Session restore: KeyError: "combine"

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.2-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> set bgColor #ffffff00

Log from Wed Jan 29 22:57:14 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/250123_Filaments_predicted_model_fit.cxs

Opened J565_2.73A_Bb as #11, grid size 360,360,360, pixel 1.35, shown at level
0.177, step 1, values float32  
Opened J788_proteus_3.43A as #17, grid size 448,448,448, pixel 1.07, shown at
level 0.114, step 1, values float32  
Opened J467_Td_FlaB3_3.47A_nosheath as #1.1, grid size 360,360,360, pixel
1.07, shown at level 0.0994, step 1, values float32  
Opened J450_Td_FlaB3_2.51A_sheath as #1.2, grid size 360,360,360, pixel 1.07,
shown at level 0.107, step 1, values float32  
Opened J371_Td_FlaB2_3.23A_nosheath as #1.3, grid size 360,360,360, pixel
1.07, shown at level 0.151, step 1, values float32  
Opened J880_Td_insitu_WT_3.39A_nosheath as #1.4, grid size 360,360,360, pixel
1.07, shown at level 0.135, step 1, values float32  
Opened J766_Td_insitu_WT_3.12A_sheath as #1.5, grid size 360,360,360, pixel
1.07, shown at level 0.158, step 1, values float32  
Opened J152_Cdiff_3.76A_Helix as #2.1, grid size 360,360,360, pixel 1.07,
shown at level 0.15, step 1, values float32  
Opened J180_Cdiff_3.31A_local as #2.2, grid size 360,360,360, pixel 1.07,
shown at level 0.185, step 1, values float32  
Log from Thu Jan 23 21:39:56 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/250123_Filaments_predicted_model_fit.cxs

Opened J565_2.73A_Bb as #11, grid size 360,360,360, pixel 1.35, shown at level
0.177, step 1, values float32  
Opened J788_proteus_3.43A as #17, grid size 448,448,448, pixel 1.07, shown at
level 0.114, step 1, values float32  
Opened J467_Td_FlaB3_3.47A_nosheath as #1.1, grid size 360,360,360, pixel
1.07, shown at level 0.0994, step 1, values float32  
Opened J450_Td_FlaB3_2.51A_sheath as #1.2, grid size 360,360,360, pixel 1.07,
shown at level 0.107, step 1, values float32  
Opened J371_Td_FlaB2_3.23A_nosheath as #1.3, grid size 360,360,360, pixel
1.07, shown at level 0.151, step 1, values float32  
Opened J880_Td_insitu_WT_3.39A_nosheath as #1.4, grid size 360,360,360, pixel
1.07, shown at level 0.135, step 1, values float32  
Opened J766_Td_insitu_WT_3.12A_sheath as #1.5, grid size 360,360,360, pixel
1.07, shown at level 0.158, step 1, values float32  
Opened J152_Cdiff_3.76A_Helix as #2.1, grid size 360,360,360, pixel 1.07,
shown at level 0.15, step 1, values float32  
Opened J180_Cdiff_3.31A_local as #2.2, grid size 360,360,360, pixel 1.07,
shown at level 0.185, step 1, values float32  
Log from Thu Jan 23 21:26:34 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Ref_Seven_Guo/Filaments.cxs

Opened J565_2.73A_Bb as #11, grid size 360,360,360, pixel 1.35, shown at level
0.177, step 1, values float32  
Opened J788_proteus_3.43A as #17, grid size 448,448,448, pixel 1.07, shown at
level 0.114, step 1, values float32  
Opened J467_Td_FlaB3_3.47A_nosheath as #1.1, grid size 360,360,360, pixel
1.07, shown at level 0.0994, step 1, values float32  
Opened J450_Td_FlaB3_2.51A_sheath as #1.2, grid size 360,360,360, pixel 1.07,
shown at level 0.107, step 1, values float32  
Opened J371_Td_FlaB2_3.23A_nosheath as #1.3, grid size 360,360,360, pixel
1.07, shown at level 0.151, step 1, values float32  
Opened J880_Td_insitu_WT_3.39A_nosheath as #1.4, grid size 360,360,360, pixel
1.07, shown at level 0.135, step 1, values float32  
Opened J766_Td_insitu_WT_3.12A_sheath as #1.5, grid size 360,360,360, pixel
1.07, shown at level 0.158, step 1, values float32  
Opened J152_Cdiff_3.76A_Helix as #2.1, grid size 360,360,360, pixel 1.07,
shown at level 0.15, step 1, values float32  
Opened J180_Cdiff_3.31A_local as #2.2, grid size 360,360,360, pixel 1.07,
shown at level 0.185, step 1, values float32  
Log from Mon Jan 20 14:14:45 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/Liulab/Desktop/TdF.cxs

Opened J444_FlaB2_Helix as #1, grid size 360,360,360, pixel 1.07, shown at
level 0.168, step 1, values float32  
Opened J442_All_Helix as #2, grid size 360,360,360, pixel 1.07, shown at level
0.19, step 1, values float32  
Opened J441_All_Home as #3, grid size 360,360,360, pixel 1.07, shown at level
0.168, step 1, values float32  
Opened J419_All_Helix as #4, grid size 360,360,360, pixel 1.07, shown at level
0.14, step 1, values float32  
Opened J404_All_Home as #5, grid size 360,360,360, pixel 1.07, shown at level
0.184, step 1, values float32  
Opened J358 as #6, grid size 360,360,360, pixel 1.07, shown at level 0.146,
step 1, values float32  
Opened J450_FlaB3_Home as #7, grid size 360,360,360, pixel 1.07, shown at
level 0.107, step 1, values float32  
Opened J565_3.71A_Bb as #8, grid size 360,360,360, pixel 1.35, shown at level
0.214, step 1, values float32  
Opened J567_4.36A_Td_WT as #10, grid size 360,360,360, pixel 1.07, shown at
level 0.0883, step 1, values float32  
Opened J565_2.73A_Bb as #11, grid size 360,360,360, pixel 1.35, shown at level
0.177, step 1, values float32  
Opened J766_Td_insitu as #9, grid size 360,360,360, pixel 1.07, shown at level
0.158, step 1, values float32  
Log from Mon Jan 13 13:36:20 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/Liulab/Desktop/TdF.cxs

Opened J444_FlaB2_Helix as #1, grid size 360,360,360, pixel 1.07, shown at
level 0.168, step 1, values float32  
Opened J442_All_Helix as #2, grid size 360,360,360, pixel 1.07, shown at level
0.19, step 1, values float32  
Opened J441_All_Home as #3, grid size 360,360,360, pixel 1.07, shown at level
0.168, step 1, values float32  
Opened J419_All_Helix as #4, grid size 360,360,360, pixel 1.07, shown at level
0.14, step 1, values float32  
Opened J404_All_Home as #5, grid size 360,360,360, pixel 1.07, shown at level
0.184, step 1, values float32  
Opened J358 as #6, grid size 360,360,360, pixel 1.07, shown at level 0.146,
step 1, values float32  
Opened J450_FlaB3_Home as #7, grid size 360,360,360, pixel 1.07, shown at
level 0.107, step 1, values float32  
Opened J565_3.71A_Bb as #8, grid size 360,360,360, pixel 1.35, shown at level
0.214, step 1, values float32  
Opened J567_4.36A_Td_WT as #10, grid size 360,360,360, pixel 1.07, shown at
level 0.0883, step 1, values float32  
Opened J565_2.73A_Bb as #11, grid size 360,360,360, pixel 1.35, shown at level
0.177, step 1, values float32  
Log from Sun Nov 17 15:17:05 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/Liulab/Desktop/TdF.cxs

Opened J444_FlaB2_Helix as #1, grid size 360,360,360, pixel 1.07, shown at
level 0.168, step 1, values float32  
Opened J442_All_Helix as #2, grid size 360,360,360, pixel 1.07, shown at level
0.19, step 1, values float32  
Opened J441_All_Home as #3, grid size 360,360,360, pixel 1.07, shown at level
0.168, step 1, values float32  
Opened J419_All_Helix as #4, grid size 360,360,360, pixel 1.07, shown at level
0.14, step 1, values float32  
Opened J404_All_Home as #5, grid size 360,360,360, pixel 1.07, shown at level
0.184, step 1, values float32  
Opened J358 as #6, grid size 360,360,360, pixel 1.07, shown at level 0.146,
step 1, values float32  
Opened J450_FlaB3_Home as #7, grid size 360,360,360, pixel 1.07, shown at
level 0.107, step 1, values float32  
Log from Wed Nov 6 12:13:11 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /Users/Liulab/Desktop/TdF.cxs

Opened J444_FlaB2_Helix as #1, grid size 360,360,360, pixel 1.07, shown at
level 0.168, step 1, values float32  
Opened J442_All_Helix as #2, grid size 360,360,360, pixel 1.07, shown at level
0.19, step 1, values float32  
Opened J441_All_Home as #3, grid size 360,360,360, pixel 1.07, shown at level
0.168, step 1, values float32  
Opened J419_All_Helix as #4, grid size 360,360,360, pixel 1.07, shown at level
0.14, step 1, values float32  
Opened J404_All_Home as #5, grid size 360,360,360, pixel 1.07, shown at level
0.184, step 1, values float32  
Opened J358 as #6, grid size 360,360,360, pixel 1.07, shown at level 0.146,
step 1, values float32  
Log from Tue Nov 5 16:10:51 2024UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/Liulab/Desktop/cryosparc_P4_J444_010_volume_map_sharp.mrc

Opened cryosparc_P4_J444_010_volume_map_sharp.mrc as #1, grid size
360,360,360, pixel 1.07, shown at level 0.168, step 2, values float32  

> open /Users/Liulab/Desktop/cryosparc_P4_J442_006_volume_map_sharp.mrc

Opened cryosparc_P4_J442_006_volume_map_sharp.mrc as #2, grid size
360,360,360, pixel 1.07, shown at level 0.19, step 2, values float32  

> open /Users/Liulab/Desktop/cryosparc_P4_J441_006_volume_map_sharp.mrc

Opened cryosparc_P4_J441_006_volume_map_sharp.mrc as #3, grid size
360,360,360, pixel 1.07, shown at level 0.168, step 2, values float32  

> open /Users/Liulab/Desktop/cryosparc_P4_J419_005_volume_map_sharp.mrc

Opened cryosparc_P4_J419_005_volume_map_sharp.mrc as #4, grid size
360,360,360, pixel 1.07, shown at level 0.14, step 2, values float32  

> open /Users/Liulab/Desktop/cryosparc_P4_J404_008_volume_map_sharp.mrc

Opened cryosparc_P4_J404_008_volume_map_sharp.mrc as #5, grid size
360,360,360, pixel 1.07, shown at level 0.184, step 2, values float32  

> volume #1 step 1

> volume #2 step 1

> volume #3 step 1

> volume #4 step 1

> volume #5 step 1

> lighting soft

> surface dust #1 size 10.7

> surface dust #2 size 10.7

> surface dust #3 size 10.7

> surface dust #4 size 10.7

> surface dust #5 size 10.7

> view orient

> turn x -90

> view orient

> turn x -90

> ui tool show "Side View"

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> rename #1 J444

> rename #1 J444_FlaB2_Helix

> rename #2 J442_

> rename #2 J442_All_Helix

> rename #3 J441_All_Home

> rename #4 J419_All_Helix

> rename #5 J404_All_Home

> open /Users/Liulab/Desktop/cryosparc_P4_J358_009_volume_map_sharp.mrc

Opened cryosparc_P4_J358_009_volume_map_sharp.mrc as #6, grid size
360,360,360, pixel 1.07, shown at level 0.146, step 2, values float32  

> volume #6 step 1

> surface dust #1 size 10.7

> surface dust #6 size 10.7

> hide #!1 models

> view orient

> turn x -90

> ui tool show "Side View"

> view orient

> rename #6 J358

> hide #!6 models

> show #!1 models

> save /Users/Liulab/Desktop/TdF.cxs includeMaps true

——— End of log from Tue Nov 5 16:10:51 2024 ———

opened ChimeraX session  

> open /Users/Liulab/Desktop/cryosparc_P4_J450_007_volume_map_sharp.mrc

Opened cryosparc_P4_J450_007_volume_map_sharp.mrc as #7, grid size
360,360,360, pixel 1.07, shown at level 0.107, step 2, values float32  

> rename #7 J450

> rename #7 J450_FlaB3_Home

> hide #!7 models

> show #!7 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #7 step 1

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!7 models

> show #!7 models

> hide #!1 models

> surface dust #7 size 10.7

> view orient

> show #!1 models

> color #1 #ccff33ff models

> fitmap #1 inMap #7

Fit map J444_FlaB2_Helix in map J450_FlaB3_Home using 465039 points  
correlation = 0.6262, correlation about mean = 0.01376, overlap = 5246  
steps = 84, shift = 2.5, angle = 6.25 degrees  
  
Position of J444_FlaB2_Helix (#1) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.99406266 0.10829236 -0.01059176 -18.42206914  
-0.10828188 0.99411901 0.00156028 21.12262575  
0.01069844 -0.00040412 0.99994269 0.34453158  
Axis -0.00902649 -0.09782886 -0.99516232  
Axis point 183.24923977 180.34815571 0.00000000  
Rotation angle (degrees) 6.24692496  
Shift along axis -2.24298064  
  

> turn x 90

> ui tool show "Side View"

> fitmap #1 inMap #7

Fit map J444_FlaB2_Helix in map J450_FlaB3_Home using 465039 points  
correlation = 0.6262, correlation about mean = 0.01374, overlap = 5246  
steps = 48, shift = 0.00369, angle = 0.0101 degrees  
  
Position of J444_FlaB2_Helix (#1) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.99405949 0.10831907 -0.01061647 -18.42487179  
-0.10830673 0.99411601 0.00173271 21.09268643  
0.01074169 -0.00057258 0.99994214 0.36898919  
Axis -0.01058986 -0.09811346 -0.99511889  
Axis point 182.92112382 180.34916163 0.00000000  
Rotation angle (degrees) 6.24869204  
Shift along axis -2.24154780  
  

> turn x -90 models #1 center #1

[Repeated 1 time(s)]

> fitmap #1 inMap #7

Fit map J444_FlaB2_Helix in map J450_FlaB3_Home using 465039 points  
correlation = 0.6886, correlation about mean = 0.07538, overlap = 6348  
steps = 80, shift = 3.02, angle = 2.68 degrees  
  
Position of J444_FlaB2_Helix (#1) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.99771766 0.06673790 0.01027231 -15.17892866  
0.06674748 -0.99776972 -0.00059210 370.78549757  
0.01020989 0.00127640 -0.99994706 383.30452352  
Axis 0.99942925 0.03339041 0.00512348  
Axis point 0.00000000 185.55668002 191.77787537  
Rotation angle (degrees) 179.94644086  
Shift along axis -0.82573361  
  

> hide #!7 models

> show #!7 models

> hide #!1 models

> ui tool show "Side View"

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!7 models

> show #!7 models

> hide #!1 models

> show #!1 models

> turn x -90 models #1 center #1

[Repeated 1 time(s)]

> view orient

> volume flip #1 axis z

Opened J444_FlaB2_Helix z flip as #8, grid size 360,360,360, pixel 1.07, shown
at step 1, values float32  

> fitmap #8 inMap #7

Fit map J444_FlaB2_Helix z flip in map J450_FlaB3_Home using 465039 points  
correlation = 0.6622, correlation about mean = 0.06535, overlap = 5861  
steps = 80, shift = 2.15, angle = 3.18 degrees  
  
Position of J444_FlaB2_Helix z flip (#8) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.29809527 0.95441213 -0.01538282 -45.89547072  
-0.95452807 0.29798802 -0.00890333 320.20706811  
-0.00391357 0.01733736 0.99984203 -1.07964169  
Axis 0.01374466 -0.00600750 -0.99988749  
Axis point 194.76004946 191.29910750 0.00000000  
Rotation angle (degrees) 72.66472290  
Shift along axis -1.47494138  
  

> surface dust #7 size 10.7

> surface dust #8 size 10.7

> ui tool show "Side View"

> view orient

> turn x 90

> turn x -90 models #8 center #8

[Repeated 1 time(s)]

> fitmap #8 inMap #7

Fit map J444_FlaB2_Helix z flip in map J450_FlaB3_Home using 465039 points  
correlation = 0.6407, correlation about mean = 0.04479, overlap = 5513  
steps = 92, shift = 3.35, angle = 3.89 degrees  
  
Position of J444_FlaB2_Helix z flip (#8) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.35723727 0.93400154 0.00475263 -56.56875507  
0.93399572 -0.35719432 -0.00801086 83.41539768  
-0.00578452 0.00730074 -0.99995661 378.81545121  
Axis 0.82377972 0.56690993 -0.00031286  
Axis point -0.00000000 60.10405441 189.63134034  
Rotation angle (degrees) 179.46751395  
Shift along axis 0.57030889  
  

> select add #8

3 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.35724,0.934,0.0047526,-58.254,0.934,-0.35719,-0.0080109,83.415,-0.0057845,0.0073007,-0.99996,357.45

> fitmap #8 inMap #7

Fit map J444_FlaB2_Helix z flip in map J450_FlaB3_Home using 465039 points  
correlation = 0.6422, correlation about mean = 0.05253, overlap = 5465  
steps = 76, shift = 2.94, angle = 1.23 degrees  
  
Position of J444_FlaB2_Helix z flip (#8) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.34979122 0.93681991 0.00380656 -56.14499956  
0.93674398 -0.34981143 0.01194320 75.81349204  
0.01252023 -0.00061184 -0.99992142 357.48979829  
Axis -0.82151646 -0.57016316 -0.00496822  
Axis point 0.00000000 58.22143925 178.73688503  
Rotation angle (degrees) 179.56217681  
Shift along axis 1.12189316  
  

> select subtract #8

Nothing selected  

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!1 models

> select add #1

3 models selected  

> view matrix models
> #1,0.27012,0.96241,0.028489,-47.064,-0.96224,0.27087,-0.026786,330.29,-0.033496,-0.020178,0.99924,39.918

> fitmap #1 inMap #7

Fit map J444_FlaB2_Helix in map J450_FlaB3_Home using 465039 points  
correlation = 0.9119, correlation about mean = 0.4002, overlap = 1.175e+04  
steps = 88, shift = 4.23, angle = 3.37 degrees  
  
Position of J444_FlaB2_Helix (#1) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.29908649 0.95408019 -0.01667909 -46.52394226  
-0.95422527 0.29906191 -0.00400967 318.47898164  
0.00116252 0.01711483 0.99985285 25.64353419  
Axis 0.01106861 -0.00934847 -0.99989504  
Axis point 193.48606278 190.56937460 0.00000000  
Rotation angle (degrees) 72.60241158  
Shift along axis -29.13308922  
  

> select subtract #1

Nothing selected  

> select add #1

3 models selected  

> select subtract #1

Nothing selected  

> close #8

> hide #!7 models

> show #!7 models

> ui tool show "Surface Color"

> color cylindrical #1.1 palette 4,#ff0000:45,#ffc0cb:70,#44ff00 center
> 191.32,191.27,222.24

> hide #!1 models

> show #!1 models

> hide #!7 models

> color cylindrical #1.1 palette 4,#ff0000:45,#ffc0cb:80,#44ff00 center
> 191.32,191.27,222.24

> color cylindrical #1.1 palette 4,#ff0000:50,#ffc0cb:80,#44ff00 center
> 191.32,191.27,222.24

> color cylindrical #7.1 palette 4,#ff0000:50,#ffc0cb:80,#44ff00 center
> 191.32,191.27,222.24

> show #!7 models

> hide #!1 models

> show #!1 models

> volume #7#1 region 0,0,0,550,380,500

> volume #7#1 region 0,0,0,550,80,500

> volume #7#1 region 0,0,0,550,180,500

> volume #7#1 region 0,100,0,550,380,500

> volume #7#1 region 0,150,0,550,580,500

> volume #7#1 region 0,120,0,550,580,500

> volume #7#1 region 0,180,0,550,580,500

> volume #7#1 region 0,160,0,550,580,500

> view orient

> turn x -90

> turn y -10

> turn y 10

[Repeated 7 time(s)]

> view name t1

> turn y 10 models #1 center #1

> turn y 10

> turn y -10

[Repeated 10 time(s)]

> turn y 10 models #1 center #1

[Repeated 8 time(s)]

> fitmap #1 inMap #7

Fit map J444_FlaB2_Helix in map J450_FlaB3_Home using 333433 points  
correlation = 0.4997, correlation about mean = 0.02261, overlap = 2446  
steps = 168, shift = 3.91, angle = 4.69 degrees  
  
Position of J444_FlaB2_Helix (#1) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.84938039 -0.52741368 -0.01969103 163.07138313  
0.52711604 0.84959185 -0.01850120 -82.24460093  
0.02648711 0.00533508 0.99963491 20.30020201  
Axis 0.02257631 -0.04373720 0.99878795  
Axis point 223.42321255 244.20564249 0.00000000  
Rotation angle (degrees) 31.86399436  
Shift along axis 27.55429549  
  

> select add #1

2 models selected  

> view matrix models
> #1,0.84938,-0.52741,-0.019691,133.55,0.52712,0.84959,-0.018501,-61.236,0.026487,0.0053351,0.99963,4.6787

> view matrix models
> #1,0.99998,0.0062294,-0.0016444,-13.561,-0.0062589,0.99981,-0.018542,9.3205,0.0015285,0.018552,0.99983,6.6142

> view matrix models
> #1,0.99998,0.0062294,-0.0016444,-9.3954,-0.0062589,0.99981,-0.018542,0.78889,0.0015285,0.018552,0.99983,0.74415

> view matrix models
> #1,0.99998,0.0062294,-0.0016444,-5.7992,-0.0062589,0.99981,-0.018542,2.9553,0.0015285,0.018552,0.99983,0.64408

> fitmap #1 inMap #7

Fit map J444_FlaB2_Helix in map J450_FlaB3_Home using 333433 points  
correlation = 0.6034, correlation about mean = 0.01422, overlap = 3555  
steps = 96, shift = 7.5, angle = 3.28 degrees  
  
Position of J444_FlaB2_Helix (#1) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.99816997 0.05952476 -0.01065087 -7.52938829  
-0.05952413 0.99822677 0.00037960 8.88792916  
0.01065456 0.00025506 0.99994320 4.42983783  
Axis -0.00102971 -0.17616474 -0.98436016  
Axis point 127.91186187 130.52649178 0.00000000  
Rotation angle (degrees) 3.46680179  
Shift along axis -5.91854257  
  

> select subtract #1

Nothing selected  

> volume #7#1 region 0,150,0,550,580,500

> volume #7#1 region 0,170,0,550,580,500

> volume #7#1 region 0,180,0,550,580,500

> surface dust #1 size 10.7

> surface dust #7 size 10.7

> ui tool show "Hide Dust"

> surface dust #1 size 1.07

> surface dust #1 size 20.93

> surface dust #7 size 10.7

> surface dust #7 size 10.5

> surface dust #7 size 16.26

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #1

2 models selected  

> color #1 #ccff00ff models

> view matrix models
> #1,0.99817,0.059525,-0.010651,-10.535,-0.059524,0.99823,0.0003796,9.0434,0.010655,0.00025506,0.99994,14.791

> fitmap #1 inMap #7

Fit map J444_FlaB2_Helix in map J450_FlaB3_Home using 235533 points  
correlation = 0.8879, correlation about mean = 0.3585, overlap = 5713  
steps = 160, shift = 17.3, angle = 3.98 degrees  
  
Position of J444_FlaB2_Helix (#1) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.99164422 0.12805326 -0.01562146 -21.20831735  
-0.12816102 0.99173461 -0.00609761 26.84712730  
0.01471151 0.00804871 0.99985938 29.35507216  
Axis 0.05474770 -0.11739169 -0.99157545  
Axis point 168.39907843 162.32088060 0.00000000  
Rotation angle (degrees) 7.42310915  
Shift along axis -33.42050538  
  

> select subtract #1

Nothing selected  

> view orient

> turn x -90

> volume #7#1 region 0,0,0,550,580,500

> color cylindrical #1.1 palette 4,#ff0000:50,#ffc0cb:80,#44ff00 center
> 191.32,191.27,222.24

> hide #!1 models

> set bgColor white

> lighting simple

> lighting soft

> show #!1 models

> hide #!7 models

> volume #7#1 region 0,180,0,550,580,500

> show #!7 models

> hide #!1 models

> volume #7#1 region 0,0,0,550,580,500

> show #!1 models

> volume #7#1 region 0,180,0,550,580,500

> hide #!1 models

> show #!1 models

> save /Users/Liulab/Desktop/TdF.cxs includeMaps true

——— End of log from Wed Nov 6 12:13:11 2024 ———

opened ChimeraX session  

> open /Users/Liulab/Desktop/cryosparc_P2_J569_004_volume_map_sharp.mrc

Opened cryosparc_P2_J569_004_volume_map_sharp.mrc as #8, grid size
360,360,360, pixel 1.35, shown at level 0.214, step 2, values float32  

> open /Users/Liulab/Desktop/cryosparc_P2_J576_008_volume_map_sharp.mrc

Opened cryosparc_P2_J576_008_volume_map_sharp.mrc as #9, grid size
360,360,360, pixel 1.07, shown at level 0.111, step 2, values float32  

> open /Users/Liulab/Desktop/cryosparc_P2_J567_008_volume_map_sharp.mrc

Opened cryosparc_P2_J567_008_volume_map_sharp.mrc as #10, grid size
360,360,360, pixel 1.07, shown at level 0.111, step 2, values float32  

> open /Users/Liulab/Desktop/cryosparc_P2_J565_003_volume_map_sharp.mrc

Opened cryosparc_P2_J565_003_volume_map_sharp.mrc as #11, grid size
360,360,360, pixel 1.35, shown at level 0.197, step 2, values float32  

> surface dust #1 size 10.7

> surface dust #7 size 10.7

> surface dust #8 size 13.5

> surface dust #9 size 10.7

> surface dust #10 size 10.7

> surface dust #11 size 13.5

> view orient

> volume #8 step 1

> volume #9 step 1

> volume #10 step 1

> volume #11 step 1

> hide #!11 models

> hide #!10 models

> hide #!9 models

> rename #11 J565_2.73A_Bb

> rename #8 J565_3.71A_Bb

> hide #!8 models

> show #!8 models

> select add #8

2 models selected  

> show #!11 models

> select add #11

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8,1,0,0,-43.423,0,1,0,-11.775,0,0,1,0.29022,#11,1,0,0,-43.423,0,1,0,-11.775,0,0,1,0.29022

> select subtract #11

2 models selected  

> select subtract #8

Nothing selected  

> hide #!7 models

> show #!6 models

> hide #!8 models

> hide #!11 models

> hide #!1 models

> view orient

> show #!8 models

> select add #8

2 models selected  

> show #!11 models

> select add #11

4 models selected  

> view matrix models
> #8,1,0,0,-47.053,0,1,0,-46.165,0,0,1,0.29022,#11,1,0,0,-47.053,0,1,0,-46.165,0,0,1,0.29022

> fitmap #8 inMap #6

Fit map J565_3.71A_Bb in map J358 using 465751 points  
correlation = 0.662, correlation about mean = 0.2816, overlap = 1.049e+04  
steps = 140, shift = 14.1, angle = 9.28 degrees  
  
Position of J565_3.71A_Bb (#8) relative to J358 (#6) coordinates:  
Matrix rotation and translation  
0.98700430 0.16046722 -0.00853096 -84.12769021  
-0.16056622 0.98694504 -0.01256884 -4.88427394  
0.00640270 0.01377528 0.99988462 8.58202150  
Axis 0.08169772 -0.04631190 -0.99558058  
Axis point -76.29530134 510.35418226 0.00000000  
Rotation angle (degrees) 9.27825387  
Shift along axis -15.19093459  
  

> fitmap #11 inMap #8

Fit map J565_2.73A_Bb in map J565_3.71A_Bb using 465633 points  
correlation = 0.8163, correlation about mean = 0.1296, overlap = 2.266e+04  
steps = 176, shift = 5.27, angle = 6 degrees  
  
Position of J565_2.73A_Bb (#11) relative to J565_3.71A_Bb (#8) coordinates:  
Matrix rotation and translation  
0.96513685 -0.26174576 0.00009393 71.84950069  
0.26174576 0.96513686 0.00000117 -54.95659906  
-0.00009096 0.00002346 1.00000000 -15.09406430  
Axis 0.00004258 0.00035318 0.99999994  
Axis point 242.20682878 242.24290073 0.00000000  
Rotation angle (degrees) 15.17367563  
Shift along axis -15.11041390  
  

> select subtract #8

2 models selected  

> select subtract #11

Nothing selected  

> hide #!11 models

> hide #!8 models

> show #!9 models

> show #!10 models

> close #9

> rename #10 J567_4.36A_Td_WT

> volume #10 level 0.08833

> fitmap #10 inMap #6

Fit map J567_4.36A_Td_WT in map J358 using 1070417 points  
correlation = 0.7931, correlation about mean = 0.3145, overlap = 1.114e+04  
steps = 104, shift = 9.14, angle = 9.44 degrees  
  
Position of J567_4.36A_Td_WT (#10) relative to J358 (#6) coordinates:  
Matrix rotation and translation  
0.98645915 -0.16388196 -0.00640729 35.38462260  
0.16385693 0.98647493 -0.00425747 -27.46637987  
0.00701836 0.00314994 0.99997041 -11.06828596  
Axis 0.02257687 -0.04091971 0.99890733  
Axis point 186.55861164 201.75901531 0.00000000  
Rotation angle (degrees) 9.44197584  
Shift along axis -9.13340168  
  

> view orient

> turn x -90

> hide #!10 models

> hide #!6 models

> show #!1 models

> hide #!1 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> show #!10 models

> volume #10 region 0,0,0,500,500,500

> volume #10 region 0,50,0,500,500,500

> volume #10 region 0,150,0,500,500,500

> volume #10 region 0,170,0,500,500,500

> view orient

> turn x -90

> hide #!10 models

> show #!10 models

> hide #!7 models

> show #!7 models

> hide #!10 models

> show #!10 models

> hide #!7 models

> show #!1 models

> show #!7 models

> hide #!7 models

> fitmap #10 inMap #1

Fit map J567_4.36A_Td_WT in map J444_FlaB2_Helix using 617605 points  
correlation = 0.6562, correlation about mean = 0.4489, overlap = 6545  
steps = 48, shift = 1.03, angle = 0.797 degrees  
  
Position of J567_4.36A_Td_WT (#10) relative to J444_FlaB2_Helix (#1)
coordinates:  
Matrix rotation and translation  
0.95835744 -0.28554087 -0.00418202 63.81744129  
0.28554285 0.95836596 -0.00013801 -46.92189946  
0.00404734 -0.00106188 0.99999125 -43.37373348  
Axis -0.00161758 -0.01440857 0.99989488  
Axis point 194.89253167 194.83159179 0.00000000  
Rotation angle (degrees) 16.59303496  
Shift along axis -42.79632642  
  

> select add #10

2 models selected  

> view matrix models
> #10,0.98685,-0.16042,-0.019786,35.04,0.16033,0.98705,-0.0056985,-20.403,0.020444,0.0024511,0.99979,35.445

> fitmap #10 inMap #1

Fit map J567_4.36A_Td_WT in map J444_FlaB2_Helix using 617605 points  
correlation = 0.4126, correlation about mean = 0.1979, overlap = 2584  
steps = 100, shift = 3.82, angle = 0.415 degrees  
  
Position of J567_4.36A_Td_WT (#10) relative to J444_FlaB2_Helix (#1)
coordinates:  
Matrix rotation and translation  
0.95973541 -0.28090320 0.00118003 60.14290983  
0.28090403 0.95973571 -0.00057170 -36.85408284  
-0.00097190 0.00088016 0.99999915 2.87324961  
Axis 0.00258424 0.00383032 0.99998933  
Axis point 158.66330290 191.33611643 0.00000000  
Rotation angle (degrees) 16.31432144  
Shift along axis 2.88747951  
  

> select subtract #10

Nothing selected  

> volume #10 region 0,0,0,500,500,500

> ui tool show "Surface Color"

> color cylindrical #10.1 palette 4,#ff0000:50,#ffc0cb:80,#44ff00 center
> 190.79,201.01,229.43

> volume #10 region 0,170,0,500,500,500

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> volume #10 region 0,180,0,500,500,500

> show #!1 models

> hide #!1 models

> show #!7 models

> hide #!10 models

> show #!10 models

> hide #!7 models

> hide #!10 models

> show #!11 models

> show #!8 models

> view orient

> turn x -90

> ui tool show "Side View"

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> turn x -90 models #8 center #8

[Repeated 1 time(s)]

> fitmap #8 inMap #11

Fit map J565_3.71A_Bb in map J565_2.73A_Bb using 465751 points  
correlation = 0.9895, correlation about mean = 0.8151, overlap = 3.92e+04  
steps = 176, shift = 20.2, angle = 5.43 degrees  
  
Position of J565_3.71A_Bb (#8) relative to J565_2.73A_Bb (#11) coordinates:  
Matrix rotation and translation  
0.99935892 -0.03580158 0.00006061 8.81470362  
-0.03580159 -0.99935892 0.00004667 493.05859730  
0.00005890 -0.00004881 -1.00000000 479.90009437  
Axis -0.99983972 0.01790366 -0.00002988  
Axis point 0.00000000 246.61394903 239.94402837  
Rotation angle (degrees) 179.99726400  
Shift along axis -0.00007561  
  

> view orient

> hide #!8 models

> show #!8 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> volume #11 level 0.2121

> view orient

> turn x -90

> hide #!8 models

> volume #11 level 0.2247

> volume #11 level 0.2132

> view orient

> hide #!11 models

> show #!8 models

> view orient

> turn x -90

> show #!11 models

> hide #!8 models

> show #!8 models

> volume #11 level 0.1663

> hide #!8 models

> volume #11 level 0.1548

> show #!8 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> volume #11 level 0.1766

> hide #!11 models

> color cylindrical #8.1 palette 4,#ff0000:50,#ffc0cb:80,#44ff00 center
> 191.95,192.64,235.74

> color cylindrical #8.1 palette 4,#ff0000:50,#ffc0cb:70,#44ff00 center
> 191.95,192.64,235.74

> color cylindrical #8.1 palette 4,#ff0000:40,#ffc0cb:60,#44ff00 center
> 191.95,192.64,235.74

> color cylindrical #8.1 palette 4,#ff0000:45,#ffc0cb:65,#44ff00 center
> 191.95,192.64,235.74

> save /Users/Liulab/Desktop/TdF.cxs includeMaps true

——— End of log from Sun Nov 17 15:17:05 2024 ———

opened ChimeraX session  

> hide #!8 models

> show #!10 models

> view orient

> hide #!10 models

> show #!5 models

> view orient

> open /Users/Liulab/Downloads/cryosparc_P2_J766_001_volume_map_sharp.mrc

Opened cryosparc_P2_J766_001_volume_map_sharp.mrc as #9, grid size
360,360,360, pixel 1.07, shown at level 0.158, step 2, values float32  

> hide #!5 models

> show #!7 models

> hide #!7 models

> show #!7 models

> volume #9 step 1

> surface dust #7 size 10.7

> surface dust #9 size 10.7

> rename #9 J766_Td_insitu

> show #!10 models

> volume #10 region 0,0,0,580,850,800

> fitmap #10 inMap #7

Fit map J567_4.36A_Td_WT in map J450_FlaB3_Home using 1070417 points  
correlation = 0.4797, correlation about mean = 0.06035, overlap = 2623  
steps = 116, shift = 5.14, angle = 1.64 degrees  
  
Position of J567_4.36A_Td_WT (#10) relative to J450_FlaB3_Home (#7)
coordinates:  
Matrix rotation and translation  
0.98289960 -0.18357226 -0.01447777 39.40454305  
0.18340990 0.98296507 -0.01185233 -21.68839937  
0.01640690 0.00899429 0.99982494 26.71946862  
Axis 0.05651496 -0.08372801 0.99488476  
Axis point 122.27336800 193.83545073 0.00000000  
Rotation angle (degrees) 10.62816479  
Shift along axis 30.62566459  
  

> fitmap #9 inMap #7

Fit map J766_Td_insitu in map J450_FlaB3_Home using 466663 points  
correlation = 0.4495, correlation about mean = 0.02082, overlap = 2305  
steps = 132, shift = 3.52, angle = 9.19 degrees  
  
Position of J766_Td_insitu (#9) relative to J450_FlaB3_Home (#7) coordinates:  
Matrix rotation and translation  
0.98716326 0.15943388 -0.00946257 -27.48955484  
-0.15944276 0.98720716 -0.00018652 32.82289173  
0.00931178 0.00169287 0.99995521 -5.44708665  
Axis 0.00588349 -0.05877373 -0.99825399  
Axis point 192.00935238 188.00282651 0.00000000  
Rotation angle (degrees) 9.19048098  
Shift along axis 3.34671772  
  

> fitmap #9 inMap #10

Fit map J766_Td_insitu in map J567_4.36A_Td_WT using 466663 points  
correlation = 0.8042, correlation about mean = 0.085, overlap = 6824  
steps = 140, shift = 11.4, angle = 6.8 degrees  
  
Position of J766_Td_insitu (#9) relative to J567_4.36A_Td_WT (#10)
coordinates:  
Matrix rotation and translation  
0.89492710 0.44621236 -0.00009940 -65.56403250  
-0.44621237 0.89492710 -0.00011413 106.01247101  
0.00003803 0.00014649 0.99999999 -27.52773515  
Axis 0.00029203 -0.00015399 -0.99999995  
Axis point 192.32418406 192.24057453 0.00000000  
Rotation angle (degrees) 26.50093307  
Shift along axis 27.49226167  
  

> hide #!10 models

> hide #!7 models

> ui tool show "Surface Color"

> color cylindrical #9.1 palette
> 4,#ff0000:45,#fffb00:77,#00f900:80,#942192:110,#ff40ff center
> 189.71,200.85,194.03

> ui tool show "Side View"

> color cylindrical #9.1 palette
> 4,#ff0000:45,#fffb00:77,#00f900:80,#942192:110,#ff40ff center
> 189.71,200.85,194.03

> view orient

[Repeated 1 time(s)]

> hide #!9 models

> save /Users/Liulab/Desktop/TdF.cxs includeMaps true

——— End of log from Mon Jan 13 13:36:20 2025 ———

opened ChimeraX session  

> show #!6 models

> view orient

[Repeated 1 time(s)]

> hide #!6 models

> show #!7 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!11 models

> hide #!11 models

> show #!10 models

> hide #!10 models

> open /Users/Liulab/Desktop/AF-Q18CX7-F1-model_v4.pdb

AF-Q18CX7-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for flagellin (Q18CX7) [more info...]  
  
Chain information for AF-Q18CX7-F1-model_v4.pdb #12  
---  
Chain | Description | UniProt  
A | flagellin | Q18CX7_CLOD6 1-290  
  
Computing secondary structure  

> open /Users/Liulab/Downloads/cryosparc_P3_J180_002_volume_map_sharp.mrc

Opened cryosparc_P3_J180_002_volume_map_sharp.mrc as #13, grid size
360,360,360, pixel 1.07, shown at level 0.159, step 2, values float32  

> open /Users/Liulab/Downloads/cryosparc_P2_J883_002_volume_map_sharp.mrc

Opened cryosparc_P2_J883_002_volume_map_sharp.mrc as #14, grid size
360,360,360, pixel 1.07, shown at level 0.143, step 2, values float32  

> open /Users/Liulab/Downloads/cryosparc_P2_J765_001_volume_map_sharp.mrc

Opened cryosparc_P2_J765_001_volume_map_sharp.mrc as #15, grid size
360,360,360, pixel 1.07, shown at level 0.158, step 2, values float32  

> open /Users/Liulab/Downloads/cryosparc_P2_J827_002_volume_map_sharp.mrc

Opened cryosparc_P2_J827_002_volume_map_sharp.mrc as #16, grid size
360,360,360, pixel 1.35, shown at level 0.208, step 2, values float32  

> open /Users/Liulab/Downloads/cryosparc_P1_J788_002_volume_map_sharp(1).mrc

Opened cryosparc_P1_J788_002_volume_map_sharp(1).mrc as #17, grid size
448,448,448, pixel 1.07, shown at level 0.114, step 2, values float32  

> rename #12 AF-Q18CX7-Cdiff.pdb

> volume #17 step 1

> volume #16 step 1

> volume #15 step 1

> volume #14 step 1

> volume #13 step 1

> surface dust #13 size 10.7

> surface dust #14 size 10.7

> surface dust #15 size 10.7

> surface dust #16 size 13.5

> surface dust #17 size 10.7

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #12 models

> show #!1 models

> show #!2 models

> show #!3 models

> show #!4 models

> show #!5 models

> show #!6 models

> show #!7 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!10 models

> hide #!10 models

> volume #1-10 region 0,0,0,700,750,800

> hide #!7 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> open /Users/Liulab/Downloads/cryosparc_P2_J371_007_volume_map_sharp(1).mrc

Opened cryosparc_P2_J371_007_volume_map_sharp(1).mrc as #18, grid size
360,360,360, pixel 1.07, shown at level 0.151, step 2, values float32  

> fitmap #18 inMap #1

Fit map cryosparc_P2_J371_007_volume_map_sharp(1).mrc in map J444_FlaB2_Helix
using 58288 points  
correlation = 0.5109, correlation about mean = 0.0306, overlap = 841.2  
steps = 116, shift = 3.45, angle = 3.28 degrees  
  
Position of cryosparc_P2_J371_007_volume_map_sharp(1).mrc (#18) relative to
J444_FlaB2_Helix (#1) coordinates:  
Matrix rotation and translation  
0.99670493 -0.08103015 -0.00366843 20.71916875  
0.08094864 0.99654452 -0.01861146 -11.69865739  
0.00516386 0.01825319 0.99982007 -37.11095176  
Axis 0.22160165 -0.05309287 0.97369084  
Axis point 179.01506776 332.98314326 0.00000000  
Rotation angle (degrees) 4.77124541  
Shift along axis -30.92207669  
  

> volume #18 step 1

> hide #!18 models

> show #!18 models

> hide #!1 models

> surface dust #18 size 10.7

> show #!1 models

> select add #18

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #18,0.99866,0.046973,-0.02164,-4.8028,-0.047491,0.99858,-0.024084,14.691,0.020478,0.025079,0.99948,-7.477

> view orient

> turn x -90

> ui tool show "Side View"

> hide #!1 models

> show #!1 models

> select clear

> hide #!18 models

> show #!18 models

> fitmap #18 inMap #1

Fit map cryosparc_P2_J371_007_volume_map_sharp(1).mrc in map J444_FlaB2_Helix
using 466767 points  
correlation = 0.5268, correlation about mean = 0.02212, overlap = 7388  
steps = 92, shift = 1.43, angle = 4.45 degrees  
  
Position of cryosparc_P2_J371_007_volume_map_sharp(1).mrc (#18) relative to
J444_FlaB2_Helix (#1) coordinates:  
Matrix rotation and translation  
0.99998380 -0.00542541 -0.00173794 1.23276015  
0.00542366 0.99998478 -0.00103064 -0.88613302  
0.00174352 0.00102121 0.99999797 -32.34306737  
Axis 0.17723078 -0.30071524 0.93710170  
Axis point 1820.33036031 1196.01784790 0.00000000  
Rotation angle (degrees) 0.33166613  
Shift along axis -29.82378660  
  

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> view orient

> rename #18 J371_FlaB2_3.23A

> rename #18 J371_Td_FlaB2_3.23A_nosheath

> close #1

> hide #!18 models

> show #!2 models

> close #2

> close #3-5

> show #!6 models

> close #6

> show #!7 models

> rename #7 J450_Td_FlaB3_2.51A_sheath

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!9 models

> rename #9 J766_Td_insitu_WT

> close #15

> show #!10 models

> close #10

> hide #!9 models

> show #!13 models

> hide #!13 models

> show #!14 models

> hide #!14 models

> show #!16 models

> hide #!16 models

> show #!17 models

> lighting soft

> hide #!17 models

> show #!18 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> open /Users/Liulab/Downloads/cryosparc_P2_J467_003_volume_map_sharp.mrc

Opened cryosparc_P2_J467_003_volume_map_sharp.mrc as #1, grid size
360,360,360, pixel 1.07, shown at level 0.101, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.09936

> show #!7 models

> fitmap #1 inMap #7

Fit map cryosparc_P2_J467_003_volume_map_sharp.mrc in map
J450_Td_FlaB3_2.51A_sheath using 488859 points  
correlation = 0.6432, correlation about mean = 0.001424, overlap = 2926  
steps = 104, shift = 1.83, angle = 6.18 degrees  
  
Position of cryosparc_P2_J467_003_volume_map_sharp.mrc (#1) relative to
J450_Td_FlaB3_2.51A_sheath (#7) coordinates:  
Matrix rotation and translation  
0.99418314 0.10733199 -0.00892889 -18.68667360  
-0.10731437 0.99422217 0.00243127 20.58086124  
0.00913825 -0.00145893 0.99995718 -0.03272747  
Axis -0.01805691 -0.08386138 -0.99631381  
Axis point 180.80792070 184.12861552 0.00000000  
Rotation angle (degrees) 6.18391508  
Shift along axis -1.35590899  
  

> rename #1 J467_Td_FlaB3_3.47A_sheath

> rename #1 J467_Td_FlaB3_3.47A_nosheath

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!1 models

> show #!18 models

> hide #!18 models

> show #!9 models

> show #!14 models

> volume #14 level 0.1837

> hide #!9 models

> volume #14 level 0.1715

> open /Users/Liulab/Downloads/cryosparc_P2_J880_002_volume_map_sharp.mrc

Opened cryosparc_P2_J880_002_volume_map_sharp.mrc as #2, grid size
360,360,360, pixel 1.07, shown at level 0.135, step 2, values float32  

> open /Users/Liulab/Downloads/cryosparc_P2_J878_002_volume_map_sharp.mrc

Opened cryosparc_P2_J878_002_volume_map_sharp.mrc as #3, grid size
360,360,360, pixel 1.07, shown at level 0.133, step 2, values float32  

> volume #2 step 1

> volume #3 step 1

> hide #!14 models

> hide #!3 models

> surface dust #2 size 10.7

> hide #!2 models

> show #!3 models

> volume #3 level 0.1345

> surface dust #3 size 10.7

> show #!14 models

> hide #!3 models

> volume #14 level 0.1703

> close #14

> show #!3 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> close #3

> rename #2 J880_Td_insitu_WT_3.39A

> rename #9 J766_Td_insitu_WT_3.12A

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> close #16

> show #!9 models

> rename #9 J766_Td_insitu_WT_3.12A_sheath

> show #!2 models

> hide #!9 models

> rename #2 J880_Td_insitu_WT_3.39A_nosheath

> rename #1#7#18#2#9 id #1

> rename #1 Td

> hide #!1.4 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.2 models

> hide #!1 models

> show #!8 models

> show #!11 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> close #8

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!13 models

> show #!17 models

> hide #!13 models

> hide #!17 models

> show #!13 models

> volume #13 level 0.236

> volume #13 level 0.1846

> open /Users/Liulab/Downloads/cryosparc_P3_J152_014_volume_map_sharp.mrc

Opened cryosparc_P3_J152_014_volume_map_sharp.mrc as #2, grid size
360,360,360, pixel 1.07, shown at level 0.15, step 2, values float32  

> open /Users/Liulab/Downloads/cryosparc_P3_J124_003_volume_map_sharp.mrc

Opened cryosparc_P3_J124_003_volume_map_sharp.mrc as #3, grid size
360,360,360, pixel 1.07, shown at level 0.131, step 2, values float32  

> hide #!13 models

> hide #!3 models

> show #!3 models

> show #!13 models

> surface dust #13 size 10.7

> surface dust #2 size 10.7

> surface dust #3 size 10.7

> volume #2 step 1

> volume #3 step 1

> hide #!13 models

> hide #!3 models

> surface dust #2 size 10.7

> hide #!2 models

> show #!3 models

> close #3

> show #!13 models

> show #!2 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> rename #2 J152_Cdiff_3.76A_Helix

> rename #13 J180_002_volume_map_sharp.mrc

> rename #13 J180_Cdiff_3.76A_local

> rename #13 J180_Cdiff_3.31A_local

> show #12 models

> select add #12

2144 atoms, 2146 bonds, 290 residues, 1 model selected  

> view matrix models #12,1,0,0,19.646,0,1,0,1.6852,0,0,1,82.751

> view matrix models
> #12,-0.85093,-0.292,-0.43663,15.341,-0.30762,0.95082,-0.036372,0.4028,0.42578,0.10336,-0.89891,115.06

> view matrix models
> #12,-0.095809,-0.15977,-0.98249,28.439,-0.19522,0.97088,-0.13884,2.6847,0.97607,0.1785,-0.12421,106.24

> view matrix models
> #12,-0.63349,-0.25143,-0.73176,21.274,-0.27775,0.95659,-0.08823,1.395,0.72218,0.14735,-0.67583,113.35

> view matrix models
> #12,-0.83507,-0.28886,-0.46821,15.931,-0.30562,0.95124,-0.041783,0.4996,0.45745,0.1082,-0.88263,115

> view matrix models
> #12,-0.83507,-0.28886,-0.46821,123.74,-0.30562,0.95124,-0.041783,17.534,0.45745,0.1082,-0.88263,139

> view matrix models
> #12,-0.83507,-0.28886,-0.46821,93.264,-0.30562,0.95124,-0.041783,164.37,0.45745,0.1082,-0.88263,167.55

> view matrix models
> #12,0.28845,0.9438,0.16137,93.018,0.82574,-0.33052,0.45706,159.46,0.48471,0.0014107,-0.87467,167.29

> view matrix models
> #12,0.13244,0.91588,0.37897,88.674,0.73128,-0.34838,0.5864,156.86,0.6691,0.19947,-0.71591,166.37

> view matrix models
> #12,0.13244,0.91588,0.37897,146.99,0.73128,-0.34838,0.5864,191.78,0.6691,0.19947,-0.71591,166.19

> view matrix models
> #12,0.13244,0.91588,0.37897,148.29,0.73128,-0.34838,0.5864,198.95,0.6691,0.19947,-0.71591,162.64

> fitmap #12 inMap #13

Fit molecule AF-Q18CX7-Cdiff.pdb (#12) to map J180_Cdiff_3.31A_local (#13)
using 2144 atoms  
average map value = 0.1016, steps = 204  
shifted from previous position = 3.7  
rotated from previous position = 17.8 degrees  
atoms outside contour = 1644, contour level = 0.18463  
  
Position of AF-Q18CX7-Cdiff.pdb (#12) relative to J180_Cdiff_3.31A_local (#13)
coordinates:  
Matrix rotation and translation  
-0.08938972 0.97961293 0.17991079 145.17204702  
0.77508254 -0.04502294 0.63025386 199.69077077  
0.62550497 0.19578394 -0.75525632 160.98790222  
Axis -0.66321550 -0.68019661 -0.31221431  
Axis point -33.78289359 0.00000000 29.45207105  
Rotation angle (degrees) 160.87997854  
Shift along axis -282.37206348  
  

> select subtract #12

Nothing selected  

> hide #12 models

> show #12 models

> select add #12

2144 atoms, 2146 bonds, 290 residues, 1 model selected  

> view matrix models
> #12,-0.54774,0.82626,-0.13146,147.06,0.63378,0.51234,0.57951,201.19,0.54618,0.2341,-0.80429,161.41

> view matrix models
> #12,-0.54774,0.82626,-0.13146,146.83,0.63378,0.51234,0.57951,199.93,0.54618,0.2341,-0.80429,161.91

> view matrix models
> #12,-0.77026,0.52363,-0.36401,148.41,0.34188,0.8209,0.45744,201.03,0.53834,0.2279,-0.81132,161.96

> view matrix models
> #12,-0.77026,0.52363,-0.36401,147.74,0.34188,0.8209,0.45744,197.57,0.53834,0.2279,-0.81132,162.29

> fitmap #12 inMap #13

Fit molecule AF-Q18CX7-Cdiff.pdb (#12) to map J180_Cdiff_3.31A_local (#13)
using 2144 atoms  
average map value = 0.09081, steps = 148  
shifted from previous position = 4.15  
rotated from previous position = 4.76 degrees  
atoms outside contour = 1714, contour level = 0.18463  
  
Position of AF-Q18CX7-Cdiff.pdb (#12) relative to J180_Cdiff_3.31A_local (#13)
coordinates:  
Matrix rotation and translation  
-0.74662970 0.58595118 -0.31496861 143.99416555  
0.40712850 0.77692111 0.48024982 197.03266175  
0.52610873 0.23033609 -0.81862984 160.39086419  
Axis -0.27909031 -0.93927028 -0.19969962  
Axis point 29.00777577 0.00000000 68.33305390  
Rotation angle (degrees) 153.40191866  
Shift along axis -257.28429433  
  

> view matrix models
> #12,-0.74663,0.58595,-0.31497,145.25,0.40713,0.77692,0.48025,203.36,0.52611,0.23034,-0.81863,161.26

> view matrix models
> #12,-0.82004,0.28805,-0.49453,146.84,0.12073,0.93172,0.34252,204.33,0.55943,0.22118,-0.79883,161.11

> view matrix models
> #12,-0.82004,0.28805,-0.49453,146.32,0.12073,0.93172,0.34252,201.59,0.55943,0.22118,-0.79883,161.52

> fitmap #12 inMap #13

Fit molecule AF-Q18CX7-Cdiff.pdb (#12) to map J180_Cdiff_3.31A_local (#13)
using 2144 atoms  
average map value = 0.09234, steps = 232  
shifted from previous position = 1.3  
rotated from previous position = 9.75 degrees  
atoms outside contour = 1704, contour level = 0.18463  
  
Position of AF-Q18CX7-Cdiff.pdb (#12) relative to J180_Cdiff_3.31A_local (#13)
coordinates:  
Matrix rotation and translation  
-0.80792053 0.41913708 -0.41423237 145.92614085  
0.28231553 0.89231139 0.35224743 201.04548865  
0.51726424 0.16764371 -0.83924563 162.27890103  
Axis -0.19241202 -0.97089667 -0.14260878  
Axis point 36.31182819 0.00000000 79.33731259  
Rotation angle (degrees) 151.33357220  
Shift along axis -246.41473490  
  

> select subtract #12

Nothing selected  

> rename #2#13#12 id #2

> rename #2 Cdiff

> hide #!2 models

> show #!11 models

> hide #!11 models

> show #!17 models

> rename #17 J788_proteus

> rename #17 J788_proteus_3.43A

> save /Users/Liulab/Desktop/Filaments.cxs includeMaps true

——— End of log from Mon Jan 20 14:14:45 2025 ———

opened ChimeraX session  

> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/FlaB2_Td_AF-Q9ACM0-F1-model_v4.pdb

FlaB2_Td_AF-Q9ACM0-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for flagellin (Q9ACM0) [more info...]  
  
Chain information for FlaB2_Td_AF-Q9ACM0-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | flagellin | Q9ACM0_TREDN 1-221  
  
Computing secondary structure  

> hide #!17 models

> hide #3 models

> show #3 models

> show #!11 models

> hide #3 models

> show #3 models

> hide #!11 models

> select add #3

1712 atoms, 1725 bonds, 221 residues, 1 model selected  

> show #!11 models

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,47.801,0,1,0,55.473,0,0,1,171.02

> view matrix models #3,1,0,0,50.104,0,1,0,69.693,0,0,1,248.97

> view matrix models #3,1,0,0,82.306,0,1,0,124.22,0,0,1,210.93

> hide #!11 models

> show #!1.3 models

> hide #!1.2 models

> view matrix models #3,1,0,0,117.56,0,1,0,173.84,0,0,1,124.91

> view matrix models #3,1,0,0,97.652,0,1,0,134.88,0,0,1,125.29

> view matrix models #3,1,0,0,120.83,0,1,0,156.12,0,0,1,118.11

> view matrix models #3,1,0,0,129.55,0,1,0,167.03,0,0,1,129.28

> view matrix models #3,1,0,0,98.962,0,1,0,114.86,0,0,1,149.88

> hide #!1.3 models

> select subtract #3

Nothing selected  

> show #3 surfaces

> show #!1.3 models

> select add #3

1712 atoms, 1725 bonds, 221 residues, 1 model selected  

> view matrix models #3,1,0,0,98.34,0,1,0,143.84,0,0,1,119.98

> view matrix models #3,1,0,0,88.383,0,1,0,130.82,0,0,1,129.39

> hide #!3 models

> show #!3 models

> select subtract #3

1 model selected  

> hide #!3 models

> hide #1.3.1 models

> select add #1.3

2 models selected  

> show #1.3.1 models

> undo

[Repeated 3 time(s)]

> select add #1.3

2 models selected  

> select subtract #1.3

Nothing selected  

> color #1.3 #f7cbc3ff models

> color #1.3 #f7c3beff models

> color #1.3 #f7c2caff models

> hide #!1 models

> hide #!1.3 models

> hide #!3 models

> select add #3

1712 atoms, 1725 bonds, 221 residues, 1 model selected  

> close #3

> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb

FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for flagellin (Q9ACM1) [more info...]  
  
Chain information for FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | flagellin | Q9ACM1_TREDN 1-234  
  
Computing secondary structure  

> show #!2 models

> hide #!2 models

> show #3 surfaces

> select add #3

1807 atoms, 1822 bonds, 234 residues, 1 model selected  

> show #!1.3 models

> view matrix models #3,1,0,0,129.12,0,1,0,150.81,0,0,1,150.8

> view matrix models #3,1,0,0,184.6,0,1,0,205.74,0,0,1,152.39

> view matrix models #3,1,0,0,168.73,0,1,0,96.459,0,0,1,135.3

> view matrix models #3,1,0,0,161.46,0,1,0,66.063,0,0,1,150.12

> view matrix models #3,1,0,0,162.1,0,1,0,95.303,0,0,1,153.58

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.49233,0.87032,-0.012593,156.27,0.78833,0.45199,0.41742,88.2,0.36898,0.19558,-0.90863,202.43

> view matrix models
> #3,-0.32717,0.94201,0.074641,154.85,0.87829,0.27399,0.39183,89.161,0.34866,0.19375,-0.91701,202.55

> view matrix models
> #3,-0.037375,0.96575,0.25676,151.6,0.89875,-0.079842,0.43114,88.158,0.43687,0.24688,-0.86498,201.66

> view matrix models
> #3,-0.62147,0.78344,0.00058389,155.35,0.75849,0.6015,0.25076,92.242,0.1961,0.15628,-0.96805,203.14

> view matrix models
> #3,-0.005999,0.85656,0.51601,145.29,0.9579,-0.1432,0.24885,92.899,0.28705,0.49578,-0.81964,199.97

> view matrix models
> #3,0.50342,0.47827,0.7196,142.33,0.73674,-0.67272,-0.06829,99.608,0.45143,0.56453,-0.69103,197.53

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.50342,0.47827,0.7196,124.99,0.73674,-0.67272,-0.06829,132.52,0.45143,0.56453,-0.69103,207.56

> view matrix models
> #3,0.50342,0.47827,0.7196,128.39,0.73674,-0.67272,-0.06829,149.61,0.45143,0.56453,-0.69103,205.62

> view matrix models
> #3,0.50342,0.47827,0.7196,133.76,0.73674,-0.67272,-0.06829,184.71,0.45143,0.56453,-0.69103,215.06

> view matrix models
> #3,0.50342,0.47827,0.7196,126.47,0.73674,-0.67272,-0.06829,181.84,0.45143,0.56453,-0.69103,196.89

> view matrix models
> #3,0.50342,0.47827,0.7196,124.81,0.73674,-0.67272,-0.06829,179.36,0.45143,0.56453,-0.69103,205.7

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.68343,0.58091,0.44212,132.48,0.59691,-0.79333,0.11969,174.07,0.42027,0.18211,-0.88894,210.33

> view matrix models
> #3,0.65821,0.5354,0.52926,130.2,0.61122,-0.79047,0.039499,176.12,0.43951,0.2975,-0.84754,209.42

> view matrix models
> #3,0.71903,-0.29615,0.62872,127.72,0.017274,-0.89676,-0.44217,185.43,0.69476,0.3288,-0.63969,205.4

> hide #!1.3 models

> show #!1.3 models

> color #1.3.1 #ffdce0ff

> color #1.3.1 #edcdd1ff

> color #1.3.1 #ffdce0ff

> color #1.3.1 #edccd0ff

> color #1.3.1 #f1cfd4ff

[Repeated 2 time(s)]

> color #1.3.1 darkgrey

> color #1.3.1 #ebebebff

> color #1.3.1 silver

> color #1.3.1 #c0c0c000

> color #1.3.1 #c0c0c080

> color #1.3.1 #797979ff

> color #1.3.1 #79797948

> color #1.3.1 #79797955

> color #1.3.1 #79797989

> color #1.3.1 #797979ff

> color #1.3.1 #929292ff

> color #1.3.1 #929292ec

> color #1.3.1 #929292ff

[Repeated 1 time(s)]

> color #1.3.1 white

> color #1.3.1 #fffbf4ff

> color #1.3.1 #b7b4afff

> color #1.3.1 #b7b4af85

> color #1.3.1 #5d5c5a85

> color #1.3.1 #5d5c5a51

> color #1.3.1 #1d1d1c51

> color #1.3.1 #1d1d1c52

> view matrix models
> #3,-0.083238,0.98992,0.11457,137.41,0.89023,0.022199,0.45498,167.32,0.44785,0.13986,-0.8831,210.29

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.083238,0.98992,0.11457,153.77,0.89023,0.022199,0.45498,187.93,0.44785,0.13986,-0.8831,206.33

> view matrix models
> #3,-0.083238,0.98992,0.11457,157.53,0.89023,0.022199,0.45498,172.14,0.44785,0.13986,-0.8831,203.39

> toolshed show

> select add #1.3.1

1807 atoms, 1822 bonds, 234 residues, 3 models selected  

> ui tool show "Modeller Comparative"

Populating font family aliases took 118 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

> ui tool show "Similar Structures"

> ui tool show "Modeller Comparative"

> ui tool show Matchmaker

> hide #1.3.1 models

> select subtract #1.3.1

1807 atoms, 1822 bonds, 234 residues, 2 models selected  

> hide #!1.3 models

> hide #!1 models

> hide #!3 models

> select subtract #3

1 model selected  

> show #!2 models

> hide #!2.1 models

> hide #!2.2 models

> hide #2.3 models

> show #2.3 models

> show #!2.2 models

> hide #!2.2 models

> hide #2.3 models

> hide #!2 models

> show #!1.3 models

> show #!3 models

> show #1.3.1 models

> ui tool show Matchmaker

> hide #3.1 models

> hide #!3 models

> hide #!1 models

> hide #!1.3 models

> hide #1.3.1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> hide #!1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.3 models

> show #!1.2 models

> hide #!1.2 models

> show #1.3.1 models

> color #1.3 #fffff952 models

> color #1.3 #ffac9b52 models

> color #1.3 #ffc49952 models

> color #1.3 #ffced452 models

> hide #!1.3 models

> hide #1.3.1 models

> show #!1.3 models

> show #1.3.1 models

> show #!1.4 models

> hide #!1.4 models

> color #1.3 #66595b52 models

> color #1.3 #5c515352 models

> color #1.3 #5c5153ff models

> color #1.3 #f0d4d8ff models

> color #1.3 #f0d5b7ff models

> color #1.3 #f0ac9cff models

> color #1.3 #f0b291ff models

> color #1.3 #f09f98ff models

> hide #!1.3 models

> hide #1.3.1 models

> show #!1.4 models

> hide #!1.4 models

> show #!1.5 models

> hide #!1.5 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.3 models

> show #1.3.1 models

> hide #1.3.1 models

> color #1.3 #eab2acff models

> show #1.3.1 models

> hide #1.3.1 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> hide #!1 models

> show #!1.3 models

> show #1.3.1 models

> show #!3 models

> show #3.1 models

> ui tool show Matchmaker

> ui dockable false Matchmaker

> ui dockable true Matchmaker

> hide #!3 models

> ui tool show "Show Sequence Viewer"

> sequence chain #3/A

Alignment identifier is 3/A  

> select #3/A:2-52,59-82,148-231

1229 atoms, 1233 bonds, 159 residues, 1 model selected  

> select #3/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #3/A

1807 atoms, 1822 bonds, 234 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> hide #!1 models

> hide #!1.3 models

> hide #1.3.1 models

> show #!2 models

> hide #!2 models

> show #!2.1 models

> show #!2.2 models

> show #2.3 models

> view matrix models
> #3,-0.083238,0.98992,0.11457,158.98,0.89023,0.022199,0.45498,168.13,0.44785,0.13986,-0.8831,233.7

> hide #!2.2 models

> show #!2.2 models

> hide #!2.1 models

> hide #2.3 models

> show #2.3 models

> show #!2.1 models

> hide #!2.2 models

> show #!2.2 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> hide #!2 models

> hide #!2.2 models

> hide #2.3 models

> show #!3 models

> select subtract #3

1 model selected  

> hide #!3 surfaces

> ui tool show "Fit in Map"

> show #!1.3 models

> show #1.3.1 models

> select add #3.1

1807 atoms, 234 residues, 1 model selected  

> view matrix models
> #3,-0.083238,0.98992,0.11457,149.99,0.89023,0.022199,0.45498,239.12,0.44785,0.13986,-0.8831,226.58

> view matrix models
> #3,-0.083238,0.98992,0.11457,156.52,0.89023,0.022199,0.45498,232.38,0.44785,0.13986,-0.8831,152.98

> view matrix models
> #3,-0.083238,0.98992,0.11457,183.74,0.89023,0.022199,0.45498,240.63,0.44785,0.13986,-0.8831,150.81

> select subtract #3.1

1 model selected  

> fitmap #3 inMap #1.3

Fit molecule FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb (#3) to map
J371_Td_FlaB2_3.23A_nosheath (#1.3) using 1807 atoms  
average map value = 0.08751, steps = 168  
shifted from previous position = 1.13  
rotated from previous position = 18 degrees  
atoms outside contour = 1339, contour level = 0.15109  
  
Position of FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb (#3) relative to
J371_Td_FlaB2_3.23A_nosheath (#1.3) coordinates:  
Matrix rotation and translation  
-0.43675572 0.89325393 -0.10649808 179.17221969  
0.75053584 0.42709506 0.50426753 238.33528124  
0.49592376 0.14031111 -0.85695531 149.05057417  
Axis -0.50679458 -0.83884801 -0.19872916  
Axis point 8.13738861 0.00000000 48.15568644  
Rotation angle (degrees) 158.95648544  
Shift along axis -320.35128020  
  

> select add #3.1

1807 atoms, 234 residues, 1 model selected  

> view matrix models
> #3,-0.35,0.93631,-0.02885,190.09,0.79505,0.3132,0.51943,238.22,0.49538,0.15886,-0.85403,150.37

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.41808,0.90517,-0.0767,190.99,0.75019,0.39164,0.53276,237.74,0.51228,0.16519,-0.84278,150.16

> view matrix models
> #3,0.23115,0.91804,0.32214,183.62,0.84034,-0.35526,0.40942,240.76,0.49031,0.17607,-0.85358,150.34

> view matrix models
> #3,0.23933,0.92761,0.28681,184.56,0.79521,-0.35676,0.49027,238.49,0.55711,0.11074,-0.82303,149.81

> view matrix models
> #3,-0.013178,0.97973,0.19987,185.73,0.9287,-0.062089,0.36559,242.48,0.37059,0.19043,-0.90906,151.25

> view matrix models
> #3,0.086607,0.96593,0.24387,185.02,0.92994,-0.16619,0.32802,243.38,0.35737,0.19837,-0.91265,151.29

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.086607,0.96593,0.24387,180.76,0.92994,-0.16619,0.32802,234.17,0.35737,0.19837,-0.91265,150.99

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.0075052,0.9622,0.27226,179.69,0.94083,-0.099038,0.32408,234.37,0.33879,0.25372,-0.90601,150.78

> view matrix models
> #3,-0.014203,0.96362,0.26691,179.73,0.9391,-0.07881,0.33449,234.11,0.34336,0.25541,-0.90381,150.75

> view matrix models
> #3,0.021323,0.99111,0.13133,183.38,0.94234,-0.063803,0.32851,234.29,0.33397,0.11675,-0.93533,151.41

> view matrix models
> #3,0.028606,0.98456,0.17269,182.35,0.92387,-0.092001,0.37149,233.09,0.38164,0.14892,-0.91224,151.05

> select subtract #3.1

1 model selected  

> fitmap #3 inMap #1.3

Fit molecule FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb (#3) to map
J371_Td_FlaB2_3.23A_nosheath (#1.3) using 1807 atoms  
average map value = 0.0822, steps = 88  
shifted from previous position = 7.26  
rotated from previous position = 7.2 degrees  
atoms outside contour = 1364, contour level = 0.15109  
  
Position of FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb (#3) relative to
J371_Td_FlaB2_3.23A_nosheath (#1.3) coordinates:  
Matrix rotation and translation  
-0.02609078 0.99930177 0.02674395 176.67842991  
0.89282995 0.01126095 0.45025311 238.19850993  
0.44963757 0.03562525 -0.89250036 147.99624579  
Axis -0.68904772 -0.70278414 -0.17693979  
Axis point -38.53440474 0.00000000 39.56437028  
Rotation angle (degrees) 162.49012248  
Shift along axis -315.32842903  
  

> ui mousemode right "translate selected models"

> select add #3.1

1807 atoms, 234 residues, 1 model selected  

> view matrix models
> #3,0.075762,0.99236,0.097362,159.65,0.88615,-0.11178,0.44971,234.69,0.45715,0.052207,-0.88785,138.31

> view matrix models
> #3,0.075762,0.99236,0.097362,179.7,0.88615,-0.11178,0.44971,241.95,0.45715,0.052207,-0.88785,149.29

> view matrix models
> #3,0.075762,0.99236,0.097362,176.78,0.88615,-0.11178,0.44971,237.39,0.45715,0.052207,-0.88785,150.69

> view matrix models
> #3,0.075762,0.99236,0.097362,182.93,0.88615,-0.11178,0.44971,237.29,0.45715,0.052207,-0.88785,148.87

> select subtract #3.1

1 model selected  

> fitmap #3 inMap #1.3

Fit molecule FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb (#3) to map
J371_Td_FlaB2_3.23A_nosheath (#1.3) using 1807 atoms  
average map value = 0.0822, steps = 56  
shifted from previous position = 2.72  
rotated from previous position = 0.0487 degrees  
atoms outside contour = 1363, contour level = 0.15109  
  
Position of FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb (#3) relative to
J371_Td_FlaB2_3.23A_nosheath (#1.3) coordinates:  
Matrix rotation and translation  
-0.02686108 0.99929087 0.02638623 176.67892202  
0.89281222 0.01210966 0.45026623 238.19577129  
0.44962741 0.03565259 -0.89250439 147.99313963  
Axis -0.68875429 -0.70308630 -0.17688184  
Axis point -38.43421360 0.00000000 39.59543055  
Rotation angle (degrees) 162.48304136  
Shift along axis -315.33784728  
  

> select add #3.1

1807 atoms, 234 residues, 1 model selected  

> view matrix models
> #3,0.074996,0.99245,0.097009,176.82,0.88623,-0.11093,0.44976,235.35,0.45713,0.052242,-0.88786,139.77

> view matrix models
> #3,0.074996,0.99245,0.097009,173.6,0.88623,-0.11093,0.44976,224.88,0.45713,0.052242,-0.88786,118.83

> view matrix models
> #3,0.074996,0.99245,0.097009,128.01,0.88623,-0.11093,0.44976,217.06,0.45713,0.052242,-0.88786,136.87

> view matrix models
> #3,0.074996,0.99245,0.097009,123.73,0.88623,-0.11093,0.44976,204.28,0.45713,0.052242,-0.88786,136.72

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.55977,0.36672,-0.74308,142.04,0.29142,0.92658,0.23775,207.86,0.77571,-0.083461,-0.62554,131.29

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.55977,0.36672,-0.74308,140.99,0.29142,0.92658,0.23775,208.26,0.77571,-0.083461,-0.62554,120.15

> view matrix models
> #3,-0.55977,0.36672,-0.74308,106.72,0.29142,0.92658,0.23775,194.46,0.77571,-0.083461,-0.62554,132.82

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.54085,0.24709,-0.80401,108.28,0.22441,0.96362,0.14518,196.56,0.81063,-0.10191,-0.57662,131.7

> view matrix models
> #3,-0.62803,0.27319,-0.72866,105.98,-0.10041,0.90008,0.42399,187.95,0.77169,0.33944,-0.53785,130.86

> view matrix models
> #3,-0.52028,-0.33581,-0.7852,107.47,-0.58237,0.81201,0.038606,195.66,0.62463,0.47736,-0.61803,132.37

> view matrix models
> #3,-0.35279,-0.60171,-0.71657,106.25,-0.76718,0.62445,-0.14665,199.47,0.5357,0.498,-0.68192,133.63

> view matrix models
> #3,-0.59063,-0.53549,-0.60367,102.36,-0.65309,0.75659,-0.032161,197.13,0.47395,0.37526,-0.79659,136.21

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.59063,-0.53549,-0.60367,108.05,-0.65309,0.75659,-0.032161,221.05,0.47395,0.37526,-0.79659,163.02

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.76081,-0.64578,0.064257,96.755,-0.56182,-0.70496,-0.43289,230.67,0.32485,0.29325,-0.89915,164.94

> view matrix models
> #3,-0.77983,-0.14635,-0.60864,107.63,-0.38441,0.87933,0.28109,214.28,0.49406,0.45317,-0.74199,161.76

> view matrix models
> #3,-0.63901,-0.60222,-0.47853,104.58,-0.70972,0.70149,0.064918,218.27,0.29659,0.38111,-0.87567,164.28

> view matrix models
> #3,0.62648,0.65694,0.41947,87.996,0.6429,-0.7398,0.19845,219.72,0.44069,0.14536,-0.88581,165

> view matrix models
> #3,-0.23866,0.95667,0.16682,90.908,0.85233,0.12404,0.50809,213.32,0.46538,0.26344,-0.845,164.14

> view matrix models
> #3,-0.5282,0.41505,-0.74077,112.52,0.40239,0.89057,0.21206,219.49,0.74772,-0.18607,-0.63741,159.73

> view matrix models
> #3,-0.92714,-0.082332,-0.36555,100.8,-0.046435,0.99329,-0.10594,225.76,0.37182,-0.08125,-0.92474,165.53

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.92714,-0.082332,-0.36555,103.24,-0.046435,0.99329,-0.10594,199.44,0.37182,-0.08125,-0.92474,150.99

> view matrix models
> #3,-0.92714,-0.082332,-0.36555,122.19,-0.046435,0.99329,-0.10594,178.69,0.37182,-0.08125,-0.92474,161.51

> view matrix models
> #3,-0.92714,-0.082332,-0.36555,138.95,-0.046435,0.99329,-0.10594,208.89,0.37182,-0.08125,-0.92474,202.21

> view matrix models
> #3,-0.92714,-0.082332,-0.36555,139.4,-0.046435,0.99329,-0.10594,209.78,0.37182,-0.08125,-0.92474,206.07

> view matrix models
> #3,-0.92714,-0.082332,-0.36555,145.12,-0.046435,0.99329,-0.10594,201.45,0.37182,-0.08125,-0.92474,209.13

> view matrix models
> #3,-0.92714,-0.082332,-0.36555,145.88,-0.046435,0.99329,-0.10594,205.92,0.37182,-0.08125,-0.92474,209

> select subtract #3.1

1 model selected  

> fitmap #3 inMap #1.3

Fit molecule FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb (#3) to map
J371_Td_FlaB2_3.23A_nosheath (#1.3) using 1807 atoms  
average map value = 0.08697, steps = 264  
shifted from previous position = 3.5  
rotated from previous position = 22.9 degrees  
atoms outside contour = 1296, contour level = 0.15109  
  
Position of FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb (#3) relative to
J371_Td_FlaB2_3.23A_nosheath (#1.3) coordinates:  
Matrix rotation and translation  
-0.74400453 -0.56566513 -0.35564055 147.83415303  
-0.46739691 0.82095771 -0.32797646 203.44948143  
0.47749070 -0.07779068 -0.87518640 206.33982851  
Axis 0.28578997 -0.95169501 0.11225287  
Axis point 77.73630042 0.00000000 137.50640451  
Rotation angle (degrees) 154.04219227  
Shift along axis -128.21009881  
  

> view #3.1 clip false

No displayed objects specified.  

> save
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/250123_Filaments_predicted_model_fit.cxs

——— End of log from Thu Jan 23 21:26:34 2025 ———

opened ChimeraX session  

> select add #3

1807 atoms, 1822 bonds, 234 residues, 1 model selected  

> select subtract #3

1 model selected  

> view #3#1.3 clip false

> select add #3.1

1807 atoms, 234 residues, 1 model selected  

> select add #3

1807 atoms, 1822 bonds, 234 residues, 2 models selected  

> select add #1.3

1807 atoms, 1822 bonds, 234 residues, 4 models selected  

> select add #1

1807 atoms, 1822 bonds, 234 residues, 13 models selected  

> help help:user/tools/modelpanel.html

> log metadata #2

No models had metadata

> log chains #2

Chain information for AF-Q18CX7-Cdiff.pdb #2.3  
---  
Chain | Description | UniProt  
A | flagellin | Q18CX7_CLOD6 1-290  
  

> log metadata #3

No models had metadata

> log chains #3

Chain information for FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | flagellin | Q9ACM1_TREDN 1-234  
  

> group #1,3

Unknown command: group #1,3  

> group

Unknown command: group  

> move

Missing or invalid "axis" argument: Expected an axis vector  

> move #3

Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 1807
atoms  

> move #3 to #1

Missing or invalid "axis" argument: Axis argument requires 2 atoms, got 1807
atoms  

> select

3951 atoms, 3968 bonds, 524 residues, 22 models selected  

> select subtract #1

3951 atoms, 3968 bonds, 524 residues, 12 models selected  

> select subtract #2

1807 atoms, 1822 bonds, 234 residues, 6 models selected  

> select subtract #3

5 models selected  

> select subtract #11

2 models selected  

> select subtract #17

Nothing selected  

> save
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/250123_Filaments_predicted_model_fit.cxs

——— End of log from Thu Jan 23 21:39:56 2025 ———

opened ChimeraX session  

> rename #3 id #1.6

> volume zone #1.3 nearAtoms #1.6:1-234 range 7 invert false newMap true
> minimalBounds true bondPointSpacing 2

Opened J371_Td_FlaB2_3.23A_nosheath zone as #3, grid size 50,48,138, pixel
1.07, shown at step 1, values float32  

> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Real_space_refine_Td_FlaB2/job016.cif

Summary of feedback from opening
/Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Real_space_refine_Td_FlaB2/job016.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for job016.cif #4  
---  
Chain | Description  
A0 | No description available  
A1 | No description available  
A2 | No description available  
A3 | No description available  
A4 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
Aa Ab | No description available  
Aa0 Aa6 Aaw | No description available  
Aa1 | No description available  
Aa2 | No description available  
Aa3 | No description available  
Aa4 | No description available  
Aa5 | No description available  
Aa7 | No description available  
Aa8 | No description available  
Aa9 | No description available  
Aaa Aae Aan Aax | No description available  
Aab | No description available  
Aac | No description available  
Aad | No description available  
Aaf | No description available  
Aag | No description available  
Aah | No description available  
Aai Abn | No description available  
Aaj | No description available  
Aak Aal Aar Aas | No description available  
Aam | No description available  
Aao | No description available  
Aap | No description available  
Aaq | No description available  
Aat | No description available  
Aau | No description available  
Aav | No description available  
Aay | No description available  
Aaz | No description available  
Ab0 | No description available  
Ab1 | No description available  
Ab2 | No description available  
Ab3 | No description available  
Ab4 | No description available  
Ab5 | No description available  
Ab6 | No description available  
Ab7 | No description available  
Ab8 | No description available  
Ab9 | No description available  
Aba | No description available  
Abb | No description available  
Abc | No description available  
Abd | No description available  
Abe | No description available  
Abf | No description available  
Abg | No description available  
Abh | No description available  
Abi | No description available  
Abj | No description available  
Abk | No description available  
Abl | No description available  
Abm | No description available  
Abo | No description available  
Abp | No description available  
Abq | No description available  
Abr | No description available  
Abs | No description available  
Abt | No description available  
Abu | No description available  
Abv | No description available  
Abw | No description available  
Abx | No description available  
Aby | No description available  
Abz | No description available  
Ac | No description available  
Ac0 Adi Adk | No description available  
Ac1 Aco Acx Acy | No description available  
Ac2 Ac4 Acp | No description available  
Ac3 Ac7 | No description available  
Ac5 Ac6 Ac9 Acw Ada Adc | No description available  
Ac8 | No description available  
Aca | No description available  
Acb Adf Adg | No description available  
Acc | No description available  
Acd | No description available  
Ace | No description available  
Acf | No description available  
Acg | No description available  
Ach | No description available  
Aci | No description available  
Acj | No description available  
Ack | No description available  
Acl | No description available  
Acm | No description available  
Acn | No description available  
Acq | No description available  
Acr | No description available  
Acs | No description available  
Act | No description available  
Acu | No description available  
Acv | No description available  
Acz | No description available  
Ad | No description available  
Adb | No description available  
Add | No description available  
Ade | No description available  
Adh | No description available  
Adj | No description available  
Adl | No description available  
Adm | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ak | No description available  
Al | No description available  
Am | No description available  
An | No description available  
Ao | No description available  
Ap | No description available  
Aq | No description available  
Ar | No description available  
As | No description available  
At | No description available  
Au | No description available  
Av | No description available  
Aw | No description available  
Ax | No description available  
Ay | No description available  
Az | No description available  
  

> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Real_space_refine_Td_FlaB2/job016.cif

Summary of feedback from opening
/Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Real_space_refine_Td_FlaB2/job016.cif  
---  
warnings | Missing entity information. Treating each chain as a separate entity.  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for job016.cif #5  
---  
Chain | Description  
A0 | No description available  
A1 | No description available  
A2 | No description available  
A3 | No description available  
A4 | No description available  
A5 | No description available  
A6 | No description available  
A7 | No description available  
A8 | No description available  
A9 | No description available  
Aa Ab | No description available  
Aa0 Aa6 Aaw | No description available  
Aa1 | No description available  
Aa2 | No description available  
Aa3 | No description available  
Aa4 | No description available  
Aa5 | No description available  
Aa7 | No description available  
Aa8 | No description available  
Aa9 | No description available  
Aaa Aae Aan Aax | No description available  
Aab | No description available  
Aac | No description available  
Aad | No description available  
Aaf | No description available  
Aag | No description available  
Aah | No description available  
Aai Abn | No description available  
Aaj | No description available  
Aak Aal Aar Aas | No description available  
Aam | No description available  
Aao | No description available  
Aap | No description available  
Aaq | No description available  
Aat | No description available  
Aau | No description available  
Aav | No description available  
Aay | No description available  
Aaz | No description available  
Ab0 | No description available  
Ab1 | No description available  
Ab2 | No description available  
Ab3 | No description available  
Ab4 | No description available  
Ab5 | No description available  
Ab6 | No description available  
Ab7 | No description available  
Ab8 | No description available  
Ab9 | No description available  
Aba | No description available  
Abb | No description available  
Abc | No description available  
Abd | No description available  
Abe | No description available  
Abf | No description available  
Abg | No description available  
Abh | No description available  
Abi | No description available  
Abj | No description available  
Abk | No description available  
Abl | No description available  
Abm | No description available  
Abo | No description available  
Abp | No description available  
Abq | No description available  
Abr | No description available  
Abs | No description available  
Abt | No description available  
Abu | No description available  
Abv | No description available  
Abw | No description available  
Abx | No description available  
Aby | No description available  
Abz | No description available  
Ac | No description available  
Ac0 Adi Adk | No description available  
Ac1 Aco Acx Acy | No description available  
Ac2 Ac4 Acp | No description available  
Ac3 Ac7 | No description available  
Ac5 Ac6 Ac9 Acw Ada Adc | No description available  
Ac8 | No description available  
Aca | No description available  
Acb Adf Adg | No description available  
Acc | No description available  
Acd | No description available  
Ace | No description available  
Acf | No description available  
Acg | No description available  
Ach | No description available  
Aci | No description available  
Acj | No description available  
Ack | No description available  
Acl | No description available  
Acm | No description available  
Acn | No description available  
Acq | No description available  
Acr | No description available  
Acs | No description available  
Act | No description available  
Acu | No description available  
Acv | No description available  
Acz | No description available  
Ad | No description available  
Adb | No description available  
Add | No description available  
Ade | No description available  
Adh | No description available  
Adj | No description available  
Adl | No description available  
Adm | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
Ah | No description available  
Ai | No description available  
Aj | No description available  
Ak | No description available  
Al | No description available  
Am | No description available  
An | No description available  
Ao | No description available  
Ap | No description available  
Aq | No description available  
Ar | No description available  
As | No description available  
At | No description available  
Au | No description available  
Av | No description available  
Aw | No description available  
Ax | No description available  
Ay | No description available  
Az | No description available  
  

> close #5

> show #!4#!1.6 surfaces

[Repeated 1 time(s)]

> ui mousemode right select

> select #4/Ay:140@CG

1 atom, 1 residue, 1 model selected  

> select #4/Ay:131@CB

1 atom, 1 residue, 1 model selected  

> select clear

> hide #!4#!1.6 surfaces

> show #!4#!1.6 cartoons

Computing secondary structure  

> style #!4#!1.6 sphere

Changed 71659 atom styles  

> style #!4#!1.6 sphere

Changed 71659 atom styles  

> hide #!4#!1.6 cartoons

> hide #!4 models

> hide #!3 models

> hide #!1 models

> show #!4 models

> hide #4.1 models

> show #4.1 models

> style #!4 sphere

Changed 69852 atom styles  

> surface hidePatches #4

> cartoon #4

> preset "initial styles" cartoon

Using preset: Initial Styles / Cartoon  
Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> select clear

> color #!4 byhetero

[Repeated 1 time(s)]

> color #!4 bychain

> show #4.2 models

> hide #4.2 models

> hide #4.1 models

> show #4.1 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #4.1 models

> show #4.1 models

> hide #4.1 models

> show #4.1 models

> show #4.2 models

> show #4.3 models

> hide #4.2 models

> hide #4.3 models

> select add #4.1

53 pseudobonds, 1 model selected  

> select subtract #4.1

Nothing selected  

> select add #4.1

53 pseudobonds, 1 model selected  

> select clear

[Repeated 1 time(s)]

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.6 models

> hide #3.1 models

> show #3.1 models

> hide #3.1 models

> hide #!3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!1.6 models

> show #!1.6 models

> hide #4.1 models

> show #4.1 models

> show #4.2 models

> hide #!4 models

> hide #4.1 models

> hide #4.2 models

> show #4.2 models

Drag select of 24 residues  

> select #1.6/A:22

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right rotate

> ui mousemode right select

> select add #1.6

1807 atoms, 1822 bonds, 234 residues, 2 models selected  

> select subtract #1.6

1 model selected  

> ui mousemode right zoom

> ui mousemode right translate

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.3 models

> hide #4.2 models

> hide #!1.3 models

> show #!1.3 models

> ui tool show "Fit in Map"

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04918, steps = 308  
shifted from previous position = 3.21  
rotated from previous position = 5.9 degrees  
atoms outside contour = 68681, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99970553 -0.02325504 -0.00693159 6.44174231  
0.02324917 0.99972927 -0.00092658 -4.34213486  
0.00695126 0.00076516 0.99997555 -6.54887196  
Axis 0.03483690 -0.28588065 0.95763179  
Axis point 249.13017787 281.04860798 0.00000000  
Rotation angle (degrees) 1.39132636  
Shift along axis -4.80566533  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04913, steps = 72  
shifted from previous position = 0.133  
rotated from previous position = 0.179 degrees  
atoms outside contour = 68685, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99977207 -0.02013608 -0.00709538 5.83438418  
0.02013000 0.99979694 -0.00092612 -3.88523304  
0.00711259 0.00078308 0.99997440 -6.57737887  
Axis 0.03999686 -0.33247902 0.94226215  
Axis point 273.16603121 295.93685186 0.00000000  
Rotation angle (degrees) 1.22431538  
Shift along axis -4.67249960  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04916, steps = 48  
shifted from previous position = 0.0423  
rotated from previous position = 0.0502 degrees  
atoms outside contour = 68684, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99975384 -0.02101083 -0.00712723 6.01935126  
0.02100461 0.99977893 -0.00094598 -4.00670521  
0.00714553 0.00079604 0.99997415 -6.57267254  
Axis 0.03922805 -0.32140305 0.94612961  
Axis point 265.66460800 292.14085399 0.00000000  
Rotation angle (degrees) 1.27229126  
Shift along axis -4.69470538  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04917, steps = 48  
shifted from previous position = 0.0293  
rotated from previous position = 0.039 degrees  
atoms outside contour = 68681, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976858 -0.02034852 -0.00698064 5.85884796  
0.02034205 0.99979258 -0.00099665 -3.90002905  
0.00699948 0.00085442 0.99997514 -6.56344611  
Axis 0.04298305 -0.32462853 0.94486442  
Axis point 269.47242514 294.75389104 0.00000000  
Rotation angle (degrees) 1.23381605  
Shift along axis -4.68367489  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04914, steps = 40  
shifted from previous position = 0.00466  
rotated from previous position = 0.0119 degrees  
atoms outside contour = 68685, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976619 -0.02040315 -0.00716071 5.90072586  
0.02039717 0.99979154 -0.00090816 -3.92715380  
0.00717775 0.00076189 0.99997395 -6.57969111  
Axis 0.03858811 -0.33130514 0.94273425  
Axis point 271.46876586 294.93573480 0.00000000  
Rotation angle (degrees) 1.23994045  
Shift along axis -4.67411600  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04913, steps = 48  
shifted from previous position = 0.0155  
rotated from previous position = 0.0184 degrees  
atoms outside contour = 68684, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976036 -0.02071301 -0.00708448 5.93998121  
0.02070682 0.99978514 -0.00094618 -3.96547422  
0.00710256 0.00079926 0.99997446 -6.57844064  
Axis 0.03983498 -0.32378000 0.94529344  
Axis point 268.00259449 292.70979585 0.00000000  
Rotation angle (degrees) 1.25536243  
Shift along axis -4.69799649  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04913, steps = 48  
shifted from previous position = 0.0155  
rotated from previous position = 0.0184 degrees  
atoms outside contour = 68684, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976036 -0.02071301 -0.00708448 5.93998121  
0.02070682 0.99978514 -0.00094618 -3.96547422  
0.00710256 0.00079926 0.99997446 -6.57844064  
Axis 0.03983498 -0.32378000 0.94529344  
Axis point 268.00259449 292.70979585 0.00000000  
Rotation angle (degrees) 1.25536243  
Shift along axis -4.69799649  
  

> ui mousemode right zoom

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> ui mousemode right "rotate selected models"

> ui mousemode right zoom

> ui mousemode right translate

> hide #!4 atoms

> hide #!4 models

> hide #!1.3 models

> show #!3 models

> show #3.1 models

> volume zone #1.3 nearAtoms #1.6:1-234 range 2 invert false newMap true
> minimalBounds true bondPointSpacing 2

Opened J371_Td_FlaB2_3.23A_nosheath zone as #5, grid size 42,38,129, pixel
1.07, shown at step 1, values float32  

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!5 models

> show #!5 models

> save
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Real_space_refine_Td_FlaB2/FlaB2_Td_3.23A_nosheath_fromJ371_mono-
> zone_2.mrc models #5

> open
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Real_space_refine_Td_FlaB2/FlaB2_Td_234aa_AF-Q9ACM1-F1_seq.fasta

Summary of feedback from opening
/Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/Real_space_refine_Td_FlaB2/FlaB2_Td_234aa_AF-Q9ACM1-F1_seq.fasta  
---  
notes | Alignment identifier is FlaB2_Td_234aa_AF-Q9ACM1-F1_seq.fasta  
Associated FlaB2_Td_234aa_AF-Q9ACM1-F1-model_v4.pdb (1.6) chain A to
tr|Q9ACM1|Q9ACM1_TREDN Flagellin (Fragment) OS=Treponema denticola OX=158
GN=flaB2 PE=3 SV=1 with 0 mismatches  
Associated job016.cif chain Aah to tr|Q9ACM1|Q9ACM1_TREDN Flagellin (Fragment)
OS=Treponema denticola OX=158 GN=flaB2 PE=3 SV=1 with 0 mismatches  
Associated job016.cif chain Abt to tr|Q9ACM1|Q9ACM1_TREDN Flagellin (Fragment)
OS=Treponema denticola OX=158 GN=flaB2 PE=3 SV=1 with 0 mismatches  
Associated job016.cif chain Abs to tr|Q9ACM1|Q9ACM1_TREDN Flagellin (Fragment)
OS=Treponema denticola OX=158 GN=flaB2 PE=3 SV=1 with 3 mismatches  
Associated job016.cif chain Abg to tr|Q9ACM1|Q9ACM1_TREDN Flagellin (Fragment)
OS=Treponema denticola OX=158 GN=flaB2 PE=3 SV=1 with 4 mismatches  
Associated job016.cif chain Abr to tr|Q9ACM1|Q9ACM1_TREDN Flagellin (Fragment)
OS=Treponema denticola OX=158 GN=flaB2 PE=3 SV=1 with 4 mismatches  
Associated job016.cif chain Aa8 to tr|Q9ACM1|Q9ACM1_TREDN Flagellin (Fragment)
OS=Treponema denticola OX=158 GN=flaB2 PE=3 SV=1 with 0 mismatches  
Associated job016.cif chain Aba to tr|Q9ACM1|Q9ACM1_TREDN Flagellin (Fragment)
OS=Treponema denticola OX=158 GN=flaB2 PE=3 SV=1 with 2 mismatches  
46 messages similar to the above omitted  
  
Opened 1 sequence from FlaB2_Td_234aa_AF-Q9ACM1-F1_seq.fasta  

> hide #3.1 models

> show #!3 models

> hide #!3 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> hide #5.1 models

> show #!4 models

> show #4.1 models

> hide #4.1 models

> show #4.1 models

> hide #4.1 models

> show #!4 surfaces

[Repeated 1 time(s)]

> show #!1.3 models

> hide #!1.3 models

> show #!1.3 models

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04915, steps = 64  
shifted from previous position = 0.0242  
rotated from previous position = 0.021 degrees  
atoms outside contour = 68684, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976820 -0.02038673 -0.00692269 5.86072543  
0.02038043 0.99979182 -0.00097899 -3.91275042  
0.00694120 0.00083768 0.99997556 -6.56240144  
Axis 0.04215171 -0.32168014 0.94590968  
Axis point 269.20148946 294.13799051 0.00000000  
Rotation angle (degrees) 1.23477283  
Shift along axis -4.70174531  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04914, steps = 44  
shifted from previous position = 0.00669  
rotated from previous position = 0.0108 degrees  
atoms outside contour = 68683, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976460 -0.02051777 -0.00705425 5.90777863  
0.02051157 0.99978916 -0.00095091 -3.93852856  
0.00707228 0.00080599 0.99997467 -6.58051779  
Axis 0.04045477 -0.32528103 0.94475164  
Axis point 269.52234615 294.10321278 0.00000000  
Rotation angle (degrees) 1.24423847  
Shift along axis -4.69682859  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04914, steps = 96  
shifted from previous position = 0.0204  
rotated from previous position = 0.0117 degrees  
atoms outside contour = 68685, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976629 -0.02038343 -0.00720225 5.90195095  
0.02037739 0.99979194 -0.00091073 -3.92198168  
0.00721932 0.00076376 0.99997365 -6.58197938  
Axis 0.03869929 -0.33329823 0.94202689  
Axis point 271.78110183 295.28681643 0.00000000  
Rotation angle (degrees) 1.23967037  
Shift along axis -4.66481069  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04914, steps = 44  
shifted from previous position = 0.0231  
rotated from previous position = 0.0173 degrees  
atoms outside contour = 68684, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99977205 -0.02017247 -0.00699486 5.82566920  
0.02016615 0.99979617 -0.00097254 -3.88245678  
0.00701306 0.00083125 0.99997506 -6.57386512  
Axis 0.04220411 -0.32774980 0.94382142  
Axis point 271.67305784 295.52743070 0.00000000  
Rotation angle (degrees) 1.22449463  
Shift along axis -4.68621312  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04915, steps = 60  
shifted from previous position = 0.0189  
rotated from previous position = 0.0145 degrees  
atoms outside contour = 68682, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976694 -0.02042307 -0.00699790 5.88715919  
0.02041697 0.99979111 -0.00094168 -3.92402515  
0.00701567 0.00079859 0.99997507 -6.55890858  
Axis 0.04027230 -0.32429436 0.94509857  
Axis point 269.68765103 294.42923188 0.00000000  
Rotation angle (degrees) 1.23804246  
Shift along axis -4.68918648  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04916, steps = 60  
shifted from previous position = 0.0158  
rotated from previous position = 0.00475 degrees  
atoms outside contour = 68683, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976619 -0.02043146 -0.00708021 5.89153545  
0.02042526 0.99979093 -0.00094700 -3.92167404  
0.00709808 0.00080216 0.99997449 -6.56784536  
Axis 0.04041290 -0.32757750 0.94395963  
Axis point 270.02544660 294.51704315 0.00000000  
Rotation angle (degrees) 1.24004241  
Shift along axis -4.67703468  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04915, steps = 64  
shifted from previous position = 0.00963  
rotated from previous position = 0.0111 degrees  
atoms outside contour = 68685, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976962 -0.02024440 -0.00713260 5.85750549  
0.02023822 0.99979475 -0.00093752 -3.89410136  
0.00715011 0.00079296 0.99997412 -6.57738740  
Axis 0.04027816 -0.33244081 0.94226364  
Axis point 272.07473483 295.52901835 0.00000000  
Rotation angle (degrees) 1.23089863  
Shift along axis -4.66714522  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04914, steps = 44  
shifted from previous position = 0.0224  
rotated from previous position = 0.0278 degrees  
atoms outside contour = 68685, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99977943 -0.01975982 -0.00711675 5.76254851  
0.01975354 0.99980443 -0.00095124 -3.82175469  
0.00713415 0.00081045 0.99997422 -6.57449095  
Axis 0.04190327 -0.33897142 0.93986302  
Axis point 276.08625117 298.39215832 0.00000000  
Rotation angle (degrees) 1.20449210  
Shift along axis -4.64218567  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04914, steps = 44  
shifted from previous position = 0.0187  
rotated from previous position = 0.0232 degrees  
atoms outside contour = 68683, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99977214 -0.02015505 -0.00703080 5.82332652  
0.02014879 0.99979653 -0.00096004 -3.87929546  
0.00704872 0.00081816 0.99997482 -6.57037858  
Axis 0.04161563 -0.32950488 0.94323628  
Axis point 271.99952194 295.50807423 0.00000000  
Rotation angle (degrees) 1.22419772  
Shift along axis -4.67683120  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04915, steps = 44  
shifted from previous position = 0.0132  
rotated from previous position = 0.0151 degrees  
atoms outside contour = 68684, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976657 -0.02038611 -0.00715641 5.89535320  
0.02037984 0.99979186 -0.00094732 -3.91564412  
0.00717423 0.00080125 0.99997394 -6.58232090  
Axis 0.04043229 -0.33136868 0.94263462  
Axis point 271.06311849 295.34088087 0.00000000  
Rotation angle (degrees) 1.23902662  
Shift along axis -4.66883907  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04915, steps = 44  
shifted from previous position = 0.00886  
rotated from previous position = 0.00987 degrees  
atoms outside contour = 68683, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976298 -0.02055753 -0.00716786 5.92997642  
0.02055135 0.99978836 -0.00093556 -3.94228548  
0.00718558 0.00078803 0.99997387 -6.57848732  
Axis 0.03955313 -0.32938312 0.94336754  
Axis point 269.75069496 294.33811962 0.00000000  
Rotation angle (degrees) 1.24848036  
Shift along axis -4.67285999  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04914, steps = 40  
shifted from previous position = 0.0146  
rotated from previous position = 0.00712 degrees  
atoms outside contour = 68682, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99976045 -0.02066128 -0.00722212 5.97283182  
0.02065535 0.99978626 -0.00089483 -3.96927180  
0.00723906 0.00074544 0.99997352 -6.58925541  
Axis 0.03744481 -0.33012601 0.94319388  
Axis point 270.02705993 294.43587008 0.00000000  
Rotation angle (degrees) 1.25502200  
Shift along axis -4.68093394  
  

> fitmap #4 inMap #3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath zone (#3)
using 69852 atoms  
average map value = 0.04914, steps = 40  
shifted from previous position = 0.0144  
rotated from previous position = 0.00716 degrees  
atoms outside contour = 68685, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath zone (#3)
coordinates:  
Matrix rotation and translation  
0.99975926 -0.02074596 -0.00714290 5.96068426  
0.02073975 0.99978446 -0.00094224 -3.97001856  
0.00716090 0.00079387 0.99997405 -6.58373063  
Axis 0.03953178 -0.32570295 0.94464534  
Axis point 268.12984753 293.14447474 0.00000000  
Rotation angle (degrees) 1.25822206  
Shift along axis -4.69060726  
  

> color #4 #e5a4faa7

> color #4 #e5a4fa60

> color #4 #e5a4fa67

> color #4 #ebf4f767

> color #4 #f6f6f767

> color #4 #f7e7ee67

> color #4 #00000067

> color #4 #80777b67

> color #4 #d3c6cc67

> color #4 #d3c6cc66

> ui tool show "Volume Viewer"

> volume #1.3 level 0.2157

> volume #1.3 level 0.1511

> hide #!4 models

> show #!4 models

> hide #1.2.1 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.2 models

> show #1.2.1 models

> hide #1.2.1 models

> hide #!1.2 models

> show #1.2.1 models

> hide #!1.2 models

> hide #1.2.1 models

> show #1.2.1 models

> hide #1.2.1 models

> hide #!1.2 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.3 models

> show #!3 models

> hide #!3 models

> show #3.1 models

> color #3.1 #bfb62dff

> color #3.1 #bfb82fff

> color #3.1 #bfbb38ff

> color #3.1 #bfb881ff

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1.6 models

> hide #!1.3 models

> color #4 #00000066

> color #4 #f1e8ed66

> color #4 #fff6fb66

> color #4 #fff6fbff

> color #4 #ffbae5ff

> color #4 #f5c4ffff

> color #4 #ffbaeaff

> color #4 #ffc9cfff

> color #4 #ffc9cfca

> color #4 #ffc9cf00

> color #4 #ffc9cfdc

> color #4 #ffc9cf9e

> color #4 #7867699e

> color #4 #937f819e

> color #4 #937f815a

> color #4 #937f8159

> hide #!4 models

> show #!4 models

> hide #4.2 models

> show #4.2 models

> show #1.6.1 models

> hide #1.6.1 models

> show #!4#!1.6 surfaces

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> hide #!4 models

> show #!1.3 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.6 models

> hide #!1.6 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 68  
shifted from previous position = 0.707  
rotated from previous position = 0.386 degrees  
atoms outside contour = 46472, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980550 -0.01971549 -0.00051652 3.83584386  
0.01971531 0.99980557 -0.00035630 -3.72170403  
0.00052344 0.00034605 0.99999980 -5.53525602  
Axis 0.01780306 -0.02636104 0.99949395  
Axis point 197.89443004 197.45312694 0.00000000  
Rotation angle (degrees) 1.13025437  
Shift along axis -5.36605713  
  

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 44  
shifted from previous position = 0.0035  
rotated from previous position = 0.00471 degrees  
atoms outside contour = 46480, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980691 -0.01964493 -0.00047557 3.81349973  
0.01964476 0.99980696 -0.00036659 -3.70630489  
0.00048268 0.00035718 0.99999982 -5.53304067  
Axis 0.01841289 -0.02437782 0.99953323  
Axis point 197.26803483 197.21546171 0.00000000  
Rotation angle (degrees) 1.12616468  
Shift along axis -5.36988888  
  

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 48  
shifted from previous position = 0.017  
rotated from previous position = 0.00582 degrees  
atoms outside contour = 46483, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980674 -0.01965254 -0.00051800 3.82211436  
0.01965240 0.99980684 -0.00027458 -3.72784300  
0.00052330 0.00026435 0.99999983 -5.53976789  
Axis 0.01370524 -0.02648096 0.99955536  
Axis point 198.87601103 196.28499232 0.00000000  
Rotation angle (degrees) 1.12657686  
Shift along axis -5.38620488  
  

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 48  
shifted from previous position = 0.0024  
rotated from previous position = 0.00664 degrees  
atoms outside contour = 46475, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980747 -0.01961800 -0.00040755 3.79286887  
0.01961789 0.99980751 -0.00028018 -3.71812766  
0.00041297 0.00027213 0.99999988 -5.52098119  
Axis 0.01407223 -0.02090603 0.99968240  
Axis point 197.18528289 195.26592850 0.00000000  
Rotation angle (degrees) 1.12445458  
Shift along axis -5.38812235  
  

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 44  
shifted from previous position = 0.00834  
rotated from previous position = 0.00612 degrees  
atoms outside contour = 46472, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980569 -0.01970694 -0.00046656 3.82305663  
0.01970681 0.99980576 -0.00027767 -3.73621148  
0.00047194 0.00026842 0.99999985 -5.52337999  
Axis 0.01384988 -0.02380250 0.99962074  
Axis point 198.01733547 195.82358208 0.00000000  
Rotation angle (degrees) 1.12962254  
Shift along axis -5.37940516  
  

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 44  
shifted from previous position = 0.000111  
rotated from previous position = 0.00103 degrees  
atoms outside contour = 46475, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980596 -0.01969370 -0.00045717 3.81864190  
0.01969357 0.99980602 -0.00028555 -3.73206006  
0.00046271 0.00027649 0.99999985 -5.52313237  
Axis 0.01426444 -0.02334594 0.99962568  
Axis point 197.81278016 195.84910033 0.00000000  
Rotation angle (degrees) 1.12885750  
Shift along axis -5.37946570  
  

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 44  
shifted from previous position = 0.00171  
rotated from previous position = 0.0039 degrees  
atoms outside contour = 46468, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980576 -0.01970406 -0.00042987 3.81577569  
0.01970391 0.99980580 -0.00034708 -3.72161434  
0.00043663 0.00033854 0.99999985 -5.52848288  
Axis 0.01739127 -0.02197921 0.99960715  
Axis point 196.81240848 196.46102997 0.00000000  
Rotation angle (degrees) 1.12947222  
Shift along axis -5.37815170  
  

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 48  
shifted from previous position = 0.0183  
rotated from previous position = 0.003 degrees  
atoms outside contour = 46474, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980500 -0.01974232 -0.00045082 3.82890054  
0.01974215 0.99980503 -0.00037612 -3.72192592  
0.00045816 0.00036714 0.99999983 -5.51992753  
Axis 0.01881577 -0.02301096 0.99955813  
Axis point 196.72071822 197.10901446 0.00000000  
Rotation angle (degrees) 1.13172025  
Shift along axis -5.35979966  
  

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 44  
shifted from previous position = 0.001  
rotated from previous position = 0.000769 degrees  
atoms outside contour = 46472, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980480 -0.01975268 -0.00044251 3.82918543  
0.01975251 0.99980483 -0.00037413 -3.72396014  
0.00044982 0.00036532 0.99999983 -5.51702764  
Axis 0.01870984 -0.02257804 0.99956999  
Axis point 196.60286393 196.98964002 0.00000000  
Rotation angle (degrees) 1.13230097  
Shift along axis -5.35893211  
  

> fitmap #4 inMap #1.3

Fit molecule job016.cif (#4) to map J371_Td_FlaB2_3.23A_nosheath (#1.3) using
69852 atoms  
average map value = 0.1062, steps = 44  
shifted from previous position = 0.00598  
rotated from previous position = 0.00647 degrees  
atoms outside contour = 46481, contour level = 0.15109  
  
Position of job016.cif (#4) relative to J371_Td_FlaB2_3.23A_nosheath (#1.3)
coordinates:  
Matrix rotation and translation  
0.99980525 -0.01972807 -0.00051093 3.83711352  
0.01972792 0.99980534 -0.00028781 -3.73753934  
0.00051651 0.00027768 0.99999983 -5.51873937  
Axis 0.01432583 -0.02602848 0.99955855  
Axis point 198.46969440 196.43618270 0.00000000  
Rotation angle (degrees) 1.13090354  
Shift along axis -5.36405077  
  

> volume #1.3 level 0.1497

> hide #3.1 models

> hide #!4 models

> show #!4 models

> hide #!1.3 models

> show #!1.2 models

> show #1.2.1 models

> hide #1.2.1 models

> hide #!1.2 models

> show #!1.3 models

> color #4 #937f81ff

> color #4 #dbc8caff

> hide #!1.3 models

> show #!1.6 models

> hide #!1.6 models

> hide #1.6.1 models

> show #!1.4 models

> hide #!1.4 models

> show #!1.3 models

> hide #!4 models

> volume #1.3 level 0.166

> show #!1.6 models

> save
> /Users/clem/Jiaqi_Wang/Yale/Tomography/Data/Data_Clem_Wang/250123_Filaments_predicted_model_fit.cxs

——— End of log from Wed Jan 29 22:57:14 2025 ———

opened ChimeraX session  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 655, in restore_snapshot  
if session.restore_options['combine']:  
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^  
KeyError: 'combine'  
  
opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.3
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Mac16,11
      Model Number: Z1JV000KLLL/A
      Chip: Apple M4 Pro
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 11881.61.3
      OS Loader Version: 11881.61.3

Software:

    System Software Overview:

      System Version: macOS 15.2 (24C101)
      Kernel Version: Darwin 24.2.0
      Time since boot: 45 days, 4 hours, 21 minutes

Graphics/Displays:

    Apple M4 Pro:

      Chipset Model: Apple M4 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 20
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        LS32D70xE:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        LG HDR 4K:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Eric Pettersen]

Duplicate of #17081