparc_P19_J504_007_volume_map_sharp.mrc as #1.1, grid size
256,256,256, pixel 1.16, shown at level 0.132, step 1, values float32  
Opened cryosparc_P19_J381_003_volume_map_sharp (1).mrc as #1.2, grid size
128,128,128, pixel 1.16, shown at level 0.401, step 1, values float32  

> volume #1.1 level 0.7391

> select #1.2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1.2,1,0,0,16.588,0,1,0,78.823,0,0,1,56.89

> ui mousemode right "rotate selected models"

> view matrix models
> #1.2,-0.46963,0.33014,0.81881,40.17,0.7027,0.70124,0.1203,41.633,-0.53447,0.63188,-0.56132,159.6

> view matrix models
> #1.2,-0.98543,0.079525,0.15035,143.6,0.1388,0.88691,0.44059,45.866,-0.098314,0.45504,-0.88503,164.19

> ui mousemode right "translate selected models"

> view matrix models
> #1.2,-0.98543,0.079525,0.15035,201.56,0.1388,0.88691,0.44059,30.914,-0.098314,0.45504,-0.88503,180.82

> ui mousemode right "rotate selected models"

> view matrix models
> #1.2,-0.99986,0.00952,0.014049,217.49,0.0093067,0.99984,-0.015169,64.288,-0.014192,-0.015036,-0.99979,217.8

> ui mousemode right "translate selected models"

> view matrix models
> #1.2,-0.99986,0.00952,0.014049,219.3,0.0093067,0.99984,-0.015169,74.817,-0.014192,-0.015036,-0.99979,220.39

> ui tool show "Fit in Map"

Fit map cryosparc_P19_J504_007_volume_map_sharp.mrc in map
cryosparc_P19_J381_003_volume_map_sharp (1).mrc using 19572 points  
correlation = 0.8115, correlation about mean = 0.2926, overlap = 1.178e+04  
steps = 104, shift = 3.22, angle = 16.3 degrees  
  
Position of cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) relative to
cryosparc_P19_J381_003_volume_map_sharp (1).mrc (#1.2) coordinates:  
Matrix rotation and translation  
-0.96318040 0.26710610 0.03062400 173.13592645  
0.26879245 0.95916047 0.08810111 -121.53610560  
-0.00584098 0.09308876 -0.99564068 207.32188537  
Axis 0.13537543 0.98973658 0.04577103  
Axis point 95.86316090 0.00000000 105.61047125  
Rotation angle (degrees) 178.94446275  
Shift along axis -87.36104327  
  

> ~select #1.2

Nothing selected  

> open "C:/Users/13146/OneDrive - Saint Louis University/Desktop/Fab-
> PT/hK1_1.pdb"

Chain information for hK1_1.pdb #2  
---  
Chain | Description  
A | No description available  
  

> select #2

623 atoms, 640 bonds, 79 residues, 1 model selected  

> view matrix models #2,1,0,0,121.33,0,1,0,192.5,0,0,1,1.3826

> view matrix models #2,1,0,0,90.745,0,1,0,140.23,0,0,1,39.542

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.91321,0.2786,-0.29738,105.78,-0.26542,0.9604,0.084711,143.97,0.3092,0.0015717,0.95099,33.083

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.91321,0.2786,-0.29738,113.41,-0.26542,0.9604,0.084711,112.04,0.3092,0.0015717,0.95099,43.043

> view matrix models
> #2,0.91321,0.2786,-0.29738,123.27,-0.26542,0.9604,0.084711,129.31,0.3092,0.0015717,0.95099,36.085

> view matrix models
> #2,0.91321,0.2786,-0.29738,123.84,-0.26542,0.9604,0.084711,129.74,0.3092,0.0015717,0.95099,35.098

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.9921,0.11011,-0.060096,110.17,0.096797,-0.36728,0.92506,97.461,0.079785,-0.92357,-0.37503,152.72

> volume #1.2 style mesh

> view matrix models
> #2,-0.63166,0.74297,-0.22136,155.08,0.3679,0.035934,-0.92917,200.06,-0.68239,-0.66836,-0.29603,164.75

> view matrix models
> #2,-0.37297,0.90116,-0.22093,142.94,0.077054,-0.2072,-0.97526,218.36,-0.92464,-0.38077,0.0078437,145.04

> view matrix models
> #2,-0.41923,0.88586,-0.19874,143.32,0.053666,-0.19435,-0.97946,219.03,-0.90629,-0.42129,0.033936,143.79

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.41923,0.88586,-0.19874,143.11,0.053666,-0.19435,-0.97946,215.51,-0.90629,-0.42129,0.033936,144.08

> view matrix models
> #2,-0.41923,0.88586,-0.19874,143.48,0.053666,-0.19435,-0.97946,214.31,-0.90629,-0.42129,0.033936,147.61

> view matrix models
> #2,-0.41923,0.88586,-0.19874,150.07,0.053666,-0.19435,-0.97946,216.42,-0.90629,-0.42129,0.033936,147.08

> view matrix models
> #2,-0.41923,0.88586,-0.19874,153.11,0.053666,-0.19435,-0.97946,214.92,-0.90629,-0.42129,0.033936,145.97

Fit molecule hK1_1.pdb (#2) to map cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) using 623 atoms  
average map value = 0.5187, steps = 76  
shifted from previous position = 1.48  
rotated from previous position = 12.5 degrees  
atoms outside contour = 224, contour level = 0.40088  
  
Position of hK1_1.pdb (#2) relative to cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.50557704 -0.82795012 0.24267358 62.78804332  
-0.07454670 -0.32213675 -0.94375352 146.09135360  
0.85955492 0.45904960 -0.22458589 84.50976624  
Axis 0.82148905 -0.36124903 0.44119709  
Axis point 0.00000000 63.41060132 79.77853256  
Rotation angle (degrees) 121.37068105  
Shift along axis 36.08979423  
  

> volume #1.2 style surface

> volume #1.1 style mesh

> volume #1.1 level 1.051

Fit molecule hK1_1.pdb (#2) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 623 atoms  
average map value = 0.9551, steps = 72  
shifted from previous position = 0.798  
rotated from previous position = 7.07 degrees  
atoms outside contour = 356, contour level = 1.0508  
  
Position of hK1_1.pdb (#2) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.51138564 0.66460740 -0.54477680 184.25633506  
0.26295905 -0.48251013 -0.83548580 209.92594349  
-0.81813036 -0.57050943 0.07198421 147.64385398  
Axis 0.47881177 0.49394934 -0.72577774  
Axis point 157.16712128 141.23828472 0.00000000  
Rotation angle (degrees) 163.93653066  
Shift along axis 84.76026049  
  

> volume #1.1 style surface

> show sel target ab

> volume #1.1 style mesh

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select #2

623 atoms, 640 bonds, 79 residues, 2 models selected  

> ~select #2

Nothing selected  

> volume #1.1 level 0.5408

> set bgColor white

> volume #1.1 style surface

Fit molecule hK1_1.pdb (#2) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 623 atoms  
average map value = 0.9552, steps = 28  
shifted from previous position = 0.0164  
rotated from previous position = 0.0623 degrees  
atoms outside contour = 178, contour level = 0.54077  
  
Position of hK1_1.pdb (#2) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
-0.51048580 0.66509896 -0.54502077 184.24758438  
0.26328167 -0.48249299 -0.83539410 209.91791600  
-0.81858844 -0.56995080 0.07119744 147.69046518  
Axis 0.47926404 0.49393278 -0.72549045  
Axis point 157.25930477 141.25926997 0.00000000  
Rotation angle (degrees) 163.92305458  
Shift along axis 84.84055917  
  

> volume #1.1 style mesh

> volume #1.1 color #64b240

> volume #1.1 color #0055ff

> volume #1.1 color #aa0000

> volume #1.1 color lime

> volume #1.1 color black

> volume #1.1 color #55007f

> volume #1.1 color #55557f

> volume #1.1 color #aa007f

> volume #1.1 color black

> volume #1.1 level 0.7533

> volume #1.1 color #aa007f

> volume #1.1 color #ff557f

> volume #1.1 color blue

> volume #1.1 color yellow

> volume #1.1 color #55ff00

> volume #1.1 level 0.3991

> volume #1.1 style surface

> volume #1.1 color #040c00

> volume #1.1 color #2d8600

> volume #1.1 color #2b8200

> volume #1.1 color #46d100

> volume #1.1 color #bbe4f9

> volume #1.1 color #f0f0f0

> volume #1.1 color #f9f9f9

> volume #1.1 color #787878

> volume #1.1 color #f9f9f9

> volume #1.1 color #f9f9f9

> volume #1.1 color #78788f

> volume #1.1 color #78788f

> volume #1.1 color #afafd1

> volume #1.1 color #c5c5eb

> volume #1.1 color #afafd0

> select #2

623 atoms, 640 bonds, 79 residues, 2 models selected  

> ~label (#!2 & sel) residues

> select #1.1

2 models selected  

> transparency #1.1.1 40

> ~select #1.1

Nothing selected  

> volume #1.1 level 1.377

> volume #1.1 level 0.8241

> volume #1.1 level 0.4699

> volume #1.1 level 0.5408

> open "C:/Users/13146/OneDrive - Saint Louis University/Desktop/Fab-
> PT/Fab0.pdb"

Chain information for Fab0.pdb #3  
---  
Chain | Description  
A | No description available  
  

> select #3

6485 atoms, 6566 bonds, 433 residues, 1 model selected  

> view matrix models #3,1,0,0,19.144,0,1,0,85.775,0,0,1,91.168

> view matrix models #3,1,0,0,20.277,0,1,0,90.335,0,0,1,98.286

> view matrix models #3,1,0,0,66.699,0,1,0,48.05,0,0,1,99.639

> view matrix models #3,1,0,0,63.479,0,1,0,50.801,0,0,1,96.93

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.42945,-0.74933,-0.50406,187.3,-0.77462,-0.59257,0.22095,194.83,-0.46426,0.29557,-0.83493,235.58

> view matrix models
> #3,-0.86692,0.4583,0.196,144.8,-0.49057,-0.71485,-0.49833,233.82,-0.088276,-0.52816,0.84454,149.2

> view matrix models
> #3,-0.13056,-0.98486,-0.11408,213.83,0.98448,-0.11516,-0.13246,68.722,0.11731,-0.1296,0.9846,98.817

> view matrix models
> #3,0.96915,-0.21842,-0.11419,88.177,0.24619,0.88004,0.4061,14.125,0.01179,-0.42168,0.90667,130.99

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.96915,-0.21842,-0.11419,81.529,0.24619,0.88004,0.4061,39.512,0.01179,-0.42168,0.90667,125.91

> view matrix models
> #3,0.96915,-0.21842,-0.11419,89.56,0.24619,0.88004,0.4061,53.648,0.01179,-0.42168,0.90667,121.63

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.015595,-0.97827,-0.20673,211.35,0.98864,0.046002,-0.14311,97.857,0.14951,-0.20215,0.96788,93.331

> view matrix models
> #3,0.50583,-0.79997,-0.32276,174.37,0.84483,0.53503,-0.0020824,64.852,0.17435,-0.27163,0.94648,97.817

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.50583,-0.79997,-0.32276,183.17,0.84483,0.53503,-0.0020824,55.87,0.17435,-0.27163,0.94648,104.15

Fit molecule Fab0.pdb (#3) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 6485 atoms  
average map value = 0.492, steps = 96  
shifted from previous position = 4.62  
rotated from previous position = 14.2 degrees  
atoms outside contour = 3775, contour level = 0.54077  
  
Position of Fab0.pdb (#3) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.57536893 -0.73744818 -0.35372415 183.42552261  
0.80461466 0.58797056 0.08298120 48.67178648  
0.14678505 -0.33235644 0.93166161 113.47720017  
Axis -0.24816862 -0.29905952 0.92139880  
Axis point 44.80172706 237.90178485 0.00000000  
Rotation angle (degrees) 56.80429149  
Shift along axis 44.48153655  
  

> volume #1.1 level 0.8525

> select #1.1

2 models selected  

> transparency #1.1.1 0

> ~select #1.1

Nothing selected  

> select #3

6485 atoms, 6566 bonds, 433 residues, 1 model selected  

> view matrix models
> #3,0.34262,-0.84836,-0.4036,208.65,0.93721,0.33847,0.084148,55.923,0.065217,-0.40709,0.91106,120.19

> volume #1.1 level 0.5266

Fit molecule Fab0.pdb (#3) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 6485 atoms  
average map value = 0.5093, steps = 84  
shifted from previous position = 3.11  
rotated from previous position = 9.83 degrees  
atoms outside contour = 3638, contour level = 0.5266  
  
Position of Fab0.pdb (#3) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.45285381 -0.78396743 -0.42463925 200.68591676  
0.85416525 0.51801296 -0.04543458 59.27459714  
0.25558787 -0.34213686 0.90422188 107.85948726  
Axis -0.16498183 -0.37824149 0.91088658  
Axis point 43.91511994 234.32815138 0.00000000  
Rotation angle (degrees) 64.05269576  
Shift along axis 42.71811818  
  

> volume #1.1 level 0.7533

> open "C:/Users/13146/OneDrive - Saint Louis University/Desktop/Fab-
> PT/complex_model_Fab_hK1.pdb"

Chain information for complex_model_Fab_hK1.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select #4

4765 atoms, 4862 bonds, 519 residues, 1 model selected  

> view matrix models #4,1,0,0,2.1286,0,1,0,68.154,0,0,1,178.66

> view matrix models #4,1,0,0,-7.573,0,1,0,89.782,0,0,1,163.35

> view matrix models #4,1,0,0,134.16,0,1,0,69.142,0,0,1,150.13

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.038201,0.10143,-0.99411,150.68,0.19152,0.97714,0.092337,66.424,0.98075,-0.18686,-0.056753,141.77

> view matrix models
> #4,-0.16161,0.12601,-0.97878,152.15,-0.052821,0.98929,0.13609,69.35,0.98544,0.073693,-0.15322,141.56

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.16161,0.12601,-0.97878,182.67,-0.052821,0.98929,0.13609,130.13,0.98544,0.073693,-0.15322,137.9

> view matrix models
> #4,-0.16161,0.12601,-0.97878,139.87,-0.052821,0.98929,0.13609,133.2,0.98544,0.073693,-0.15322,137.06

> view matrix models
> #4,-0.16161,0.12601,-0.97878,152.49,-0.052821,0.98929,0.13609,143.25,0.98544,0.073693,-0.15322,137.43

> hide #3 models

Fit molecule complex_model_Fab_hK1.pdb (#4) to map
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) using 4765 atoms  
average map value = 0.4479, steps = 152  
shifted from previous position = 5.58  
rotated from previous position = 19.2 degrees  
atoms outside contour = 3519, contour level = 0.7533  
  
Position of complex_model_Fab_hK1.pdb (#4) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.03972745 0.19551438 -0.97989584 153.35632699  
-0.31588968 0.93283169 0.17331691 148.53157421  
0.94796384 0.30265355 0.09882000 134.55557072  
Axis 0.06470954 -0.96454433 -0.25586504  
Axis point 32.43527599 0.00000000 135.79598893  
Rotation angle (degrees) 87.95470419  
Shift along axis -167.76973554  
  

> volume #1.1 level 0.578

> show #3 models

> hide #4 models

Fit molecule Fab0.pdb (#3) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 6485 atoms  
average map value = 0.5093, steps = 60  
shifted from previous position = 0.0235  
rotated from previous position = 0.0359 degrees  
atoms outside contour = 3893, contour level = 0.578  
  
Position of Fab0.pdb (#3) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.45312682 -0.78364114 -0.42495017 200.68084052  
0.85389006 0.51845513 -0.04556367 59.28400621  
0.25602316 -0.34221461 0.90406931 107.83151441  
Axis -0.16497840 -0.37871410 0.91069081  
Axis point 43.87417024 234.44679701 0.00000000  
Rotation angle (degrees) 64.03477037  
Shift along axis 42.64147574  
  

> volume #1.1 level 0.2238

> volume #1.1 level 0.3088

> volume #1.1 level 0.4788

> volume #1.1 level 0.4505

> volume #1.1 level 0.7055

> volume #1.1 level 0.5072

> volume #1.1 level 1.216

> volume #1.1 level 0.9181

> volume #1.1 level 0.9322

> volume #1.1 level 0.7197

> volume #1.1 level 0.8047

> volume #1.1 level 0.7905

> volume #1.1 level 1.584

> volume #1.1 level 1.102

> volume #1.1 level 0.9464

> volume #1.1 level 1.499

> volume #1.1 level 1.145

> select #2

623 atoms, 640 bonds, 79 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.49667,0.84538,-0.1966,155.68,-0.077227,-0.26866,-0.96013,219.51,-0.8645,-0.46169,0.19872,135.37

> view matrix models
> #2,-0.44939,0.88669,-0.10876,147.57,-0.23747,-0.23594,-0.94231,222.44,-0.86119,-0.39764,0.31659,126.1

> view matrix models
> #2,-0.0041734,0.90942,-0.41585,153.44,-0.064446,-0.41524,-0.90743,219.19,-0.99791,0.023013,0.060342,136.87

> view matrix models
> #2,0.53047,0.11011,0.84052,74.742,-0.43318,-0.81709,0.38043,156.43,0.72867,-0.5659,-0.38575,127.34

Fit molecule hK1_1.pdb (#2) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 623 atoms  
average map value = 0.7291, steps = 168  
shifted from previous position = 3.38  
rotated from previous position = 28.3 degrees  
atoms outside contour = 460, contour level = 1.1448  
  
Position of hK1_1.pdb (#2) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.58818071 -0.10402369 0.80201156 80.83779288  
-0.25358409 -0.96540335 0.06075779 175.97039071  
0.76794439 -0.23911393 -0.59421037 136.07041330  
Axis -0.89028603 0.10114166 -0.44402831  
Axis point 0.00000000 96.63475364 38.94249115  
Rotation angle (degrees) 170.30443203  
Shift along axis -114.58993584  
  

> volume #1.1 level 0.833

> volume #1.1 level 0.6488

Fit molecule Fab0.pdb (#3) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 6485 atoms  
average map value = 0.5093, steps = 44  
shifted from previous position = 0.00144  
rotated from previous position = 0.00624 degrees  
atoms outside contour = 4189, contour level = 0.64884  
  
Position of Fab0.pdb (#3) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.45318390 -0.78359045 -0.42498277 200.67613709  
0.85383731 0.51853924 -0.04559496 59.28524902  
0.25609802 -0.34220324 0.90405240 107.82738203  
Axis -0.16496023 -0.37878661 0.91066395  
Axis point 43.86213387 234.46509282 0.00000000  
Rotation angle (degrees) 64.03080972  
Shift along axis 42.63446821  
  

> ui mousemode right "translate selected models"

> select #3

6485 atoms, 6566 bonds, 433 residues, 1 model selected  

> view matrix models
> #3,0.20723,-0.87467,-0.4382,221.82,0.96402,0.2588,-0.060671,70.995,0.16647,-0.40986,0.89683,112.63

> view matrix models
> #3,0.20723,-0.87467,-0.4382,218.51,0.96402,0.2588,-0.060671,73.285,0.16647,-0.40986,0.89683,113.6

> view matrix models
> #3,0.20723,-0.87467,-0.4382,220.43,0.96402,0.2588,-0.060671,84.065,0.16647,-0.40986,0.89683,85.773

> view matrix models
> #3,0.20723,-0.87467,-0.4382,224.24,0.96402,0.2588,-0.060671,70.159,0.16647,-0.40986,0.89683,109.69

Fit molecule Fab0.pdb (#3) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 6485 atoms  
average map value = 0.5124, steps = 84  
shifted from previous position = 4.23  
rotated from previous position = 8.55 degrees  
atoms outside contour = 4085, contour level = 0.64884  
  
Position of Fab0.pdb (#3) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.55143998 -0.77026435 -0.32032292 186.33920219  
0.80225340 0.59492767 -0.04950311 56.75624290  
0.22869945 -0.22968216 0.94601410 96.41851859  
Axis -0.10754894 -0.32771165 0.93863640  
Axis point 26.17624616 233.91352729 0.00000000  
Rotation angle (degrees) 56.89391874  
Shift along axis 51.86166621  
  

> volume #1.1 level 0.493

> show #!1.2 models

> hide #!1.1 models

> volume #1.2 style mesh

> select #2

623 atoms, 640 bonds, 79 residues, 1 model selected  

> hide sel target a

> view matrix models
> #2,0.59936,0.15778,0.78477,73.545,-0.011146,-0.97864,0.20527,154.37,0.8004,-0.13178,-0.5848,129.41

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.28268,-0.82694,0.48606,145.78,0.45259,-0.56176,-0.69252,188.02,0.84573,0.024219,0.53307,50.835

> view matrix models
> #2,-0.91729,0.073012,-0.39146,199.92,0.052798,-0.95207,-0.30129,184.86,-0.39469,-0.29704,0.86947,75.662

> view matrix models
> #2,-0.94017,0.027741,-0.33958,198.4,0.1064,-0.92293,-0.36997,186.94,-0.32367,-0.38397,0.86476,75.986

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.94017,0.027741,-0.33958,200.48,0.1064,-0.92293,-0.36997,188.91,-0.32367,-0.38397,0.86476,75.425

> view matrix models
> #2,-0.94017,0.027741,-0.33958,201.51,0.1064,-0.92293,-0.36997,192.91,-0.32367,-0.38397,0.86476,73.069

> view matrix models
> #2,-0.94017,0.027741,-0.33958,201.24,0.1064,-0.92293,-0.36997,192.46,-0.32367,-0.38397,0.86476,73.501

> view matrix models
> #2,-0.94017,0.027741,-0.33958,200.22,0.1064,-0.92293,-0.36997,189.89,-0.32367,-0.38397,0.86476,74.255

Fit molecule hK1_1.pdb (#2) to map cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) using 623 atoms  
average map value = 0.4279, steps = 124  
shifted from previous position = 2.78  
rotated from previous position = 27.9 degrees  
atoms outside contour = 302, contour level = 0.40088  
  
Position of hK1_1.pdb (#2) relative to cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.86180072 -0.00815060 0.50718153 14.60750777  
-0.02609444 -0.99925936 0.02828109 95.69359521  
0.50657538 -0.03760728 -0.86137511 149.48460218  
Axis -0.96482134 0.00887596 -0.26275653  
Axis point 0.00000000 49.11481580 71.90218837  
Rotation angle (degrees) 178.04323387  
Shift along axis -52.52231851  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.69231,0.11943,-0.71165,212.15,0.1352,-0.94728,-0.2905,184.07,-0.70882,-0.29733,0.63966,98.187

> view matrix models
> #2,-0.60969,0.05581,-0.79068,216.38,0.027048,-0.99547,-0.091122,175.62,-0.79218,-0.076942,0.60542,97.38

> view matrix models
> #2,-0.7827,-0.10107,-0.61414,214.23,0.26949,-0.94447,-0.18802,173.11,-0.56103,-0.31267,0.76647,85.678

Fit molecule hK1_1.pdb (#2) to map cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) using 623 atoms  
average map value = 0.4279, steps = 152  
shifted from previous position = 1.26  
rotated from previous position = 22.8 degrees  
atoms outside contour = 301, contour level = 0.40088  
  
Position of hK1_1.pdb (#2) relative to cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.86206877 -0.00858411 0.50671862 14.64223627  
-0.02632176 -0.99926544 0.02785247 95.73797295  
0.50610731 -0.03734847 -0.86166147 149.51982484  
Axis -0.96489103 0.00904653 -0.26249467  
Axis point 0.00000000 49.12620299 71.92574139  
Rotation angle (degrees) 178.06379704  
Shift along axis -52.51022306  
  

> view matrix models
> #2,-0.81568,0.19059,-0.5462,203.34,0.20664,-0.78589,-0.58281,196.85,-0.54034,-0.58826,0.60166,102.87

> view matrix models
> #2,-0.38038,-0.051415,-0.9234,220.67,0.44446,-0.88575,-0.13377,162.61,-0.81103,-0.4613,0.35977,123.88

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.38038,-0.051415,-0.9234,218.19,0.44446,-0.88575,-0.13377,159.24,-0.81103,-0.4613,0.35977,124.06

> view matrix models
> #2,-0.38038,-0.051415,-0.9234,217.69,0.44446,-0.88575,-0.13377,158,-0.81103,-0.4613,0.35977,123.65

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.40413,-0.061907,-0.9126,217.99,0.3858,-0.91616,-0.1087,158.97,-0.82936,-0.39601,0.39413,120.3

> view matrix models
> #2,-0.64916,0.28984,-0.70327,202.91,0.19925,-0.82748,-0.52495,189.75,-0.7341,-0.4809,0.47941,113.93

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.64916,0.28984,-0.70327,206.38,0.19925,-0.82748,-0.52495,192.92,-0.7341,-0.4809,0.47941,112.59

> view matrix models
> #2,-0.64916,0.28984,-0.70327,205.87,0.19925,-0.82748,-0.52495,191.67,-0.7341,-0.4809,0.47941,113.31

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.67697,0.58107,-0.45173,182.82,-0.039734,-0.64172,-0.76591,210.13,-0.73493,-0.50055,0.45752,115.28

> view matrix models
> #2,-0.61631,0.59186,-0.51949,185.09,0.18391,-0.53325,-0.82573,204.3,-0.76573,-0.60444,0.21979,134.46

> view matrix models
> #2,-0.71417,0.62317,-0.31877,174.19,-0.08094,-0.52588,-0.8467,213.73,-0.69527,-0.57889,0.42601,118.11

Fit molecule hK1_1.pdb (#2) to map cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) using 623 atoms  
average map value = 0.5188, steps = 76  
shifted from previous position = 4.81  
rotated from previous position = 19.3 degrees  
atoms outside contour = 223, contour level = 0.40088  
  
Position of hK1_1.pdb (#2) relative to cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.50503375 -0.82819676 0.24296304 62.78231988  
-0.07375628 -0.32188333 -0.94390208 146.07604690  
0.85994240 0.45878236 -0.22364665 84.41807148  
Axis 0.82122923 -0.36122272 0.44170204  
Axis point 0.00000000 63.42335622 79.74429176  
Rotation angle (degrees) 121.34889583  
Shift along axis 36.08032372  
  

> volume #1.2 style surface

> volume #1.2 style mesh

> volume #1.2 level 0.6307

> volume #1.2 level 0.3603

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.49358,0.83146,-0.25506,159.12,-0.082089,-0.3365,-0.9381,219.17,-0.86582,-0.44209,0.23434,133.38

Fit molecule hK1_1.pdb (#2) to map cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) using 623 atoms  
average map value = 0.5188, steps = 48  
shifted from previous position = 1.11  
rotated from previous position = 0.0251 degrees  
atoms outside contour = 195, contour level = 0.36031  
  
Position of hK1_1.pdb (#2) relative to cryosparc_P19_J381_003_volume_map_sharp
(1).mrc (#1.2) coordinates:  
Matrix rotation and translation  
0.50482790 -0.82824981 0.24320990 62.77331026  
-0.07340393 -0.32191577 -0.94391848 146.06719205  
0.86009341 0.45866382 -0.22330885 84.39790813  
Axis 0.82114030 -0.36115378 0.44192370  
Axis point 0.00000000 63.42283122 79.73330512  
Rotation angle (degrees) 121.34555792  
Shift along axis 36.09041153  
  

> lighting full

> ~select #2

Nothing selected  

> lighting soft

> lighting full

> lighting flat

> volume #1.2 style surface

> volume #1.2 style image

> volume #1.2 colorMode opaque8 showOutlineBox true orthoplanes xyz
> positionPlanes 63,63,63 imageMode orthoplanes

> volume #1.2 region 0,0,63,127,127,63 step 1 colorMode auto8 imageMode "full
> region"

> volume #1.2 region 0,0,0,127,127,127 step 1

> volume #1.2 region 0,0,0,127,127,127 step 1 colorMode opaque8 imageMode "box
> faces"

> volume #1.2 style mesh

> volume #1.2 style image

> volume #1.2

> volume #1.2 maximumIntensityProjection true colorMode auto8 imageMode "full
> region"

> volume #1.2 style surface maximumIntensityProjection false

> volume #1.2 style mesh

> graphics silhouettes false

> lighting flat

> lighting shadows true intensity 0.5

> lighting simple

> volume #1.1 level 0.4646

> volume #1.2 change image level -0.03948,0 level 0.4007,0.8 level 2.047,1

> volume #1.1 level 0.8071

> select #2

623 atoms, 640 bonds, 79 residues, 1 model selected  

> show sel target ab

> volume #1.1 level 0.4035

> ui tool show "Map Coordinates"

> ui tool show "Hide Dust"

> surface dust #1.1 size 10

> select #1.1

2 models selected  

> transparency #1.1.1 20

> ~select #1.1

Nothing selected  

> select #1.1

2 models selected  

> ~select #1.1

Nothing selected  

> select #1.2

3 models selected  

> select #1.2

3 models selected  

> select #1.2

3 models selected  

> select #1.1

2 models selected  

> select #1.2

3 models selected  

> select #1.2

3 models selected  

> select #1

6 models selected  

> ~select #1.1

4 models selected  

> select #1.2

3 models selected  

> select #1

6 models selected  

> volume #1.1 level 0.4288

Fit molecule Fab0.pdb (#3) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 6485 atoms  
average map value = 0.5124, steps = 72  
shifted from previous position = 0.00682  
rotated from previous position = 0.0211 degrees  
atoms outside contour = 3162, contour level = 0.42878  
  
Position of Fab0.pdb (#3) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.55151038 -0.77009193 -0.32061614 186.33910565  
0.80212990 0.59508924 -0.04956223 56.75365943  
0.22896269 -0.22984171 0.94591167 96.42267181  
Axis -0.10761431 -0.32806034 0.93850710  
Axis point 26.16142744 233.97565387 0.00000000  
Rotation angle (degrees) 56.88948830  
Shift along axis 51.82198302  
  
Fit molecule Fab0.pdb (#3) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 6485 atoms  
average map value = 0.5124, steps = 60  
shifted from previous position = 0.0146  
rotated from previous position = 0.0252 degrees  
atoms outside contour = 3166, contour level = 0.42878  
  
Position of Fab0.pdb (#3) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.55153377 -0.77020232 -0.32031061 186.33520443  
0.80223184 0.59497343 -0.04930203 56.73985821  
0.22854884 -0.22977164 0.94602877 96.44720878  
Axis -0.10772884 -0.32763407 0.93864286  
Axis point 26.19632983 233.93137515 0.00000000  
Rotation angle (degrees) 56.88864437  
Shift along axis 51.86589767  
  
Fit molecule Fab0.pdb (#3) to map cryosparc_P19_J504_007_volume_map_sharp.mrc
(#1.1) using 6485 atoms  
average map value = 0.5124, steps = 100  
shifted from previous position = 0.0146  
rotated from previous position = 0.0148 degrees  
atoms outside contour = 3165, contour level = 0.42878  
  
Position of Fab0.pdb (#3) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.55163697 -0.77007371 -0.32044211 186.32178830  
0.80210660 0.59513508 -0.04938871 56.73195191  
0.22873929 -0.22978409 0.94597971 96.44489273  
Axis -0.10769358 -0.32785380 0.93857018  
Axis point 26.17146648 233.96709157 0.00000000  
Rotation angle (degrees) 56.88126358  
Shift along axis 51.85485388  
  

> volume #1.1 level 0.5679

> volume #1.1 level 0.3529

> volume #1.1 level 0.5552

> preset "molecular surfaces" "ghostly white"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color white targ s trans 80

  

> preset "molecular surfaces" "atomic coloring (transparent)"

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    surface
    color fromatoms targ s trans 70

  

> volume #1.1 level 0.8333

> volume #1.1 level 0.9345

> volume #1.1 level 1.251

> ~select #1.1

4 models selected  

> select #1

6 models selected  

> select #1

6 models selected  

> ~select #1.1

4 models selected  

> select #1.2

3 models selected  

> select #1.2

3 models selected  

> select #1.2

3 models selected  

> select #1.2

3 models selected  

> select #1.2

3 models selected  

> select #1.2

3 models selected  

> select #1.2

3 models selected  

> show #!1.2 models

> hide #!1.2 models

> select #2

623 atoms, 640 bonds, 79 residues, 1 model selected  

> ~select #2

1 model selected  

> select #2

623 atoms, 640 bonds, 79 residues, 1 model selected  

> label (#!2 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select #2

623 atoms, 640 bonds, 79 residues, 2 models selected  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> ~label (#!2 & sel) residues

> show #!1.1 models

> hide #!1.1 models

> show #!1.1 models

> volume #1.1 level 0.8333

> volume #1.1 level 1.301

No map chosen to save  

> ~select #2

1 model selected  

> save C:/Users/13146/Downloads/Fab-PT.mrc models #1.1

> open C:/Users/13146/Downloads/Fab-PT.mrc

Opened Fab-PT.mrc as #5, grid size 256,256,256, pixel 1.16, shown at level
0.132, step 1, values float32  

> volume #5 level 0.8653

> volume #5 level 1.169

Fit map Fab-PT.mrc in map cryosparc_P19_J504_007_volume_map_sharp.mrc using
8966 points  
correlation = 1, correlation about mean = 0.9997, overlap = 2.791e+04  
steps = 92, shift = 3.3, angle = 16.3 degrees  
  
Position of Fab-PT.mrc (#5) relative to
cryosparc_P19_J504_007_volume_map_sharp.mrc (#1.1) coordinates:  
Matrix rotation and translation  
0.99999990 0.00000999 0.00045491 -0.07606278  
-0.00000998 1.00000000 -0.00003489 -0.00625583  
-0.00045491 0.00003489 0.99999990 0.06751821  
Axis 0.07645068 0.99683332 -0.02187762  
Axis point 147.73174442 0.00000000 164.96322412  
Rotation angle (degrees) 0.02614738  
Shift along axis -0.01352821  
  

> volume #5 level 1.245

> volume #1.1 level 1.01

> volume #1.2 style surface

> volume #5 level 0.7642

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> select #2

623 atoms, 640 bonds, 79 residues, 1 model selected  

> label (#!2 & sel) text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> ~label (#!2 & sel) residues

> label (#!2 & sel) attribute label_specifier

> ~label (#!2 & sel) residues

> label (#!2 & sel) attribute label_one_letter_code

> label (#!2 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> ~label (#!2 & sel) residues

> label (#!2 & sel) attribute label_specifier

> ~label (#!2 & sel) residues

> select #3

6485 atoms, 6566 bonds, 433 residues, 1 model selected  

> show (#!3 & sel) target ab

> ~select #3

1 model selected  

> hide #2-3#!1 target a

> save C:\Users\Public\Desktop\image1.png supersample 3

Permission denied writing file C:\Users\Public\Desktop\image1.png  

> save D:/Fab-PT.mtz

You need to specify at least one crystallographic map set to save!  
No map chosen to save  

> select #2

623 atoms, 640 bonds, 79 residues, 1 model selected  

> show (#!2 & sel) target ab

> ~select #2

1 model selected  

> save D:/PT-Fab.cxs

——— End of log from Fri Oct 14 22:31:01 2022 ———

opened ChimeraX session  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> molmap # 2 #3 5

Opened map 5 as #6, grid size 74,60,49, pixel 1.67, shown at level 0.117, step
1, values float32  

> molmap # 2 #3 3

Opened map 3 as #6, grid size 111,88,69, pixel 1, shown at level 0.119, step
1, values float32  

> molmap # 2 #3 2

Opened map 2 as #6, grid size 157,122,94, pixel 0.667, shown at level 0.156,
step 1, values float32  

> hide #!2 models

> hide #!3 models

> molmap # 2 #3 3

Opened map 3 as #6, grid size 111,88,69, pixel 1, shown at level 0.119, step
1, values float32  

> save C:/Users/Public/Desktop/PT-Fab.mrc models #6

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 87, in provider_save  
provider_info.bundle_info.run_provider(session, provider_info.format_name,  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\\__init__.py", line 164, in save  
save_map(session, path, _name, **kw)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map\volume.py", line 3974, in save_map  
save_grid_data(grids, path, session, format_name, options)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\fileformats.py", line 314, in save_grid_data  
ff.save_func(garg, tpath, options = options, progress = p)  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\mrc\writemrc.py", line 58, in
write_mrc2000_grid_data  
f = open(path, 'wb')  
PermissionError: [Errno 13] Permission denied: 'C:/Users/Public/Desktop/PT-
Fab.mrc'  
  
PermissionError: [Errno 13] Permission denied: 'C:/Users/Public/Desktop/PT-
Fab.mrc'  
  
File "C:\Program Files\ChimeraX 1.2.5\bin\lib\site-
packages\chimerax\map_data\mrc\writemrc.py", line 58, in
write_mrc2000_grid_data  
f = open(path, 'wb')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.101.1029
OpenGL renderer: Intel(R) Iris(R) Xe Graphics
OpenGL vendor: Intel
Manufacturer: HP
Model: HP Laptop 15t-dy200
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 16,805,040,128
MaxProcessMemory: 137,438,953,344
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
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
    biopython: 1.79
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StrudelScore: 0.1.10
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    MolecularDynamicsViewer: 1.2
    mrcfile: 1.3.0
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    pandas: 1.3.4
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    recordtype: 1.3
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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
    threed-strudel: 0.9.13
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

[Eric Pettersen]

In current versions, this is a UserError.