Opened 5 months ago

Closed 5 months ago

#17857 closed defect (nonchimerax)

Cannot save command history: No space left on device

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation2.cxs

Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.86, shown at level 0.0606, step 1, values float32  
Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448,
pixel 0.86, shown at level 0.029, step 1, values float32  
Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448,
pixel 0.86, shown at level 0.11, step 1, values float32  
Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448,
pixel 0.86, shown at level 0.0778, step 1, values float32  
Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448,
pixel 0.86, shown at level 0.0308, step 1, values float32  
Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448,
pixel 0.86, shown at level 0.08, step 1, values float32  
Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size
448,448,448, pixel 0.86, shown at level 0.13, step 1, values float32  
Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size
448,448,448, pixel 0.86, shown at level 0.135, step 1, values float32  
Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size
448,448,448, pixel 0.86, shown at level 0.105, step 1, values float32  
Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size
448,448,448, pixel 0.86, shown at level 0.1, step 1, values float32  
Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size
448,448,448, pixel 0.86, shown at level 0.14, step 1, values float32  
Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size
448,448,448, pixel 0.86, shown at level 0.12, step 1, values float32  
Log from Mon Feb 3 13:09:17 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation2.cxs

Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.86, shown at level 0.0606, step 1, values float32  
Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448,
pixel 0.86, shown at level 0.029, step 1, values float32  
Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448,
pixel 0.86, shown at level 0.11, step 1, values float32  
Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448,
pixel 0.86, shown at level 0.0778, step 1, values float32  
Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448,
pixel 0.86, shown at level 0.0308, step 1, values float32  
Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448,
pixel 0.86, shown at level 0.08, step 1, values float32  
Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size
448,448,448, pixel 0.86, shown at level 0.13, step 1, values float32  
Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size
448,448,448, pixel 0.86, shown at level 0.135, step 1, values float32  
Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size
448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32  
Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size
448,448,448, pixel 0.86, shown at level 0.1, step 1, values float32  
Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size
448,448,448, pixel 0.86, shown at level 0.14, step 1, values float32  
Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size
448,448,448, pixel 0.86, shown at level 0.12, step 1, values float32  
Log from Fri Jan 31 04:00:50 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation1.cxs

Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.86, shown at level 0.0606, step 1, values float32  
Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448,
pixel 0.86, shown at level 0.029, step 1, values float32  
Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448,
pixel 0.86, shown at level 0.11, step 1, values float32  
Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448,
pixel 0.86, shown at level 0.0778, step 1, values float32  
Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448,
pixel 0.86, shown at level 0.0308, step 1, values float32  
Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448,
pixel 0.86, shown at level 0.08, step 1, values float32  
Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size
448,448,448, pixel 0.86, shown at level 0.13, step 1, values float32  
Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size
448,448,448, pixel 0.86, shown at level 0.135, step 1, values float32  
Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size
448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32  
Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size
448,448,448, pixel 0.86, shown at level 0.1, step 1, values float32  
Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size
448,448,448, pixel 0.86, shown at level 0.14, step 1, values float32  
Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size
448,448,448, pixel 0.86, shown at level 0.12, step 1, values float32  
Log from Fri Jan 31 02:27:14 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new.cxs

Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.86, shown at level 0.0282, step 1, values float32  
Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448,
pixel 0.86, shown at level 0.029, step 1, values float32  
Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448,
pixel 0.86, shown at level 0.0379, step 1, values float32  
Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448,
pixel 0.86, shown at level 0.0281, step 1, values float32  
Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448,
pixel 0.86, shown at level 0.0308, step 1, values float32  
Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448,
pixel 0.86, shown at level 0.08, step 1, values float32  
Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size
448,448,448, pixel 0.86, shown at level 0.13, step 1, values float32  
Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size
448,448,448, pixel 0.86, shown at level 0.135, step 1, values float32  
Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size
448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32  
Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size
448,448,448, pixel 0.86, shown at level 0.11, step 1, values float32  
Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size
448,448,448, pixel 0.86, shown at level 0.14, step 1, values float32  
Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size
448,448,448, pixel 0.86, shown at level 0.12, step 1, values float32  
Log from Mon Jan 27 17:38:14 2025UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended.cxs

Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.86, shown at level 0.0282, step 1, values float32  
Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448,
pixel 0.86, shown at level 0.029, step 1, values float32  
Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448,
pixel 0.86, shown at level 0.0379, step 1, values float32  
Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448,
pixel 0.86, shown at level 0.0281, step 1, values float32  
Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448,
pixel 0.86, shown at level 0.0308, step 1, values float32  
Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448,
pixel 0.86, shown at level 0.08, step 1, values float32  
Log from Sun Jan 26 19:47:57 2025 Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/walz/Downloads/cryosparc_P91_J558_009_volume_map.mrc

Opened cryosparc_P91_J558_009_volume_map.mrc as #1, grid size 448,448,448,
pixel 0.86, shown at level 0.0282, step 2, values float32  

> open /Users/walz/Downloads/cryosparc_P91_J556_008_volume_map.mrc

Opened cryosparc_P91_J556_008_volume_map.mrc as #2, grid size 448,448,448,
pixel 0.86, shown at level 0.029, step 2, values float32  

> open /Users/walz/Downloads/cryosparc_P91_J554_008_volume_map.mrc

Opened cryosparc_P91_J554_008_volume_map.mrc as #3, grid size 448,448,448,
pixel 0.86, shown at level 0.0379, step 2, values float32  

> open /Users/walz/Downloads/cryosparc_P91_J552_008_volume_map.mrc

Opened cryosparc_P91_J552_008_volume_map.mrc as #4, grid size 448,448,448,
pixel 0.86, shown at level 0.0281, step 2, values float32  

> open /Users/walz/Downloads/cryosparc_P91_J550_008_volume_map.mrc

Opened cryosparc_P91_J550_008_volume_map.mrc as #5, grid size 448,448,448,
pixel 0.86, shown at level 0.0308, step 2, values float32  

> open /Users/walz/Downloads/cryosparc_P91_J548_008_volume_map.mrc

Opened cryosparc_P91_J548_008_volume_map.mrc as #6, grid size 448,448,448,
pixel 0.86, shown at level 0.0325, step 2, values float32  

> set bgColor white

> surface dust #1 size 8.6

> surface dust #2 size 8.6

> surface dust #3 size 8.6

> surface dust #4 size 8.6

> surface dust #5 size 8.6

> surface dust #6 size 8.6

> tile

6 models tiled  

> volume all step 1

> open /Users/walz/Desktop/aIIbb3_21D/21D_extend_model/thigh_PSI_I-
> EGF1_2_21D10Fab/Refinement/semi-extended_aIIbb3_21D10/submission/semi-
> extended_aIIbb3_21D10_final_new4.pdb

Chain information for semi-extended_aIIbb3_21D10_final_new4.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
  

> ~tile

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> hide #!1 models

> select add #7

11697 atoms, 11945 bonds, 1 pseudobond, 1569 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.19118,-0.77657,-0.60032,441.69,-0.69023,-0.54121,0.48029,420.28,-0.69788,0.32254,-0.63948,365.99

> view matrix models
> #7,0.19118,-0.77657,-0.60032,342.52,-0.69023,-0.54121,0.48029,336.24,-0.69788,0.32254,-0.63948,462.89

> color #6 #ffb2b26f models

> color #6 #ffb2b26e models

> volume #6 level 0.1062

> open /Users/walz/Desktop/aIIbb3_21D/21D_extend_model/thigh_PSI_I-
> EGF1_2_21D10Fab/overall_structure_comparison/overall_semi_extended/full_21D10_semi_extended_aIIbb3_refine_new.pdb

Summary of feedback from opening
/Users/walz/Desktop/aIIbb3_21D/21D_extend_model/thigh_PSI_I-
EGF1_2_21D10Fab/overall_structure_comparison/overall_semi_extended/full_21D10_semi_extended_aIIbb3_refine_new.pdb  
---  
notes | Combining 3 symmetry atoms into CA /C:2 CA  
Combining 3 symmetry atoms into MG /I:1 MG  
Combining 3 symmetry atoms into CA /C:1 CA  
  
Chain information for full_21D10_semi_extended_aIIbb3_refine_new.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
D | No description available  
E | No description available  
F | No description available  
H | No description available  
L | No description available  
  

> select subtract #7

Nothing selected  

> select add #8

14944 atoms, 15264 bonds, 4 pseudobonds, 1970 residues, 2 models selected  

> hide (#!8 & sel) target a

> cartoon (#!8 & sel)

> hide #!7 models

> view matrix models #8,1,0,0,74.674,0,1,0,14.932,0,0,1,64.535

> view matrix models #8,1,0,0,96.902,0,1,0,51.797,0,0,1,2.6908

> ui mousemode right "rotate selected models"

> view matrix models
> #8,-0.58626,-0.79174,-0.17161,556.77,0.10786,0.13366,-0.98514,340.08,0.80291,-0.59606,0.0070336,116.08

> view matrix models
> #8,-0.95891,-0.14169,0.2458,447.89,0.13487,-0.98987,-0.044445,371.52,0.24961,-0.0094681,0.9683,-37.3

> view matrix models
> #8,-0.11837,-0.75612,0.64364,329.39,0.92144,-0.3252,-0.21257,138.81,0.37004,0.56792,0.73521,-119.67

> view matrix models
> #8,-0.40188,-0.5142,0.75769,322.79,0.18394,-0.85592,-0.48329,411.51,0.89703,-0.054854,0.43856,-64.14

> view matrix models
> #8,-0.25181,-0.56129,0.78838,297.62,0.69428,-0.6723,-0.25689,247.57,0.67422,0.48267,0.55898,-133.34

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.25181,-0.56129,0.78838,205.32,0.69428,-0.6723,-0.25689,220.48,0.67422,0.48267,0.55898,-62.62

> view matrix models
> #8,-0.25181,-0.56129,0.78838,214.22,0.69428,-0.6723,-0.25689,240.81,0.67422,0.48267,0.55898,-50.402

> ui tool show "Fit in Map"

> fitmap #8 inMap #6

Fit molecule full_21D10_semi_extended_aIIbb3_refine_new.pdb (#8) to map
cryosparc_P91_J548_008_volume_map.mrc (#6) using 14944 atoms  
average map value = 0.1808, steps = 332  
shifted from previous position = 10.2  
rotated from previous position = 19.9 degrees  
atoms outside contour = 6390, contour level = 0.10618  
  
Position of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#8) relative to
cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.95283509 0.23650967 -0.19017993 355.35625335  
0.24690090 0.96849253 -0.03259015 -7.03996872  
0.17647996 -0.07800863 -0.98120815 350.12189933  
Axis -0.12288274 -0.99202290 0.02811416  
Axis point 161.63097867 0.00000000 191.49987239  
Rotation angle (degrees) 169.35028574  
Shift along axis -26.83995675  
  

> hide #!6 models

> show #!6 models

> volume #6 level 0.05726

> volume #6 level 0.0706

> hide #!6 models

> open /Users/walz/Desktop/aIIbb3_21D/21D_extend_model/thigh_PSI_I-
> EGF1_2_21D10Fab/overall_structure_comparison/overall_semi_extended/b-tail.pdb

Chain information for b-tail.pdb #9  
---  
Chain | Description  
B | No description available  
  

> view matrix models
> #8,-0.47985,-0.66006,0.57799,319.59,0.60881,-0.72487,-0.32235,268.83,0.63174,0.19721,0.74968,-2.8445

> show #!6 models

> fitmap #8 inMap #6

Fit molecule full_21D10_semi_extended_aIIbb3_refine_new.pdb (#8) to map
cryosparc_P91_J548_008_volume_map.mrc (#6) using 14944 atoms  
average map value = 0.1808, steps = 1468  
shifted from previous position = 21.5  
rotated from previous position = 0.0227 degrees  
atoms outside contour = 5408, contour level = 0.070601  
  
Position of full_21D10_semi_extended_aIIbb3_refine_new.pdb (#8) relative to
cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.95291596 0.23649509 -0.18979249 355.28808959  
0.24685947 0.96850221 -0.03261625 -7.03180936  
0.17610087 -0.07793261 -0.98128230 350.18862920  
Axis -0.12286365 -0.99202565 0.02810036  
Axis point 161.62837102 0.00000000 191.49498248  
Rotation angle (degrees) 169.37283895  
Shift along axis -26.83583113  
  

> combine #8

> hide #9 models

> hide #!8 models

> hide #!6 models

> select #10/A:531

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

50 atoms, 49 bonds, 7 residues, 1 model selected  

> select up

5067 atoms, 5188 bonds, 667 residues, 1 model selected  

> select up

5116 atoms, 5237 bonds, 673 residues, 1 model selected  

> select down

5067 atoms, 5188 bonds, 667 residues, 1 model selected  

> select down

50 atoms, 49 bonds, 7 residues, 1 model selected  

> select up

5067 atoms, 5188 bonds, 667 residues, 1 model selected  

> delete sel

> select #10/B:369

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

59 atoms, 59 bonds, 8 residues, 1 model selected  

> select up

3455 atoms, 3519 bonds, 446 residues, 1 model selected  

> delete sel

> select clear

> select #10/F:949

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

102 atoms, 103 bonds, 12 residues, 1 model selected  

> select up

675 atoms, 694 bonds, 86 residues, 1 model selected  

> select up

745 atoms, 766 bonds, 96 residues, 1 model selected  

> delete sel

> select #10/B:43

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

> select up

51 atoms, 50 bonds, 6 residues, 1 model selected  

> select up

548 atoms, 557 bonds, 74 residues, 1 model selected  

> delete sel

> select #10/D:604

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

136 atoms, 139 bonds, 19 residues, 1 model selected  

> select up

296 atoms, 299 bonds, 43 residues, 1 model selected  

> delete sel

> select #10/F:780

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

89 atoms, 91 bonds, 10 residues, 1 model selected  

> select up

426 atoms, 440 bonds, 55 residues, 1 model selected  

> select up

436 atoms, 449 bonds, 57 residues, 1 model selected  

> select down

426 atoms, 440 bonds, 55 residues, 1 model selected  

> delete sel

> select #10/F:752

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

64 atoms, 64 bonds, 8 residues, 1 model selected  

> delete sel

> select #10/E:531

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

83 atoms, 84 bonds, 10 residues, 1 model selected  

> select up

296 atoms, 302 bonds, 39 residues, 1 model selected  

> select up

4343 atoms, 4428 bonds, 581 residues, 1 model selected  

> select down

296 atoms, 302 bonds, 39 residues, 1 model selected  

> delete sel

> select #10/F:759

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

> select up

28 atoms, 27 bonds, 4 residues, 1 model selected  

> select up

50 atoms, 50 bonds, 8 residues, 1 model selected  

> select up

78 atoms, 77 bonds, 12 residues, 1 model selected  

> select up

4047 atoms, 4126 bonds, 542 residues, 1 model selected  

> select down

78 atoms, 77 bonds, 12 residues, 1 model selected  

> delete sel

> select #10/A:703

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

> select up

75 atoms, 74 bonds, 11 residues, 1 model selected  

> select up

585 atoms, 589 bonds, 76 residues, 1 model selected  

> select up

3969 atoms, 4049 bonds, 530 residues, 1 model selected  

> select down

585 atoms, 589 bonds, 76 residues, 1 model selected  

> delete sel

> rename #10 Fab

> show #9 models

> show #!6 models

> select add #10

3384 atoms, 3460 bonds, 454 residues, 1 model selected  

> view matrix models
> #10,-0.4796,-0.66011,0.57813,263.4,0.60871,-0.72483,-0.32264,290.03,0.63203,0.19717,0.74944,-61.389

> view matrix models
> #10,-0.4796,-0.66011,0.57813,233.83,0.60871,-0.72483,-0.32264,257.94,0.63203,0.19717,0.74944,-38.805

> view matrix models
> #10,-0.4796,-0.66011,0.57813,237.38,0.60871,-0.72483,-0.32264,260.49,0.63203,0.19717,0.74944,-39.471

> view matrix models
> #10,-0.4796,-0.66011,0.57813,277.45,0.60871,-0.72483,-0.32264,294.4,0.63203,0.19717,0.74944,-55.096

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.0035973,0.88908,-0.45775,38.884,-0.80498,-0.27416,-0.52617,454.27,-0.5933,0.36658,0.71667,107.5

> view matrix models
> #10,0.013861,0.89276,-0.45032,34.679,-0.79634,-0.2625,-0.54492,452.92,-0.6047,0.36616,0.7073,110.4

> view matrix models
> #10,0.16463,0.82004,-0.54811,35.517,-0.90023,-0.10218,-0.42326,426.25,-0.4031,0.56311,0.7214,41.863

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.16463,0.82004,-0.54811,38.796,-0.90023,-0.10218,-0.42326,427.38,-0.4031,0.56311,0.7214,53.816

> fitmap #10 inMap #6

Fit molecule Fab (#10) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using
3384 atoms  
average map value = 0.05594, steps = 196  
shifted from previous position = 18.6  
rotated from previous position = 14.8 degrees  
atoms outside contour = 2228, contour level = 0.070601  
  
Position of Fab (#10) relative to cryosparc_P91_J548_008_volume_map.mrc (#6)
coordinates:  
Matrix rotation and translation  
0.97764717 -0.19678280 -0.07404376 100.81760441  
0.01420978 -0.28952043 0.95706633 156.07404631  
-0.20977138 -0.93672537 -0.28025259 545.94553186  
Axis -0.99133915 0.07104905 0.11044784  
Axis point 0.00000000 285.75438766 219.82084075  
Rotation angle (degrees) 107.22128610  
Shift along axis -28.55701943  
  

> select add #9

4058 atoms, 4143 bonds, 538 residues, 2 models selected  

> select subtract #9

3384 atoms, 3460 bonds, 454 residues, 1 model selected  

> select subtract #10

Nothing selected  

> show #!7 models

> hide #!7 models

> show #!8 models

> rename #8

No name or id option specified for renaming  

> combine #8

> hide #!6 models

> hide #!10 models

> hide #9 models

> select #8/L:145

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

55 atoms, 56 bonds, 6 residues, 1 model selected  

> select up

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> select up

14944 atoms, 15264 bonds, 1970 residues, 1 model selected  

> select down

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> select up

14944 atoms, 15264 bonds, 1970 residues, 1 model selected  

> select down

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> delete sel

> show #!10 models

> hide #!10 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> hide #!8 models

> hide #!11 models

> show #!11 models

> select #11/H:195

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

81 atoms, 81 bonds, 11 residues, 1 model selected  

> select up

1734 atoms, 1783 bonds, 227 residues, 1 model selected  

> delete sel

> select #11/L:8

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

> select up

119 atoms, 120 bonds, 17 residues, 1 model selected  

> select up

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> delete sel

> combine #11

> hide #!11 models

> select #12/F:906

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

> select up

77 atoms, 77 bonds, 10 residues, 1 model selected  

> select up

675 atoms, 694 bonds, 86 residues, 1 model selected  

> combine #11

> select add #12

11574 atoms, 11804 bonds, 4 pseudobonds, 1530 residues, 2 models selected  

> select subtract #12

Nothing selected  

> select add #12

11574 atoms, 11804 bonds, 4 pseudobonds, 1530 residues, 2 models selected  

> select subtract #12

Nothing selected  

> hide #!12 models

> show #!12 models

> hide #!13 models

> hide #!12 models

> show #!13 models

> select #13/F:927

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

105 atoms, 109 bonds, 12 residues, 1 model selected  

> select up

675 atoms, 694 bonds, 86 residues, 1 model selected  

> delete

Missing or invalid "atoms" argument: empty atom specifier  

> select #13/F:927

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

105 atoms, 109 bonds, 12 residues, 1 model selected  

> select up

675 atoms, 694 bonds, 86 residues, 1 model selected  

> delete sel

> select #13/F:761

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

28 atoms, 27 bonds, 4 residues, 1 model selected  

> select up

142 atoms, 143 bonds, 20 residues, 1 model selected  

> select up

173 atoms, 176 bonds, 24 residues, 1 model selected  

> select up

638 atoms, 656 bonds, 85 residues, 1 model selected  

> select up

10899 atoms, 11110 bonds, 1444 residues, 1 model selected  

> select down

638 atoms, 656 bonds, 85 residues, 1 model selected  

> delete sel

> select #13/B:45

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

> select up

51 atoms, 50 bonds, 6 residues, 1 model selected  

> select up

548 atoms, 557 bonds, 74 residues, 1 model selected  

> select up

609 atoms, 618 bonds, 82 residues, 1 model selected  

> select up

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> select up

10261 atoms, 10454 bonds, 1359 residues, 1 model selected  

> select down

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> delete sel

> select #13/E:559

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

> select up

116 atoms, 119 bonds, 14 residues, 1 model selected  

> select up

296 atoms, 302 bonds, 39 residues, 1 model selected  

> delete sel

> select #13/D:602

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

> select up

136 atoms, 139 bonds, 19 residues, 1 model selected  

> select up

296 atoms, 299 bonds, 43 residues, 1 model selected  

> delete sel

> show #!6 models

> fitmap #13 inMap #6

Fit molecule copy of copy of full_21D10_semi_extended_aIIbb3_refine_new.pdb
(#13) to map cryosparc_P91_J548_008_volume_map.mrc (#6) using 5666 atoms  
average map value = 0.2909, steps = 124  
shifted from previous position = 2.86  
rotated from previous position = 2.16 degrees  
atoms outside contour = 492, contour level = 0.070601  
  
Position of copy of copy of full_21D10_semi_extended_aIIbb3_refine_new.pdb
(#13) relative to cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.94842327 0.25593793 -0.18705352 351.07511089  
0.27110992 0.96066547 -0.06017652 -1.96816652  
0.16429440 -0.10778487 -0.98050483 356.29542546  
Axis -0.13415216 -0.99003811 0.04275207  
Axis point 159.52100929 0.00000000 193.78030278  
Rotation angle (degrees) 169.77922344  
Shift along axis -29.91655776  
  

> combine #13

> hide #!13 models

> hide #!6 models

> select #14/A:609-1000

1011 atoms, 1021 bonds, 1 pseudobond, 135 residues, 2 models selected  

> delete sel

> rename #14 propeller_thigh

> show #!13 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> show #!13 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> select #13/A:1-608

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> delete sel

> show #!14 models

> hide #!14 models

> show #!14 models

> rename #13 calf1

> show #!12 models

> hide #!12 models

> show #!12 models

> fitmap #13 inMap #6

Fit molecule calf1 (#13) to map cryosparc_P91_J548_008_volume_map.mrc (#6)
using 1025 atoms  
average map value = 0.222, steps = 108  
shifted from previous position = 5.46  
rotated from previous position = 9.85 degrees  
atoms outside contour = 51, contour level = 0.070601  
  
Position of calf1 (#13) relative to cryosparc_P91_J548_008_volume_map.mrc (#6)
coordinates:  
Matrix rotation and translation  
-0.90479885 0.36361028 -0.22164510 332.88455411  
0.35411327 0.93154374 0.08264379 -37.35376888  
0.23652224 -0.00371146 -0.97161896 328.13909024  
Axis -0.18518010 -0.98249355 -0.02036536  
Axis point 150.26067531 0.00000000 184.13040294  
Rotation angle (degrees) 166.51648597  
Shift along axis -31.62642825  
  

> hide #!13 models

> hide #!14 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> combine #12

> hide #!12 models

Drag select of 1262 residues, 1 pseudobonds  

> delete sel

Drag select of 38 residues, 1 pseudobonds  

> delete sel

Drag select of 39 residues, 2 pseudobonds  

> delete sel

> select clear

> select #15/A:742

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

41 atoms, 38 bonds, 6 residues, 1 model selected  

> select down

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

41 atoms, 38 bonds, 6 residues, 1 model selected  

> select up

1368 atoms, 1388 bonds, 191 residues, 1 model selected  

> select down

41 atoms, 38 bonds, 6 residues, 1 model selected  

> delete sel

> rename #15 calf2

> show #!6 models

> show #!14 models

> show #!13 models

> fitmap #15 inMap #6

Fit molecule calf2 (#15) to map cryosparc_P91_J548_008_volume_map.mrc (#6)
using 1327 atoms  
average map value = 0.1854, steps = 540  
shifted from previous position = 43.6  
rotated from previous position = 16.1 degrees  
atoms outside contour = 144, contour level = 0.070601  
  
Position of calf2 (#15) relative to cryosparc_P91_J548_008_volume_map.mrc (#6)
coordinates:  
Matrix rotation and translation  
-0.86244881 0.24947347 -0.44039186 374.61925651  
0.32238960 0.94152009 -0.09800418 -45.90381986  
0.39018835 -0.22650134 -0.89244056 295.70901122  
Axis -0.15231671 -0.98454508 0.08643261  
Axis point 157.77064194 0.00000000 188.16220864  
Rotation angle (degrees) 155.05114162  
Shift along axis 13.69250747  
  

> select add #15

1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected  

> view matrix models
> #15,-0.64948,-0.54749,0.52766,333.27,0.60821,-0.79054,-0.071614,241.5,0.45635,0.27442,0.84643,-37.123

> volume #6 level 0.1105

> view matrix models
> #15,-0.64948,-0.54749,0.52766,335.65,0.60821,-0.79054,-0.071614,247.58,0.45635,0.27442,0.84643,-17.459

> fitmap #15 inMap #6

Fit molecule calf2 (#15) to map cryosparc_P91_J548_008_volume_map.mrc (#6)
using 1327 atoms  
average map value = 0.1265, steps = 212  
shifted from previous position = 10.1  
rotated from previous position = 10.9 degrees  
atoms outside contour = 547, contour level = 0.11051  
  
Position of calf2 (#15) relative to cryosparc_P91_J548_008_volume_map.mrc (#6)
coordinates:  
Matrix rotation and translation  
-0.93563714 0.22353157 -0.27316062 371.31123811  
0.27402663 0.94780873 -0.16299683 -0.88558265  
0.22246909 -0.22735917 -0.94805868 374.18117390  
Axis -0.12812617 -0.98665055 0.10052055  
Axis point 161.45266616 0.00000000 210.98590850  
Rotation angle (degrees) 165.45337216  
Shift along axis -9.08802905  
  

> view matrix models
> #15,-0.52523,-0.55682,0.6435,296.33,0.60435,-0.77645,-0.17858,265.58,0.59908,0.2951,0.74433,-46.558

> view matrix models
> #15,-0.52523,-0.55682,0.6435,295.45,0.60435,-0.77645,-0.17858,266.57,0.59908,0.2951,0.74433,-49.223

> fitmap #15 inMap #6

Fit molecule calf2 (#15) to map cryosparc_P91_J548_008_volume_map.mrc (#6)
using 1327 atoms  
average map value = 0.1265, steps = 60  
shifted from previous position = 2.04  
rotated from previous position = 0.0231 degrees  
atoms outside contour = 547, contour level = 0.11051  
  
Position of calf2 (#15) relative to cryosparc_P91_J548_008_volume_map.mrc (#6)
coordinates:  
Matrix rotation and translation  
-0.93554884 0.22392329 -0.27314223 371.23060592  
0.27438936 0.94772549 -0.16287060 -0.97904661  
0.22239334 -0.22732072 -0.94808567 374.20391052  
Axis -0.12832251 -0.98662919 0.10047976  
Axis point 161.42087184 0.00000000 210.98369961  
Rotation angle (degrees) 165.45587401  
Shift along axis -9.07136900  
  

> hide #!15 models

> hide #!14 models

> hide #!13 models

> select subtract #15

Nothing selected  

> show #!12 models

> combine #12

> hide #!12 models

> hide #!6 models

> select #16/A:635

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

> select up

83 atoms, 82 bonds, 11 residues, 1 model selected  

> select up

5067 atoms, 5188 bonds, 667 residues, 1 model selected  

> select up

5116 atoms, 5237 bonds, 673 residues, 1 model selected  

> select up

5652 atoms, 5777 bonds, 743 residues, 1 model selected  

> select down

5116 atoms, 5237 bonds, 673 residues, 1 model selected  

> select up

5652 atoms, 5777 bonds, 743 residues, 1 model selected  

> delete sel

> select clear

Drag select of 171 residues, 2 pseudobonds  

> delete sel

> show #!6 models

> fitmap #16 inMap #6

Fit molecule copy of copy of copy of
full_21D10_semi_extended_aIIbb3_refine_new.pdb (#16) to map
cryosparc_P91_J548_008_volume_map.mrc (#6) using 4609 atoms  
average map value = 0.2719, steps = 104  
shifted from previous position = 4.41  
rotated from previous position = 3.17 degrees  
atoms outside contour = 884, contour level = 0.11051  
  
Position of copy of copy of copy of
full_21D10_semi_extended_aIIbb3_refine_new.pdb (#16) relative to
cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.96079585 0.20309126 -0.18874647 362.78748781  
0.22143338 0.97175763 -0.08157396 1.47448981  
0.16684886 -0.12017068 -0.97863191 360.66818396  
Axis -0.10776577 -0.99285637 0.05121297  
Axis point 164.86676653 0.00000000 196.75577933  
Rotation angle (degrees) 169.68400198  
Shift along axis -22.08913961  
  

> volume #6 level 0.2049

> volume #6 color #ffb2b23b

> combine #16

> hide #!16 models

> hide #!6 models

Drag select of 82 residues  

> delete sel

> fitmap #17 inMap #6

Fit molecule copy of copy of copy of copy of
full_21D10_semi_extended_aIIbb3_refine_new.pdb (#17) to map
cryosparc_P91_J548_008_volume_map.mrc (#6) using 4017 atoms  
average map value = 0.3004, steps = 92  
shifted from previous position = 0.289  
rotated from previous position = 0.52 degrees  
atoms outside contour = 1238, contour level = 0.2049  
  
Position of copy of copy of copy of copy of
full_21D10_semi_extended_aIIbb3_refine_new.pdb (#17) relative to
cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
-0.96121156 0.20615041 -0.18323292 361.10306955  
0.22481572 0.97046412 -0.08750557 2.47385898  
0.15978167 -0.12530500 -0.97916721 362.94502097  
Axis -0.10937480 -0.99253220 0.05400915  
Axis point 164.44559355 0.00000000 197.26854577  
Rotation angle (degrees) 170.04947598  
Shift along axis -22.34860817  
  

> show #!6 models

> show #!14 models

> hide #!14 models

> hide #!6 models

> combine #16

> hide #!17 models

> select #18/B:1-1000

4003 atoms, 4076 bonds, 1 pseudobond, 520 residues, 2 models selected  

> delete sel

> combine #18

> hide #!18 models

> select #19/E:537

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 4 residues, 1 model selected  

> select up

296 atoms, 302 bonds, 39 residues, 1 model selected  

> delete sel

> rename #19 I-EGF4

> rename #18 I-EGF3

> show #!18 models

> hide #!19 models

> select #18/D:600

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

> select up

136 atoms, 139 bonds, 19 residues, 1 model selected  

> select up

296 atoms, 299 bonds, 43 residues, 1 model selected  

> delete sel

> show #!19 models

> show #!17 models

> show #!16 models

> hide #!16 models

> show #!15 models

> show #!14 models

> show #!13 models

> show #9 models

> select add #9

674 atoms, 683 bonds, 84 residues, 1 model selected  

> view matrix models #9,1,0,0,-59.731,0,1,0,-51.145,0,0,1,99.266

> view matrix models #9,1,0,0,-61.475,0,1,0,26.841,0,0,1,130.08

> show #!6 models

> volume #6 level 0.14

> select subtract #9

Nothing selected  

> select add #18

310 atoms, 302 bonds, 53 residues, 1 model selected  

> select add #19

620 atoms, 601 bonds, 110 residues, 2 models selected  

> volume #6 level 0.12

> volume #6 level 0.1

> fitmap #18 inMap #6

Fit molecule I-EGF3 (#18) to map cryosparc_P91_J548_008_volume_map.mrc (#6)
using 310 atoms  
average map value = 0.2148, steps = 240  
shifted from previous position = 12.7  
rotated from previous position = 10.2 degrees  
atoms outside contour = 62, contour level = 0.1  
  
Position of I-EGF3 (#18) relative to cryosparc_P91_J548_008_volume_map.mrc
(#6) coordinates:  
Matrix rotation and translation  
-0.98025301 0.07888826 -0.18133017 391.51409030  
0.07692240 0.99687709 0.01785957 -0.08929022  
0.18217280 0.00355855 -0.98326007 334.22344253  
Axis -0.03931124 -0.99921240 -0.00540383  
Axis point 180.42475586 0.00000000 185.04858781  
Rotation angle (degrees) 169.51985707  
Shift along axis -17.10777214  
  

> select subtract #19

310 atoms, 302 bonds, 53 residues, 1 model selected  

> view matrix models
> #18,-0.35651,-0.7612,0.54174,312.45,0.72246,-0.59226,-0.35675,234.89,0.59241,0.2642,0.76108,-36.986

> fitmap #18 inMap #6

Fit molecule I-EGF3 (#18) to map cryosparc_P91_J548_008_volume_map.mrc (#6)
using 310 atoms  
average map value = 0.2137, steps = 432  
shifted from previous position = 11.8  
rotated from previous position = 6.33 degrees  
atoms outside contour = 60, contour level = 0.1  
  
Position of I-EGF3 (#18) relative to cryosparc_P91_J548_008_volume_map.mrc
(#6) coordinates:  
Matrix rotation and translation  
-0.97566674 -0.01329218 -0.21885537 411.73725830  
-0.02386391 0.99866863 0.04573219 15.82705778  
0.21795611 0.04984214 -0.97468500 317.92856772  
Axis 0.00940579 -0.99966304 -0.02419389  
Axis point 188.38591307 0.00000000 181.55464502  
Rotation angle (degrees) 167.38026585  
Shift along axis -19.64093810  
  

> hide #!6 models

> hide #9 models

> show #9 models

> show #!6 models

> view matrix models
> #18,-0.29884,-0.808,0.50777,309.57,0.79103,-0.50738,-0.34182,199.54,0.53382,0.29951,0.79078,-38.045

> select add #19

620 atoms, 601 bonds, 110 residues, 2 models selected  

> select subtract #18

310 atoms, 299 bonds, 57 residues, 1 model selected  

> view matrix models
> #19,-0.45581,-0.64367,0.61476,301.16,0.62346,-0.72382,-0.2956,270.6,0.63524,0.24854,0.73123,-43.674

> view matrix models
> #19,-0.45581,-0.64367,0.61476,301.62,0.62346,-0.72382,-0.2956,269.69,0.63524,0.24854,0.73123,-42.848

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.28768,-0.9536,-0.088831,399.8,0.8518,-0.21236,-0.4789,148.38,0.43781,-0.21343,0.87337,67.435

> fitmap #19 inMap #6

Fit molecule I-EGF4 (#19) to map cryosparc_P91_J548_008_volume_map.mrc (#6)
using 310 atoms  
average map value = 0.1095, steps = 420  
shifted from previous position = 4.25  
rotated from previous position = 21.3 degrees  
atoms outside contour = 114, contour level = 0.1  
  
Position of I-EGF4 (#19) relative to cryosparc_P91_J548_008_volume_map.mrc
(#6) coordinates:  
Matrix rotation and translation  
-0.96549508 0.25668139 0.04397558 333.89860864  
0.22004319 0.71376560 0.66492076 -36.20855798  
0.13928454 0.65165428 -0.74561818 210.20718209  
Axis -0.12884238 -0.92562835 -0.35582552  
Axis point 166.96183400 0.00000000 116.55795343  
Rotation angle (degrees) 177.04891462  
Shift along axis -84.30170199  
  

> select subtract #19

Nothing selected  

> select add #9

674 atoms, 683 bonds, 84 residues, 1 model selected  

> view matrix models
> #9,0.99966,0.0083186,-0.024648,-60.857,0.0077285,0.80974,0.58674,10.693,0.024839,-0.58674,0.8094,255.55

> view matrix models
> #9,0.99873,-0.013055,-0.048604,-54.433,0.04181,0.7528,0.65692,8.8559,0.028013,-0.65812,0.75239,273.75

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.99873,-0.013055,-0.048604,-33.494,0.04181,0.7528,0.65692,32.539,0.028013,-0.65812,0.75239,231.9

> volume #6 level 0.08

> view matrix models
> #9,0.99873,-0.013055,-0.048604,-19.36,0.04181,0.7528,0.65692,40.626,0.028013,-0.65812,0.75239,249.85

> view matrix models
> #9,0.99873,-0.013055,-0.048604,-19.195,0.04181,0.7528,0.65692,40.956,0.028013,-0.65812,0.75239,249.96

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.37609,-0.1564,-0.91329,206.98,0.50694,0.85978,0.061517,-19.077,0.77561,-0.48612,0.40264,100.19

> view matrix models
> #9,-0.38756,-0.31481,-0.86643,383.85,0.35824,0.81458,-0.45621,64.366,0.84939,-0.4872,-0.20292,139

> view matrix models
> #9,-0.81818,-0.17624,-0.54729,413.77,0.23062,0.77135,-0.59316,109.87,0.52669,-0.61152,-0.59046,260.59

> view matrix models
> #9,-0.5182,-0.68635,-0.51028,450.27,-0.65467,0.70225,-0.27972,270,0.55034,0.18911,-0.81324,120.43

> view matrix models
> #9,-0.3335,-0.40981,-0.84902,390.08,-0.54187,0.82028,-0.18309,216.46,0.77147,0.39899,-0.49562,8.394

> view matrix models
> #9,-0.09313,0.38884,-0.91659,194.02,0.10176,0.91949,0.37973,21.194,0.99044,-0.057904,-0.1252,21.284

> view matrix models
> #9,0.72079,0.69313,0.0055702,-106.01,-0.62134,0.64253,0.44843,211.12,0.30724,-0.32669,0.8938,118.41

> view matrix models
> #9,0.65758,-0.62774,-0.41658,199.28,0.19007,0.67328,-0.71454,147.49,0.72902,0.39068,0.56205,-74.43

> view matrix models
> #9,-0.58219,-0.7427,0.33083,399.99,-0.14274,-0.30721,-0.94087,422.74,0.80042,-0.59499,0.072842,145.33

> view matrix models
> #9,-0.83198,-0.55101,-0.064729,446.73,0.29514,-0.34077,-0.89262,338.82,0.46978,-0.76175,0.44614,209.95

> view matrix models
> #9,-0.92229,-0.29043,-0.25503,430.73,0.36161,-0.41537,-0.83469,335.11,0.13649,-0.86204,0.48811,291.29

> view matrix models
> #9,-0.8213,-0.51089,-0.2539,453.45,0.48422,-0.38889,-0.78377,301.38,0.30168,-0.76665,0.56678,233.4

> show #!10 models

> view matrix models
> #9,-0.50825,-0.57264,0.64325,325.09,-0.41045,-0.49557,-0.76547,496.52,0.75711,-0.65307,0.016831,170.01

> view matrix models
> #9,-0.61715,0.14533,0.77331,196.07,-0.78517,-0.049694,-0.61728,470.93,-0.05128,-0.98813,0.14478,382.79

> view matrix models
> #9,-0.13456,0.99039,0.032029,2.4549,-0.23074,-0.062752,0.97099,224.99,0.96367,0.12326,0.23697,-40.305

> view matrix models
> #9,-0.34305,0.91314,-0.2202,80.578,-0.55303,-0.0068632,0.83313,289.7,0.75926,0.40758,0.50735,-78.856

> view matrix models
> #9,-0.39561,0.9008,-0.17904,89.705,-0.50118,-0.04838,0.86399,284.82,0.76962,0.43154,0.4706,-82.311

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.39561,0.9008,-0.17904,87.796,-0.50118,-0.04838,0.86399,294.69,0.76962,0.43154,0.4706,-78.163

> view matrix models
> #9,-0.39561,0.9008,-0.17904,91.681,-0.50118,-0.04838,0.86399,297.87,0.76962,0.43154,0.4706,-72.863

> view matrix models
> #9,-0.39561,0.9008,-0.17904,90.944,-0.50118,-0.04838,0.86399,291.78,0.76962,0.43154,0.4706,-74.977

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.39655,0.75393,-0.52376,149.81,-0.76806,0.040017,0.63912,346.91,0.50282,0.65573,0.5632,-74.007

> view matrix models
> #9,-0.90774,0.14834,-0.39242,356.19,-0.38999,-0.64312,0.65902,403.06,-0.15461,0.75126,0.64163,30.007

> view matrix models
> #9,-0.42349,0.77359,-0.4714,146.71,-0.83024,-0.12324,0.54361,399.15,0.36244,0.62159,0.69445,-51.28

> view matrix models
> #9,0.37723,0.54633,-0.74782,57.38,-0.9247,0.17748,-0.33679,436.74,-0.051277,0.81855,0.57214,2.7336

> view matrix models
> #9,0.92867,0.36517,-0.064926,-75.984,-0.18027,0.29141,-0.93946,321.03,-0.32415,0.88416,0.33645,64.412

> view matrix models
> #9,0.26151,0.51347,0.81729,-50.788,0.5244,0.6353,-0.56693,83.049,-0.81032,0.57684,-0.10312,258.18

> view matrix models
> #9,-0.75157,-0.096853,0.65251,281.26,0.11855,0.95323,0.27803,27.229,-0.64892,0.28631,-0.70493,335.48

> view matrix models
> #9,0.060311,-0.35426,0.9332,146.69,0.61328,0.75079,0.24537,-28.074,-0.78756,0.55751,0.26254,225.37

> view matrix models
> #9,0.084195,-0.27473,0.95783,124.43,0.63438,0.75605,0.16109,-25.852,-0.76842,0.59407,0.23794,216.68

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.084195,-0.27473,0.95783,108.64,0.63438,0.75605,0.16109,-27.947,-0.76842,0.59407,0.23794,224.81

> view matrix models
> #9,0.084195,-0.27473,0.95783,107.27,0.63438,0.75605,0.16109,-26.987,-0.76842,0.59407,0.23794,222.16

> hide #!6 models

> select subtract #9

Nothing selected  

> show #!11 models

> hide #!11 models

> delete #11

> delete #12

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> delete #16

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> delete #7

> delete #8

> select clear

> save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/b-tail.pdb models
> #9 relModel #6

> save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/Fab.pdb models #10
> relModel #6

> save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/calf1.pdb models
> #13 relModel #6

> save
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/propeller_thigh.pdb
> models #14 relModel #6

> save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/calf2.pdb models
> #15 relModel #6

> hide #!17 models

> show #!17 models

> rename #17 PSI_hybrid_BI_I-EGF-2

> save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/PSI_hybrid_BI_I-
> EGF-2.pdb models #17 relModel #6

> save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/I-EGF3.pdb models
> #18 relModel #6

> save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/I-EGF4.pdb models
> #19

> save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/I-EGF4.pdb models
> #19 relModel #6

[Repeated 1 time(s)]

> save /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended.cxs
> includeMaps true

——— End of log from Sun Jan 26 19:47:57 2025 ———

opened ChimeraX session  

> show #!6 models

> open /Users/walz/Downloads/cryosparc_P91_J548_008_volume_map_sharp.mrc

Opened cryosparc_P91_J548_008_volume_map_sharp.mrc as #7, grid size
448,448,448, pixel 0.86, shown at level 0.0706, step 2, values float32  

> volume #7 step 1

> surface dust #6 size 8.6

> surface dust #7 size 8.6

> volume #7 level 0.09

> select add #7

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #7,1,0,0,3.1183,0,1,0,2.9994,0,0,1,2.6409

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.80916,0.17976,-0.55941,439.44,0.41754,0.84577,-0.33218,31.815,0.41342,-0.50236,-0.75942,432.82

> view matrix models
> #7,0.18299,0.3227,-0.92864,308.72,0.90003,-0.43503,0.026182,113.2,-0.39554,-0.8406,-0.37005,563.21

> view matrix models
> #7,0.35075,0.12761,-0.92773,315.72,0.73315,-0.65378,0.18725,151.12,-0.58263,-0.74585,-0.32287,568.75

> view matrix models
> #7,0.16739,0.53309,-0.82933,246.61,0.95798,0.11081,0.26458,-62.1,0.23295,-0.83877,-0.49214,472.18

> view matrix models
> #7,-0.85003,-0.27787,-0.44747,512.63,-0.48067,0.75663,0.44324,39.796,0.21541,0.59185,-0.77673,255.75

> view matrix models
> #7,0.4788,-0.82099,-0.311,337.91,-0.54174,-0.55505,0.63121,269.77,-0.69084,-0.13374,-0.71053,556.88

> view matrix models
> #7,0.10168,-0.9613,-0.25605,424.58,-0.76631,-0.23981,0.59604,257.47,-0.63438,0.13561,-0.76104,504.11

> view matrix models
> #7,0.60537,-0.71386,-0.35204,302.07,-0.56214,-0.69658,0.44584,344.9,-0.56349,-0.072,-0.82298,546.53

> view matrix models
> #7,-0.058499,-0.80041,-0.59659,501.75,-0.99499,-0.0018066,0.099989,368.27,-0.08111,0.59944,-0.7963,314.9

> view matrix models
> #7,-0.086114,-0.83673,-0.5408,501.3,-0.82387,-0.24541,0.51089,289.23,-0.56019,0.48955,-0.66823,397.84

> ui tool show "Fit in Map"

> fitmap #7 inMap #1

Fit map cryosparc_P91_J548_008_volume_map_sharp.mrc in map
cryosparc_P91_J558_009_volume_map.mrc using 581439 points  
correlation = 0.8818, correlation about mean = 0.7621, overlap = 3.252e+04  
steps = 392, shift = 14.3, angle = 19.9 degrees  
  
Position of cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) relative to
cryosparc_P91_J558_009_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998836 0.00093539 0.00472847 -0.94260289  
-0.00093004 0.99999890 -0.00113479 0.24010156  
-0.00472952 0.00113038 0.99998816 0.68694229  
Axis 0.22874171 0.95508751 -0.18837483  
Axis point 140.15211701 0.00000000 194.09372244  
Rotation angle (degrees) 0.28369412  
Shift along axis -0.11569724  
  

> fitmap #7 inMap #1

Fit map cryosparc_P91_J548_008_volume_map_sharp.mrc in map
cryosparc_P91_J558_009_volume_map.mrc using 581439 points  
correlation = 0.8819, correlation about mean = 0.7623, overlap = 3.252e+04  
steps = 44, shift = 0.0102, angle = 0.0186 degrees  
  
Position of cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) relative to
cryosparc_P91_J558_009_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99998975 0.00096269 0.00442035 -0.89219072  
-0.00095810 0.99999898 -0.00103878 0.22868018  
-0.00442134 0.00103454 0.99998967 0.64152730  
Axis 0.22336035 0.95251825 -0.20692786  
Axis point 139.29483880 0.00000000 196.38890302  
Rotation angle (degrees) 0.26592301  
Shift along axis -0.11420786  
  

> fitmap #7 inMap #6

Fit map cryosparc_P91_J548_008_volume_map_sharp.mrc in map
cryosparc_P91_J548_008_volume_map.mrc using 581439 points  
correlation = 0.9517, correlation about mean = 0.8865, overlap = 3.796e+04  
steps = 48, shift = 0.275, angle = 0.26 degrees  
  
Position of cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) relative to
cryosparc_P91_J548_008_volume_map.mrc (#6) coordinates:  
Matrix rotation and translation  
0.99999997 0.00009315 0.00011460 -0.03808621  
-0.00009316 0.99999997 0.00006790 0.00451226  
-0.00011459 -0.00006790 0.99999997 0.04777578  
Axis -0.41771513 0.70502145 -0.57311328  
Axis point 375.41814221 0.00000000 362.58970348  
Rotation angle (degrees) 0.00931321  
Shift along axis -0.00829051  
  

> hide #!6 models

> color #7 #b2b2b238 models

> volume #7 level 0.12

> color #7 #b2b2b2e0 models

> open /Users/walz/Downloads/cryosparc_P91_J550_008_volume_map_sharp.mrc

Opened cryosparc_P91_J550_008_volume_map_sharp.mrc as #8, grid size
448,448,448, pixel 0.86, shown at level 0.073, step 2, values float32  

> open /Users/walz/Downloads/cryosparc_P91_J558_009_volume_map_sharp.mrc

Opened cryosparc_P91_J558_009_volume_map_sharp.mrc as #11, grid size
448,448,448, pixel 0.86, shown at level 0.0567, step 2, values float32  

> open /Users/walz/Downloads/cryosparc_P91_J556_008_volume_map_sharp.mrc

Opened cryosparc_P91_J556_008_volume_map_sharp.mrc as #12, grid size
448,448,448, pixel 0.86, shown at level 0.0544, step 2, values float32  

> open /Users/walz/Downloads/cryosparc_P91_J554_008_volume_map_sharp.mrc

Opened cryosparc_P91_J554_008_volume_map_sharp.mrc as #16, grid size
448,448,448, pixel 0.86, shown at level 0.0797, step 2, values float32  

> open /Users/walz/Downloads/cryosparc_P91_J552_008_volume_map_sharp.mrc

Opened cryosparc_P91_J552_008_volume_map_sharp.mrc as #20, grid size
448,448,448, pixel 0.86, shown at level 0.0663, step 2, values float32  

> surface dust #7 size 8.6

[Repeated 2 time(s)]

> select subtract #7

Nothing selected  

> surface dust #7 size 8.6

> surface dust #8 size 8.6

> surface dust #11 size 8.6

> surface dust #12 size 8.6

> surface dust #16 size 8.6

> surface dust #20 size 8.6

> select add #8

2 models selected  

> select add #20

4 models selected  

> select add #16

6 models selected  

> select add #12

8 models selected  

> select add #11

10 models selected  

> view matrix models
> #8,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974,#11,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974,#12,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974,#16,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974,#20,0.030018,0.34261,-0.939,304.53,-0.48758,0.82509,0.28547,69.806,0.87256,0.44927,0.19182,-93.974

> view matrix models
> #8,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61,#11,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61,#12,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61,#16,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61,#20,-0.36928,-0.56472,-0.73806,512.34,-0.92932,0.22371,0.29381,266.15,-0.00080532,0.79439,-0.60741,166.61

> view matrix models
> #8,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253,#11,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253,#12,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253,#16,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253,#20,-0.71606,0.13594,-0.68468,440.69,-0.28116,0.8416,0.46115,-0.57466,0.63891,0.52271,-0.56441,86.253

> view matrix models
> #8,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12,#11,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12,#12,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12,#16,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12,#20,-0.34141,-0.58968,-0.73193,508.77,-0.9276,0.085723,0.36362,276.9,-0.15167,0.80308,-0.57625,188.12

> view matrix models
> #8,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44,#11,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44,#12,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44,#16,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44,#20,0.20056,-0.8304,-0.51982,401.39,-0.79116,-0.45022,0.41397,334.18,-0.57779,0.32823,-0.74727,392.44

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73,#11,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73,#12,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73,#16,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73,#20,0.20056,-0.8304,-0.51982,429.98,-0.79116,-0.45022,0.41397,340.59,-0.57779,0.32823,-0.74727,449.73

> view matrix models
> #8,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57,#11,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57,#12,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57,#16,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57,#20,0.20056,-0.8304,-0.51982,427.24,-0.79116,-0.45022,0.41397,342.91,-0.57779,0.32823,-0.74727,447.57

> view matrix models
> #8,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88,#11,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88,#12,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88,#16,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88,#20,0.20056,-0.8304,-0.51982,427.9,-0.79116,-0.45022,0.41397,342.89,-0.57779,0.32823,-0.74727,447.88

> view matrix models
> #8,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17,#11,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17,#12,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17,#16,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17,#20,0.20056,-0.8304,-0.51982,438.57,-0.79116,-0.45022,0.41397,346.84,-0.57779,0.32823,-0.74727,445.17

> view matrix models
> #8,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07,#11,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07,#12,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07,#16,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07,#20,0.20056,-0.8304,-0.51982,446.26,-0.79116,-0.45022,0.41397,355.21,-0.57779,0.32823,-0.74727,444.07

> view matrix models
> #8,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67,#11,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67,#12,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67,#16,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67,#20,0.20056,-0.8304,-0.51982,444.37,-0.79116,-0.45022,0.41397,352.3,-0.57779,0.32823,-0.74727,445.67

> view matrix models
> #8,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28,#11,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28,#12,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28,#16,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28,#20,0.20056,-0.8304,-0.51982,443.33,-0.79116,-0.45022,0.41397,354.1,-0.57779,0.32823,-0.74727,446.28

> fitmap #8 inMap #5

Fit map cryosparc_P91_J550_008_volume_map_sharp.mrc in map
cryosparc_P91_J550_008_volume_map.mrc using 112244 points  
correlation = 0.9412, correlation about mean = 0.895, overlap = 5284  
steps = 196, shift = 3.53, angle = 9.8 degrees  
  
Position of cryosparc_P91_J550_008_volume_map_sharp.mrc (#8) relative to
cryosparc_P91_J550_008_volume_map.mrc (#5) coordinates:  
Matrix rotation and translation  
0.99999998 -0.00005942 0.00001803 0.00333361  
0.00005942 0.99999998 0.00000680 -0.01378749  
-0.00001802 -0.00000679 0.99999998 0.01280236  
Axis -0.10875476 0.28857693 0.95126009  
Axis point 270.09212416 70.43598055 0.00000000  
Rotation angle (degrees) 0.00357903  
Shift along axis 0.00783708  
  

> fitmap #11 inMap #1

Fit map cryosparc_P91_J558_009_volume_map_sharp.mrc in map
cryosparc_P91_J558_009_volume_map.mrc using 111773 points  
correlation = 0.9587, correlation about mean = 0.9178, overlap = 4340  
steps = 276, shift = 4.63, angle = 9.8 degrees  
  
Position of cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) relative to
cryosparc_P91_J558_009_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999997 -0.00012472 0.00007221 0.00739204  
0.00012472 0.99999997 0.00009108 -0.04069274  
-0.00007221 -0.00009106 0.99999997 0.04352525  
Axis -0.53418804 0.42358484 0.73158665  
Axis point 362.49134482 104.88224097 0.00000000  
Rotation angle (degrees) 0.00976758  
Shift along axis 0.01065692  
  

> fitmap #12 inMap #2

Fit map cryosparc_P91_J556_008_volume_map_sharp.mrc in map
cryosparc_P91_J556_008_volume_map.mrc using 111628 points  
correlation = 0.966, correlation about mean = 0.9291, overlap = 4100  
steps = 240, shift = 5.34, angle = 9.81 degrees  
  
Position of cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) relative to
cryosparc_P91_J556_008_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999997 0.00011427 -0.00006802 -0.00710718  
-0.00011427 0.99999997 -0.00002242 0.02860082  
0.00006802 0.00002244 0.99999998 -0.01395664  
Axis 0.16632071 -0.50434360 -0.84733403  
Axis point 233.59226008 56.71006184 0.00000000  
Rotation angle (degrees) 0.00772706  
Shift along axis -0.00378078  
  

> fitmap #12 inMap #2

Fit map cryosparc_P91_J556_008_volume_map_sharp.mrc in map
cryosparc_P91_J556_008_volume_map.mrc using 111628 points  
correlation = 0.9659, correlation about mean = 0.929, overlap = 4100  
steps = 44, shift = 0.0116, angle = 0.000429 degrees  
  
Position of cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) relative to
cryosparc_P91_J556_008_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999997 0.00011255 -0.00006076 -0.01795682  
-0.00011255 0.99999997 -0.00002178 0.02850161  
0.00006076 0.00002179 0.99999998 -0.01894104  
Axis 0.16790249 -0.46832584 -0.86745586  
Axis point 253.50692337 159.66648917 0.00000000  
Rotation angle (degrees) 0.00743391  
Shift along axis 0.00006748  
  

> fitmap #12 inMap #2

Fit map cryosparc_P91_J556_008_volume_map_sharp.mrc in map
cryosparc_P91_J556_008_volume_map.mrc using 111628 points  
correlation = 0.9659, correlation about mean = 0.9289, overlap = 4099  
steps = 64, shift = 0.0138, angle = 0.00106 degrees  
  
Position of cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) relative to
cryosparc_P91_J556_008_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999997 0.00011471 -0.00007550 -0.01168166  
-0.00011471 0.99999997 -0.00001090 0.02858760  
0.00007550 0.00001092 0.99999998 -0.00644372  
Axis 0.07922118 -0.54806253 -0.83267729  
Axis point 195.56697791 94.09905921 0.00000000  
Rotation angle (degrees) 0.00789307  
Shift along axis -0.01122769  
  

> fitmap #12 inMap #2

Fit map cryosparc_P91_J556_008_volume_map_sharp.mrc in map
cryosparc_P91_J556_008_volume_map.mrc using 111628 points  
correlation = 0.9659, correlation about mean = 0.929, overlap = 4099  
steps = 48, shift = 0.00571, angle = 0.00269 degrees  
  
Position of cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) relative to
cryosparc_P91_J556_008_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999997 0.00011567 -0.00003175 -0.01630674  
-0.00011567 0.99999997 -0.00002789 0.02942150  
0.00003175 0.00002790 0.99999998 -0.00086915  
Axis 0.22652468 -0.25778928 -0.93927166  
Axis point 231.03251441 120.50255951 0.00000000  
Rotation angle (degrees) 0.00705590  
Shift along axis -0.01046206  
  

> fitmap #16 inMap #3

Fit map cryosparc_P91_J554_008_volume_map_sharp.mrc in map
cryosparc_P91_J554_008_volume_map.mrc using 111264 points  
correlation = 0.9451, correlation about mean = 0.8943, overlap = 5413  
steps = 220, shift = 4.39, angle = 9.79 degrees  
  
Position of cryosparc_P91_J554_008_volume_map_sharp.mrc (#16) relative to
cryosparc_P91_J554_008_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99999996 -0.00006647 0.00019113 -0.01517210  
0.00006647 0.99999998 0.00002949 -0.01589606  
-0.00019113 -0.00002947 0.99999996 0.04861121  
Axis -0.14415236 0.93465011 0.32503734  
Axis point 249.00601794 0.00000000 77.04793762  
Rotation angle (degrees) 0.01171651  
Shift along axis 0.00313030  
  

> fitmap #20 inMap #4

Fit map cryosparc_P91_J552_008_volume_map_sharp.mrc in map
cryosparc_P91_J552_008_volume_map.mrc using 111514 points  
correlation = 0.9457, correlation about mean = 0.8978, overlap = 4659  
steps = 252, shift = 4.15, angle = 9.79 degrees  
  
Position of cryosparc_P91_J552_008_volume_map_sharp.mrc (#20) relative to
cryosparc_P91_J552_008_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99999996 -0.00016035 0.00013379 0.00869009  
0.00016034 0.99999996 0.00005400 -0.04213159  
-0.00013380 -0.00005397 0.99999997 0.04478127  
Axis -0.25028123 0.62028692 0.74337301  
Axis point 282.03118324 61.92978627 0.00000000  
Rotation angle (degrees) 0.01235881  
Shift along axis 0.00498055  
  

> fitmap #20 inMap #4

Fit map cryosparc_P91_J552_008_volume_map_sharp.mrc in map
cryosparc_P91_J552_008_volume_map.mrc using 111514 points  
correlation = 0.9457, correlation about mean = 0.8978, overlap = 4659  
steps = 104, shift = 0.0171, angle = 0.00287 degrees  
  
Position of cryosparc_P91_J552_008_volume_map_sharp.mrc (#20) relative to
cryosparc_P91_J552_008_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99999996 -0.00017266 0.00009051 0.01524728  
0.00017266 0.99999996 0.00003213 -0.04231769  
-0.00009051 -0.00003211 0.99999998 0.01586544  
Axis -0.16256390 0.45811166 0.87390313  
Axis point 223.86924828 80.74831448 0.00000000  
Rotation angle (degrees) 0.01132044  
Shift along axis -0.00800003  
  

> volume all step 1

> surface dust #8 size 8.6

> surface dust #11 size 8.6

> surface dust #12 size 8.6

> surface dust #16 size 8.6

> surface dust #20 size 8.6

> surface dust #8 size 8.6

> surface dust #11 size 8.6

> surface dust #12 size 8.6

> surface dust #16 size 8.6

> surface dust #20 size 8.6

> volume #16 level 0.1589

> volume #16 level 0.2452

> volume #20 level 0.168

> volume #12 level 0.2036

> volume #11 level 0.13

> volume #8 level 0.2948

> select subtract #12

8 models selected  

> select subtract #11

6 models selected  

> select subtract #16

4 models selected  

> select subtract #20

2 models selected  

> hide #!12 models

> hide #!13 models

> show #!12 models

> hide #!12 models

> hide #!11 models

> hide #!20 models

> hide #!16 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #9 models

> hide #!10 models

> hide #!14 models

> hide #!15 models

> hide #!17 models

> hide #!19 models

> hide #!8 models

> show #!8 models

> hide #!18 models

> hide #!7 models

> volume #8 level 0.2

> volume #8 level 0.15

> volume #8 level 0.1

> surface dust #8 size 8.6

[Repeated 3 time(s)]

> volume #8 level 0.12

> lighting soft

> volume #7 level 0.13

> fitmap #8 inMap #7

Fit map cryosparc_P91_J550_008_volume_map_sharp.mrc in map
cryosparc_P91_J548_008_volume_map_sharp.mrc using 382518 points  
correlation = 0.8942, correlation about mean = 0.808, overlap = 4.607e+04  
steps = 160, shift = 0.604, angle = 0.82 degrees  
  
Position of cryosparc_P91_J550_008_volume_map_sharp.mrc (#8) relative to
cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99996146 -0.00543594 -0.00689322 2.18293687  
0.00551398 0.99992035 0.01135269 -2.73838618  
0.00683096 -0.01139026 0.99991179 0.97591746  
Axis -0.79157027 -0.47767094 0.38111282  
Axis point 0.00000000 85.39674467 243.82763462  
Rotation angle (degrees) 0.82312338  
Shift along axis -0.04796577  
  

> show #!20 models

> fitmap #20 inMap #7

Fit map cryosparc_P91_J552_008_volume_map_sharp.mrc in map
cryosparc_P91_J548_008_volume_map_sharp.mrc using 250306 points  
correlation = 0.9199, correlation about mean = 0.8061, overlap = 4.124e+04  
steps = 120, shift = 0.45, angle = 0.541 degrees  
  
Position of cryosparc_P91_J552_008_volume_map_sharp.mrc (#20) relative to
cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99999605 -0.00266984 -0.00087684 0.70675136  
0.00267767 0.99995547 0.00904943 -1.81387975  
0.00085264 -0.00905174 0.99995867 1.60797784  
Axis -0.95502489 -0.09124776 0.28213702  
Axis point 0.00000000 178.45984098 201.88203609  
Rotation angle (degrees) 0.54298902  
Shift along axis -0.05578259  
  

> hide #!8 models

> volume #20 level 0.12

> hide #!7 models

> show #!8 models

> show #!7 models

> show #!12 models

> hide #!8 models

> volume #12 level 0.12

> hide #!7 models

> hide #!20 models

> volume #12 level 0.1

> volume #12 level 0.11

> show #!20 models

> hide #!20 models

> show #!8 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!7 models

> hide #!12 models

> volume #8 level 0.11

> volume #8 level 0.08192

> volume #8 level 0.1

> volume #8 level 0.11

> volume #8 level 0.12

> volume #8 level 0.13

> volume #8 level 0.125

> volume #8 level 0.135

> volume #8 level 0.14

> volume #8 level 0.135

> show #!12 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!20 models

> show #!16 models

> hide #!12 models

> hide #!20 models

> volume #16 level 0.12

> show #!7 models

> show #!8 models

> show #!12 models

> hide #!12 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #!7 models

> show #!7 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!12 models

> show #!8 models

> show #!11 models

> hide #!12 models

> hide #!8 models

> hide #!7 models

> hide #!16 models

> volume #11 level 0.11

> show #!7 models

> show #!8 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #!7 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #!7 models

> hide #!11 models

> show #!11 models

> show #!8 models

> show #!7 models

> show #!20 models

> show #!16 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #!11 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #!20 models

> volume #16 level 0.11

> volume #16 level 0.14

> surface dust #16 size 8.6

> show #!12 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!12 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> volume #11 level 0.12

> volume #11 level 0.11

> volume #11 level 0.12

> volume #11 level 0.11

> surface dust #11 size 8.6

[Repeated 1 time(s)]

> show #!12 models

> hide #!12 models

> show #!12 models

> show #!8 models

> show #!7 models

> hide #!7 models

> show #!20 models

> show #!16 models

> show #!7 models

> hide #!7 models

> hide #!8 models

> hide #!20 models

> hide #!16 models

> volume #12 level 0.1

> volume #12 level 0.11

> show #!12 models

> hide #!12 models

> show #!12 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!12 models

> hide #!11 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> save
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new.cxs
> includeMaps true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 630, in save  
fserialize(stream, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/serialize.py", line 65, in msgpack_serialize  
stream.write(packer.pack(obj))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 136, in write  
self._f.write(buf)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/lz4/frame/__init__.py", line 741, in write  
self._fp.write(compressed)  
OSError: [Errno 28] No space left on device  
  
OSError: [Errno 28] No space left on device  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/lz4/frame/__init__.py", line 741, in write  
self._fp.write(compressed)  
  
See log for complete Python traceback.  
  
Cannot save
'/Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new.cxs':
[Errno 28] No space left on device  

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> fitmap #8 inMap #7

Fit map cryosparc_P91_J550_008_volume_map_sharp.mrc in map
cryosparc_P91_J548_008_volume_map_sharp.mrc using 328138 points  
correlation = 0.9013, correlation about mean = 0.802, overlap = 4.571e+04  
steps = 84, shift = 0.0136, angle = 0.0102 degrees  
  
Position of cryosparc_P91_J550_008_volume_map_sharp.mrc (#8) relative to
cryosparc_P91_J548_008_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.99996237 -0.00547745 -0.00672681 2.16862670  
0.00555389 0.99991961 0.01139809 -2.75241339  
0.00666384 -0.01143502 0.99991241 1.02460814  
Axis -0.79622622 -0.46695284 0.38468021  
Axis point 0.00000000 89.32530792 244.04885445  
Rotation angle (degrees) 0.82155430  
Shift along axis -0.04732373  
  

> save
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new.cxs

——— End of log from Mon Jan 27 17:38:14 2025 ———

opened ChimeraX session  

> hide #!8 models

> show #!8 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!7 models

> hide #!8 models

> show #!3 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> volume #4 level 0.04

> show #!19 models

> color #4 #b2b2ff38 models

> color #4 #b2b2ffc0 models

> color #4 #b2b2ffe3 models

> color #4 #b2b2ffff models

[Repeated 1 time(s)]

> volume #4 color #b2b2ff8c

> show #!18 models

> hide #!4 models

> show #!4 models

> show #!17 models

> show #!15 models

> show #!14 models

> show #!13 models

> volume #4 level 0.06

> show #!10 models

> show #9 models

> show #!7 models

> volume #4 level 0.1135

> hide #!4 models

> show #!4 models

> volume #4 level 0.07785

> hide #!4 models

> show #!3 models

> volume #3 level 0.1214

> volume #3 color #b2ffff6e

> volume #3 level 0.07588

> volume #3 color #009193

> volume #3 color #00919350

> volume #3 color #00fdff

> volume #3 color #00fdff2d

> volume #3 level 0.1101

> show #!4 models

> hide #!3 models

> hide #!4 models

> show #!1 models

> volume #1 level 0.06056

> show #!4 models

> hide #!1 models

> show #!12 models

> hide #!4 models

> hide #!12 models

> show #!12 models

> color #12 #b2b2ff7d models

> volume #12 level 0.1777

> volume #12 level 0.11

> show #!11 models

> hide #!12 models

> hide #!11 models

> show #!12 models

> select add #10

3384 atoms, 3460 bonds, 454 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.30181,0.74955,-0.58914,28.753,-0.78324,-0.15738,-0.60147,463.83,-0.54355,0.64297,0.53958,83.745

> view matrix models
> #10,0.30181,0.74955,-0.58914,25.455,-0.78324,-0.15738,-0.60147,469.14,-0.54355,0.64297,0.53958,85.999

> view matrix models
> #10,0.30181,0.74955,-0.58914,22.058,-0.78324,-0.15738,-0.60147,465.97,-0.54355,0.64297,0.53958,88.156

> ui tool show "Fit in Map"

> fitmap #10 inMap #12

Fit molecule Fab (#10) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 3384 atoms  
average map value = 0.06266, steps = 116  
shifted from previous position = 3.72  
rotated from previous position = 5.05 degrees  
atoms outside contour = 2774, contour level = 0.11  
  
Position of Fab (#10) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) coordinates:  
Matrix rotation and translation  
0.98849879 -0.11361862 -0.09980451 70.83207994  
0.06080833 -0.30563479 0.95020509 148.41424462  
-0.13846472 -0.94534553 -0.29521067 541.19291392  
Axis -0.99558763 0.02030525 0.09161312  
Axis point 0.00000000 273.62288874 219.39825162  
Rotation angle (degrees) 107.82876842  
Shift along axis -17.92558395  
  

> volume #12 level 0.1438

> hide #!12 models

> show #!12 models

> select add #18

3694 atoms, 3762 bonds, 507 residues, 2 models selected  

> select subtract #10

310 atoms, 302 bonds, 53 residues, 1 model selected  

> view matrix models
> #18,-0.29884,-0.808,0.50777,310.21,0.79103,-0.50738,-0.34182,201.78,0.53382,0.29951,0.79078,-35.662

> fitmap #18 inMap #12

Fit molecule I-EGF3 (#18) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 310 atoms  
average map value = 0.1618, steps = 204  
shifted from previous position = 2.44  
rotated from previous position = 8.48 degrees  
atoms outside contour = 133, contour level = 0.14384  
  
Position of I-EGF3 (#18) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.96435014 0.09915673 -0.24535025 390.98644598  
0.10659231 0.99415437 -0.01718040 13.93866547  
0.24221247 -0.04272037 -0.96928225 337.14979433  
Axis -0.05230516 -0.99851504 0.01522787  
Axis point 174.17503509 0.00000000 192.85317726  
Rotation angle (degrees) 165.86875303  
Shift along axis -29.23450314  
  

> select add #19

620 atoms, 601 bonds, 110 residues, 2 models selected  

> select subtract #18

310 atoms, 299 bonds, 57 residues, 1 model selected  

> view matrix models
> #19,-0.43908,-0.89642,-0.060339,419.02,0.61422,-0.25049,-0.74832,234.78,0.6557,-0.36564,0.66058,75.809

> fitmap #19 inMap #12

Fit molecule I-EGF4 (#19) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 310 atoms  
average map value = 0.1045, steps = 208  
shifted from previous position = 4.09  
rotated from previous position = 8 degrees  
atoms outside contour = 226, contour level = 0.14384  
  
Position of I-EGF4 (#19) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.92089228 0.37749684 0.09722930 290.22890707  
0.34559583 0.67523483 0.65162983 -52.43453428  
0.18033559 0.63368293 -0.75227988 203.94421091  
Axis -0.19763181 -0.91516864 -0.35129479  
Axis point 148.59838551 0.00000000 115.43880334  
Rotation angle (degrees) 177.39759608  
Shift along axis -81.01656192  
  

> volume #12 level 0.09872

> select add #10

3694 atoms, 3759 bonds, 511 residues, 2 models selected  

> select subtract #19

3384 atoms, 3460 bonds, 454 residues, 1 model selected  

> view matrix models
> #10,0.22495,0.78311,-0.57977,13.125,-0.78164,-0.21022,-0.58724,461.92,-0.58176,0.58527,0.56482,104.55

> view matrix models
> #10,0.22495,0.78311,-0.57977,12.27,-0.78164,-0.21022,-0.58724,459.88,-0.58176,0.58527,0.56482,106.33

[Repeated 1 time(s)]

> select add #15

4711 atoms, 4810 bonds, 2 pseudobonds, 639 residues, 3 models selected  

> select subtract #10

1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected  

> view matrix models
> #15,-0.52545,-0.5567,0.64342,302.56,0.60405,-0.77666,-0.17867,269.51,0.59918,0.29477,0.74437,-43.358

> fitmap #15 inMap #12

Fit molecule calf2 (#15) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 1327 atoms  
average map value = 0.1701, steps = 768  
shifted from previous position = 42.2  
rotated from previous position = 11.2 degrees  
atoms outside contour = 347, contour level = 0.098719  
  
Position of calf2 (#15) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.87648818 0.40146766 -0.26569189 327.63686451  
0.45185340 0.87646330 -0.16625459 -59.25651157  
0.16612335 -0.26577396 -0.94961425 358.31728090  
Axis -0.22314254 -0.96821695 0.11297500  
Axis point 149.91524935 0.00000000 195.12896599  
Rotation angle (degrees) 167.11499011  
Shift along axis 24.74433088  
  

> volume #12 level 0.1551

> view matrix models
> #15,-0.52545,-0.5567,0.64342,297.09,0.60405,-0.77666,-0.17867,270.97,0.59918,0.29477,0.74437,-45.106

> volume #12 level 0.1156

> hide #!15 models

> show #!15 models

> select add #13

2352 atoms, 2371 bonds, 3 pseudobonds, 334 residues, 4 models selected  

> select subtract #15

1025 atoms, 1021 bonds, 1 pseudobond, 149 residues, 2 models selected  

> view matrix models
> #13,-0.58997,-0.65166,0.47673,345.78,0.54647,-0.75692,-0.3584,291.79,0.5944,0.049077,0.80267,-4.3884

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.60257,-0.64676,0.46756,348.9,0.53993,-0.76181,-0.35794,293.84,0.58769,0.036763,0.80825,-1.875

> view matrix models
> #13,-0.31096,-0.80971,0.49767,310.21,0.42529,-0.58683,-0.68903,337.04,0.84996,-0.0026099,0.52684,-9.6238

> view matrix models
> #13,-0.18751,-0.82396,0.53473,281.81,0.90332,-0.35848,-0.2356,138.64,0.38581,0.43885,0.81151,-23.802

> view matrix models
> #13,-0.37606,-0.84146,0.38796,344.15,0.2492,-0.49512,-0.83232,379.22,0.89245,-0.21633,0.39589,33.706

> view matrix models
> #13,-0.56967,-0.72727,0.38282,366.79,0.5866,-0.68604,-0.4304,282.68,0.57565,-0.020624,0.81744,8.2783

> view matrix models
> #13,0.18303,-0.98259,0.031768,301.96,0.39778,0.044468,-0.9164,276.16,0.89904,0.18037,0.399,-30.191

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.18303,-0.98259,0.031768,304.33,0.39778,0.044468,-0.9164,276.47,0.89904,0.18037,0.399,-30.511

> fitmap #13 inMap #12

Fit molecule calf1 (#13) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 1025 atoms  
average map value = 0.1995, steps = 308  
shifted from previous position = 11.5  
rotated from previous position = 29.2 degrees  
atoms outside contour = 233, contour level = 0.11564  
  
Position of calf1 (#13) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.57633215 -0.74739022 0.33052851 370.93471022  
-0.27813437 0.55970271 0.78062420 54.20471398  
-0.76842860 0.35796749 -0.53044958 415.07317739  
Axis -0.33345799 0.86702994 0.37022271  
Axis point 275.55183482 0.00000000 114.23649383  
Rotation angle (degrees) 140.67280684  
Shift along axis 76.97548371  
  

> volume #12 level 0.2454

> volume #12 level 0.189

> view matrix models
> #13,0.56706,-0.79248,-0.22456,235.75,0.17921,0.3848,-0.90544,296.58,0.80395,0.47319,0.36022,-52.786

> view matrix models
> #13,0.56706,-0.79248,-0.22456,238.72,0.17921,0.3848,-0.90544,299.95,0.80395,0.47319,0.36022,-51.436

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.68382,-0.70419,0.19108,422.89,-0.70346,0.56674,-0.4289,385.15,0.19373,-0.4277,-0.88291,391.6

> view matrix models
> #13,-0.66931,-0.64212,0.37377,384.24,-0.74298,0.57711,-0.339,378.87,0.0019698,-0.5046,-0.86335,440.27

> view matrix models
> #13,-0.61736,-0.58293,0.52826,342.35,-0.78069,0.53672,-0.3201,390.26,-0.096927,-0.61002,-0.78643,466.17

> ui mousemode right "translate selected models"

> view matrix models
> #13,-0.61736,-0.58293,0.52826,334.39,-0.78069,0.53672,-0.3201,358.05,-0.096927,-0.61002,-0.78643,474.02

> view matrix models
> #13,-0.61736,-0.58293,0.52826,334.24,-0.78069,0.53672,-0.3201,353.3,-0.096927,-0.61002,-0.78643,469.83

> fitmap #13 inMap #12

Fit molecule calf1 (#13) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 1025 atoms  
average map value = 0.1951, steps = 212  
shifted from previous position = 4.43  
rotated from previous position = 36.1 degrees  
atoms outside contour = 487, contour level = 0.18897  
  
Position of calf1 (#13) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.50319207 0.27336220 0.81979927 -87.65948442  
0.68063836 0.45915770 -0.57088144 59.97575740  
-0.53247456 0.84524984 0.04498371 205.93326038  
Axis 0.70807040 0.67614146 0.20363945  
Axis point 0.00000000 -71.16457947 148.29408539  
Rotation angle (degrees) 89.78991060  
Shift along axis 20.41914501  
  

> volume #12 level 0.1213

> view matrix models
> #13,-0.11267,-0.81169,0.57311,261.64,-0.97145,-0.0312,-0.23518,472.25,0.20877,-0.58325,-0.78501,397.62

> fitmap #13 inMap #12

Fit molecule calf1 (#13) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 1025 atoms  
average map value = 0.1973, steps = 152  
shifted from previous position = 3.36  
rotated from previous position = 14 degrees  
atoms outside contour = 236, contour level = 0.12128  
  
Position of calf1 (#13) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.37728647 0.44780172 0.81063465 -87.54190524  
0.60533824 0.54320089 -0.58180615 62.92894147  
-0.70087126 0.71021574 -0.06612916 277.28118686  
Axis 0.64773065 0.75776480 0.07897795  
Axis point 98.79766814 0.00000000 194.17857056  
Rotation angle (degrees) 94.17602654  
Shift along axis 12.88086028  
  

> view matrix models
> #13,0.022812,-0.76253,0.64655,217.54,-0.92468,-0.26194,-0.27631,504.3,0.38005,-0.59155,-0.71108,350.88

> fitmap #13 inMap #12

Fit molecule calf1 (#13) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 1025 atoms  
average map value = 0.1973, steps = 88  
shifted from previous position = 4.59  
rotated from previous position = 0.0124 degrees  
atoms outside contour = 238, contour level = 0.12128  
  
Position of calf1 (#13) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.37722813 0.44763916 0.81075157 -87.52700647  
0.60537059 0.54332717 -0.58165455 62.86981898  
-0.70087472 0.71022162 -0.06602929 277.27170471  
Axis 0.64765362 0.75782050 0.07907517  
Axis point 98.83074693 0.00000000 194.16452601  
Rotation angle (degrees) 94.17120650  
Shift along axis 12.88216273  
  

> select subtract #13

Nothing selected  

> select add #15

1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected  

> view matrix models
> #15,-0.52545,-0.5567,0.64342,296.68,0.60405,-0.77666,-0.17867,266.6,0.59918,0.29477,0.74437,-43.542

> fitmap #15 inMap #12

Fit molecule calf2 (#15) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 1327 atoms  
average map value = 0.1701, steps = 1108  
shifted from previous position = 47.7  
rotated from previous position = 11.2 degrees  
atoms outside contour = 433, contour level = 0.12128  
  
Position of calf2 (#15) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.87681153 0.40052901 -0.26604142 327.91627250  
0.45107304 0.87679974 -0.16659928 -59.10119741  
0.16653721 -0.26608028 -0.94945597 358.27367084  
Axis -0.22268277 -0.96830353 0.11314003  
Axis point 149.99134622 0.00000000 195.15882427  
Rotation angle (degrees) 167.09299228  
Shift along axis 24.74168755  
  

> volume #12 level 0.08744

> view matrix models
> #15,-0.52545,-0.5567,0.64342,301.01,0.60405,-0.77666,-0.17867,268.36,0.59918,0.29477,0.74437,-42.462

> view matrix models
> #15,-0.52545,-0.5567,0.64342,300.02,0.60405,-0.77666,-0.17867,271.61,0.59918,0.29477,0.74437,-41.738

> fitmap #15 inMap #12

Fit molecule calf2 (#15) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 1327 atoms  
average map value = 0.1701, steps = 1120  
shifted from previous position = 44.9  
rotated from previous position = 11.2 degrees  
atoms outside contour = 300, contour level = 0.087438  
  
Position of calf2 (#15) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.87644563 0.40162544 -0.26559378 327.58304345  
0.45196947 0.87641891 -0.16617307 -59.28717539  
0.16603208 -0.26568194 -0.94965596 358.32658500  
Axis -0.22321428 -0.96820570 0.11292968  
Axis point 149.90239475 0.00000000 195.12189039  
Rotation angle (degrees) 167.12058576  
Shift along axis 24.74667455  
  

> hide #!12 models

> select subtract #15

Nothing selected  

> select add #13

1025 atoms, 1021 bonds, 1 pseudobond, 149 residues, 2 models selected  

> view matrix models
> #13,0.022777,-0.76267,0.64639,218.2,-0.92466,-0.26189,-0.27642,502.78,0.3801,-0.5914,-0.71118,354.69

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.10105,-0.63942,0.76218,207.9,-0.80472,-0.39794,-0.44054,522.74,0.58499,-0.65786,-0.47434,289.35

> view matrix models
> #13,-0.19184,-0.97932,0.064308,378.91,-0.08431,-0.048839,-0.99524,398.86,0.9778,-0.19635,-0.073197,79.392

> view matrix models
> #13,-0.69313,-0.66949,0.26713,404.6,-0.1521,-0.2264,-0.96208,435.88,0.70459,-0.70748,0.055093,197.32

> view matrix models
> #13,-0.63302,-0.71008,0.30833,392.75,-0.36466,-0.077825,-0.92788,451.44,0.68287,-0.69981,-0.20967,238.2

> select add #15

2352 atoms, 2371 bonds, 3 pseudobonds, 334 residues, 4 models selected  

> select subtract #13

1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected  

> view matrix models
> #15,-0.57419,-0.54668,0.60947,313.14,0.56863,-0.80186,-0.18353,284.99,0.58904,0.24118,0.77127,-32.418

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.57419,-0.54668,0.60947,311.56,0.56863,-0.80186,-0.18353,280.1,0.58904,0.24118,0.77127,-33.952

> view matrix models
> #15,-0.57419,-0.54668,0.60947,309.7,0.56863,-0.80186,-0.18353,275.36,0.58904,0.24118,0.77127,-35.768

> show #!12 models

> view matrix models
> #15,-0.57419,-0.54668,0.60947,309.8,0.56863,-0.80186,-0.18353,276.81,0.58904,0.24118,0.77127,-35.994

> view matrix models
> #15,-0.57419,-0.54668,0.60947,307.07,0.56863,-0.80186,-0.18353,278.06,0.58904,0.24118,0.77127,-37.186

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.35874,-0.85709,0.36974,342.8,0.93306,-0.31803,0.1681,64.378,-0.026486,0.40529,0.9138,57.11

> view matrix models
> #15,-0.44855,-0.605,0.65786,283.74,0.76857,-0.6368,-0.06159,187.61,0.45619,0.47799,0.75061,-48.718

> view matrix models
> #15,-0.12867,-0.66409,0.7365,212.62,0.98977,-0.1321,0.053807,29.472,0.061561,0.73589,0.67429,2.067

> view matrix models
> #15,-0.12879,-0.66001,0.74013,211.48,0.98987,-0.13059,0.055793,28.945,0.05983,0.73982,0.67014,2.1975

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.12879,-0.66001,0.74013,213.42,0.98987,-0.13059,0.055793,34.669,0.05983,0.73982,0.67014,2.1546

> ui mousemode right "rotate selected models"

> view matrix models
> #15,0.18418,-0.43587,0.88096,83.882,0.9127,-0.25677,-0.31787,118.08,0.36476,0.8626,0.35053,-54.678

> view matrix models
> #15,0.27455,-0.37285,0.88634,50.773,0.96148,0.093754,-0.25839,34.608,0.01324,0.92314,0.38423,10.756

> view matrix models
> #15,0.10994,-0.65328,0.7491,156.44,0.4758,-0.62711,-0.61672,321.19,0.87266,0.42422,0.24188,-76.808

> view matrix models
> #15,-0.65147,-0.3551,0.67044,284.01,-0.50591,-0.4552,-0.7327,527.08,0.56537,-0.81651,0.1169,239.86

> view matrix models
> #15,-0.22713,-0.30991,0.92324,149.81,-0.63605,-0.67068,-0.38161,557.65,0.73746,-0.6739,-0.044787,191.96

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.22713,-0.30991,0.92324,149.88,-0.63605,-0.67068,-0.38161,552.63,0.73746,-0.6739,-0.044787,195.07

> view matrix models
> #15,-0.22713,-0.30991,0.92324,149.7,-0.63605,-0.67068,-0.38161,555.06,0.73746,-0.6739,-0.044787,197.28

> view matrix models
> #15,-0.22713,-0.30991,0.92324,149.3,-0.63605,-0.67068,-0.38161,554.75,0.73746,-0.6739,-0.044787,196.96

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.20841,-0.54579,0.81159,201.73,0.23293,-0.83363,-0.5008,399.52,0.9499,0.084675,0.30087,-32.629

> view matrix models
> #15,-0.13967,-0.60843,0.78122,201.12,0.55362,-0.7021,-0.44784,295.44,0.82097,0.36995,0.4349,-71.567

> view matrix models
> #15,-0.19995,-0.65291,0.73057,228.97,0.44066,-0.72588,-0.52812,334.83,0.87512,0.21634,0.43285,-55.002

> view matrix models
> #15,-0.30093,-0.70218,0.64528,270.94,0.19139,-0.70735,-0.68046,405.66,0.93424,-0.081271,0.34726,-3.2183

> view matrix models
> #15,-0.12543,-0.58229,0.80325,190.48,0.19567,-0.80826,-0.55536,409.46,0.97261,0.087516,0.21532,-28.723

> view matrix models
> #15,-0.58269,-0.6462,0.49284,342.23,0.057639,-0.63776,-0.76807,433.17,0.81065,-0.41914,0.40887,81.383

> view matrix models
> #15,-0.44025,-0.64171,0.628,293.51,0.6964,-0.68553,-0.2123,233.07,0.56675,0.34388,0.74869,-43.793

> view matrix models
> #15,-0.49847,-0.5342,0.68276,280.56,0.52443,-0.81294,-0.25318,300.93,0.69029,0.23186,0.68538,-44.009

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.49847,-0.5342,0.68276,279.29,0.52443,-0.81294,-0.25318,300.92,0.69029,0.23186,0.68538,-44.601

> view matrix models
> #15,-0.49847,-0.5342,0.68276,279.51,0.52443,-0.81294,-0.25318,300.74,0.69029,0.23186,0.68538,-44.439

> view matrix models
> #15,-0.49847,-0.5342,0.68276,281.14,0.52443,-0.81294,-0.25318,302.84,0.69029,0.23186,0.68538,-45.134

> volume #12 level 0.09872

> select add #10

4711 atoms, 4810 bonds, 2 pseudobonds, 639 residues, 3 models selected  

> select subtract #15

3384 atoms, 3460 bonds, 454 residues, 1 model selected  

> view matrix models
> #10,0.22495,0.78311,-0.57977,34.527,-0.78164,-0.21022,-0.58724,475.48,-0.58176,0.58527,0.56482,97.146

> select add #9

4058 atoms, 4143 bonds, 538 residues, 2 models selected  

> select subtract #10

674 atoms, 683 bonds, 84 residues, 1 model selected  

> view matrix models
> #9,0.084195,-0.27473,0.95783,68.859,0.63438,0.75605,0.16109,-50.508,-0.76842,0.59407,0.23794,219.09

> hide #!12 models

> view matrix models
> #9,0.084195,-0.27473,0.95783,76.215,0.63438,0.75605,0.16109,-47.745,-0.76842,0.59407,0.23794,223.92

> view matrix models
> #9,0.084195,-0.27473,0.95783,73.993,0.63438,0.75605,0.16109,-48.618,-0.76842,0.59407,0.23794,222.73

> view matrix models
> #9,0.084195,-0.27473,0.95783,74.684,0.63438,0.75605,0.16109,-48.521,-0.76842,0.59407,0.23794,224.32

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.28696,0.41509,0.86334,-90.53,0.92891,0.099637,-0.35666,66.057,-0.23407,0.90431,-0.35699,111.25

> view matrix models
> #9,0.80627,0.45421,0.37898,-157.83,0.59124,-0.63943,-0.4915,287.48,0.019086,0.62035,-0.7841,153.89

> view matrix models
> #9,0.92669,-0.25525,-0.27584,13.318,-0.26057,-0.96529,0.017858,473.56,-0.27082,0.055325,-0.96104,335.9

> view matrix models
> #9,0.93195,-0.25961,-0.25312,11.135,-0.26082,-0.96494,0.029393,472.53,-0.25188,0.038626,-0.96699,335.93

> view matrix models
> #9,0.5527,-0.35332,-0.75478,147.94,0.085812,-0.87674,0.47325,348.28,-0.82895,-0.32633,-0.45426,475.21

> view matrix models
> #9,0.5908,-0.60613,-0.53251,169.9,-0.25916,-0.7676,0.58619,385.14,-0.76407,-0.20831,-0.61058,453.29

> view matrix models
> #9,0.88779,-0.2864,-0.36027,34.415,-0.14264,-0.91546,0.37628,409.25,-0.43758,-0.28267,-0.85359,424.75

> view matrix models
> #9,0.94371,-0.26699,-0.19524,5.1708,-0.22009,-0.94751,0.2319,443.37,-0.2469,-0.17588,-0.95295,375.26

> view matrix models
> #9,0.92098,-0.2522,0.29697,-36.4,-0.38961,-0.59908,0.69951,368.23,0.001495,-0.75993,-0.65,412.9

> view matrix models
> #9,0.82731,-0.55688,0.073702,60.63,-0.32694,-0.37066,0.86932,296.76,-0.45679,-0.7433,-0.48872,485.73

> view matrix models
> #9,0.74202,-0.66812,-0.055038,110.25,-0.18845,-0.28667,0.93931,247.1,-0.64335,-0.68661,-0.33863,498.3

> show #!12 models

> view matrix models
> #9,0.7454,-0.66392,-0.060001,109.21,-0.18864,-0.29641,0.93625,249.29,-0.63937,-0.68656,-0.34618,498.17

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.7454,-0.66392,-0.060001,102.95,-0.18864,-0.29641,0.93625,246.88,-0.63937,-0.68656,-0.34618,491.38

> view matrix models
> #9,0.7454,-0.66392,-0.060001,105.95,-0.18864,-0.29641,0.93625,237.94,-0.63937,-0.68656,-0.34618,488.03

> view matrix models
> #9,0.7454,-0.66392,-0.060001,108.14,-0.18864,-0.29641,0.93625,237.2,-0.63937,-0.68656,-0.34618,490.24

> view matrix models
> #9,0.7454,-0.66392,-0.060001,106.92,-0.18864,-0.29641,0.93625,236.03,-0.63937,-0.68656,-0.34618,489.9

> view matrix models
> #9,0.7454,-0.66392,-0.060001,110.46,-0.18864,-0.29641,0.93625,238.57,-0.63937,-0.68656,-0.34618,490.71

> hide #!12 models

> show #!12 models

> select add #10

4058 atoms, 4143 bonds, 538 residues, 2 models selected  

> select subtract #9

3384 atoms, 3460 bonds, 454 residues, 1 model selected  

> view matrix models
> #10,0.22495,0.78311,-0.57977,35.194,-0.78164,-0.21022,-0.58724,476.94,-0.58176,0.58527,0.56482,97.169

> view matrix models
> #10,0.22495,0.78311,-0.57977,36.606,-0.78164,-0.21022,-0.58724,480.32,-0.58176,0.58527,0.56482,95.513

> view matrix models
> #10,0.22495,0.78311,-0.57977,36.452,-0.78164,-0.21022,-0.58724,480.22,-0.58176,0.58527,0.56482,95.67

> select add #9

4058 atoms, 4143 bonds, 538 residues, 2 models selected  

> select subtract #10

674 atoms, 683 bonds, 84 residues, 1 model selected  

> view matrix models
> #9,0.7454,-0.66392,-0.060001,109.94,-0.18864,-0.29641,0.93625,239.58,-0.63937,-0.68656,-0.34618,486.89

> view matrix models
> #9,0.7454,-0.66392,-0.060001,109.35,-0.18864,-0.29641,0.93625,239.22,-0.63937,-0.68656,-0.34618,486.84

> view matrix models
> #9,0.7454,-0.66392,-0.060001,109.45,-0.18864,-0.29641,0.93625,239.26,-0.63937,-0.68656,-0.34618,486.9

> view matrix models
> #9,0.7454,-0.66392,-0.060001,113.36,-0.18864,-0.29641,0.93625,240.55,-0.63937,-0.68656,-0.34618,489.7

> view matrix models
> #9,0.7454,-0.66392,-0.060001,113.19,-0.18864,-0.29641,0.93625,240.6,-0.63937,-0.68656,-0.34618,489.34

> view matrix models
> #9,0.7454,-0.66392,-0.060001,112.21,-0.18864,-0.29641,0.93625,240.26,-0.63937,-0.68656,-0.34618,488.66

> view matrix models
> #9,0.7454,-0.66392,-0.060001,111.03,-0.18864,-0.29641,0.93625,238.65,-0.63937,-0.68656,-0.34618,487.05

> view matrix models
> #9,0.7454,-0.66392,-0.060001,112.88,-0.18864,-0.29641,0.93625,238.51,-0.63937,-0.68656,-0.34618,487.67

> volume #12 level 0.12

> volume #12 level 0.1

> select subtract #9

Nothing selected  

> select add #10

3384 atoms, 3460 bonds, 454 residues, 1 model selected  

> view matrix models
> #10,0.22495,0.78311,-0.57977,34.772,-0.78164,-0.21022,-0.58724,479.07,-0.58176,0.58527,0.56482,96.507

> fitmap #10 inMap #12

Fit molecule Fab (#10) to map cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) using 3384 atoms  
average map value = 0.0571, steps = 100  
shifted from previous position = 7.49  
rotated from previous position = 3.07 degrees  
atoms outside contour = 2686, contour level = 0.1  
  
Position of Fab (#10) relative to cryosparc_P91_J556_008_volume_map_sharp.mrc
(#12) coordinates:  
Matrix rotation and translation  
0.97928041 -0.14481400 -0.14155840 83.61835583  
0.08949133 -0.31760009 0.94399231 139.44098174  
-0.18166226 -0.93710143 -0.29805995 549.68289905  
Axis -0.99210977 0.02115122 0.12357523  
Axis point 0.00000000 270.38783251 229.41553400  
Rotation angle (degrees) 108.55348773  
Shift along axis -12.08204694  
  

> save
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation1.cxs

——— End of log from Fri Jan 31 02:27:14 2025 ———

opened ChimeraX session  

> combine #9,10,13,14,15,17,18,19 conformation1 true

Expected a keyword  

> combine #9,10,13,14,15,17,18,19 conformation1 keepModels true

Expected a keyword  

> combine #9,10,13,14,15,17,18,19 name conformation1 keepModels true

Expected a keyword  

> combine #9, 10, 13, 14, 15, 17, 18, 19 name conformation1 keepModels true

Expected a keyword  

> combine #9, 10, 13, 14, 15, 17, 18, 19 conformation1

Expected a keyword  

> combine #9, 10, 13, 14, 15, 17, 18, 19 conformation1

Expected a keyword  

> combine #9, 10, 13, 14, 15, 17, 18, 19 conformation1

Expected a keyword  

> combine #9, 10, 13, 14, 15, 17, 18, 19

Remapping chain ID 'C' in calf1 #13 to 'D'  
Remapping chain ID 'I' in calf1 #13 to 'K'  
Remapping chain ID 'J' in calf1 #13 to 'M'  
Remapping chain ID 'A' in propeller_thigh #14 to 'E'  
Remapping chain ID 'C' in propeller_thigh #14 to 'F'  
Remapping chain ID 'I' in propeller_thigh #14 to 'N'  
Remapping chain ID 'J' in propeller_thigh #14 to 'O'  
Remapping chain ID 'C' in calf2 #15 to 'G'  
Remapping chain ID 'F' in calf2 #15 to 'P'  
Remapping chain ID 'I' in calf2 #15 to 'Q'  
Remapping chain ID 'J' in calf2 #15 to 'R'  
Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S'  
Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T'  
Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U'  
Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V'  
Remapping chain ID 'C' in I-EGF3 #18 to 'W'  
Remapping chain ID 'E' in I-EGF3 #18 to 'X'  
Remapping chain ID 'I' in I-EGF3 #18 to 'Y'  
Remapping chain ID 'J' in I-EGF3 #18 to 'Z'  
Remapping chain ID 'C' in I-EGF4 #19 to 'a'  
Remapping chain ID 'D' in I-EGF4 #19 to 'b'  
Remapping chain ID 'I' in I-EGF4 #19 to 'c'  
Remapping chain ID 'J' in I-EGF4 #19 to 'd'  

> hide #!21 models

> show #!21 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!10 models

> hide #9 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> hide #!21 models

> show #!21 models

> select #21/E:459

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

> select up

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select #21/E:547

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

70 atoms, 71 bonds, 9 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> color sel blue

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select up

31404 atoms, 31892 bonds, 4276 residues, 33 models selected  

> select down

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select clear

> select #21/A:632

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

> select clear

> select #21/A:631

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

> select up

83 atoms, 82 bonds, 11 residues, 1 model selected  

> select up

426 atoms, 432 bonds, 59 residues, 1 model selected  

> select up

475 atoms, 481 bonds, 65 residues, 1 model selected  

> select up

1011 atoms, 1021 bonds, 135 residues, 1 model selected  

> color sel blue

> select #21/P:927

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

105 atoms, 109 bonds, 12 residues, 1 model selected  

> select up

675 atoms, 694 bonds, 86 residues, 1 model selected  

> select up

745 atoms, 766 bonds, 96 residues, 1 model selected  

> color sel blue

> select #21/B:615

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

46 atoms, 45 bonds, 6 residues, 1 model selected  

> select up

674 atoms, 683 bonds, 84 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

674 atoms, 683 bonds, 84 residues, 1 model selected  

> color sel blue

> select #21/P:828

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

> select up

42 atoms, 43 bonds, 5 residues, 1 model selected  

> select up

496 atoms, 513 bonds, 65 residues, 1 model selected  

> select up

514 atoms, 529 bonds, 68 residues, 1 model selected  

> color sel blue

> select #21/S:350

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

> select up

110 atoms, 110 bonds, 14 residues, 1 model selected  

> select up

3455 atoms, 3519 bonds, 446 residues, 1 model selected  

> select up

3522 atoms, 3586 bonds, 455 residues, 1 model selected  

> select up

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> color sel red

> select #21/X:536

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

24 atoms, 23 bonds, 4 residues, 1 model selected  

> select up

296 atoms, 302 bonds, 39 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

296 atoms, 302 bonds, 39 residues, 1 model selected  

> color sel red

> select #21/b:569

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

107 atoms, 106 bonds, 16 residues, 1 model selected  

> select up

296 atoms, 299 bonds, 43 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

296 atoms, 299 bonds, 43 residues, 1 model selected  

> color sel red

> select #21/H:4

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

> select up

35 atoms, 34 bonds, 4 residues, 1 model selected  

> select up

1734 atoms, 1783 bonds, 227 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

1734 atoms, 1783 bonds, 227 residues, 1 model selected  

> color sel forest green

> select #21/L:87

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

46 atoms, 47 bonds, 5 residues, 1 model selected  

> select up

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> show #!12 models

> ui tool show "Color Zone"

> color zone #12 near #21 distance 15

> color zone #12 near #21 distance 2

> color zone #12 near #21 distance 25

[Repeated 2 time(s)]

> hide #!12 models

> show #!12 models

> volume #12 level 0.1592

> volume #12 level 0.1296

> volume #12 level 0.12

> hide #!21 models

> volume #12 level 0.1

> color zone #12 near #21 distance 3

> color zone #12 near #21 distance 30

[Repeated 2 time(s)]

> hide #!12 models

> show #!12 models

> show #!21 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> volume #12 level 0.2629

> hide #!21 models

> show #!14 models

> ui tool show "Fit in Map"

> fitmap #14 inMap #12

Fit molecule propeller_thigh (#14) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4655 atoms  
average map value = 0.3683, steps = 64  
shifted from previous position = 0.362  
rotated from previous position = 0.848 degrees  
atoms outside contour = 1979, contour level = 0.26287  
  
Position of propeller_thigh (#14) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.94940963 0.24528192 -0.19610742 354.76956495  
0.26078501 0.96370214 -0.05717829 -1.66005707  
0.17496434 -0.10542750 -0.97891395 353.82671079  
Axis -0.12883067 -0.99080226 0.04139494  
Axis point 160.56747216 0.00000000 193.61017366  
Rotation angle (degrees) 169.20717929  
Shift along axis -29.41377446  
  

> fitmap #14 inMap #12

Fit molecule propeller_thigh (#14) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4655 atoms  
average map value = 0.3683, steps = 40  
shifted from previous position = 0.00842  
rotated from previous position = 0.0144 degrees  
atoms outside contour = 1980, contour level = 0.26287  
  
Position of propeller_thigh (#14) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.94947078 0.24508837 -0.19605335 354.79344879  
0.26056554 0.96376718 -0.05708260 -1.65492422  
0.17495950 -0.10528301 -0.97893036 353.80249907  
Axis -0.12872296 -0.99081885 0.04133298  
Axis point 160.58355030 0.00000000 193.59629166  
Rotation angle (degrees) 169.20909591  
Shift along axis -29.40662240  
  

> show #!21 models

> hide #!21 models

> show #!21 models

> close #21

> combine #9, 10, 13, 14, 15, 17, 18, 19

Remapping chain ID 'C' in calf1 #13 to 'D'  
Remapping chain ID 'I' in calf1 #13 to 'K'  
Remapping chain ID 'J' in calf1 #13 to 'M'  
Remapping chain ID 'A' in propeller_thigh #14 to 'E'  
Remapping chain ID 'C' in propeller_thigh #14 to 'F'  
Remapping chain ID 'I' in propeller_thigh #14 to 'N'  
Remapping chain ID 'J' in propeller_thigh #14 to 'O'  
Remapping chain ID 'C' in calf2 #15 to 'G'  
Remapping chain ID 'F' in calf2 #15 to 'P'  
Remapping chain ID 'I' in calf2 #15 to 'Q'  
Remapping chain ID 'J' in calf2 #15 to 'R'  
Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S'  
Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T'  
Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U'  
Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V'  
Remapping chain ID 'C' in I-EGF3 #18 to 'W'  
Remapping chain ID 'E' in I-EGF3 #18 to 'X'  
Remapping chain ID 'I' in I-EGF3 #18 to 'Y'  
Remapping chain ID 'J' in I-EGF3 #18 to 'Z'  
Remapping chain ID 'C' in I-EGF4 #19 to 'a'  
Remapping chain ID 'D' in I-EGF4 #19 to 'b'  
Remapping chain ID 'I' in I-EGF4 #19 to 'c'  
Remapping chain ID 'J' in I-EGF4 #19 to 'd'  

> volume #12 level 0.12

> hide #!14 models

> hide #!12 models

> select #21/E:456

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> color sel blue

> select #21/E:456

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select up

31404 atoms, 31892 bonds, 4276 residues, 33 models selected  

> select down

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> color sel medium blue

> select #21/S:346

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

> select up

110 atoms, 110 bonds, 14 residues, 1 model selected  

> select up

3455 atoms, 3519 bonds, 446 residues, 1 model selected  

> color sel orange red

> select #21/S:369

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

59 atoms, 59 bonds, 8 residues, 1 model selected  

> select up

3455 atoms, 3519 bonds, 446 residues, 1 model selected  

> select up

3522 atoms, 3586 bonds, 455 residues, 1 model selected  

> select up

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> color sel red

> select #21/X:548

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

> select up

28 atoms, 27 bonds, 4 residues, 1 model selected  

> select up

296 atoms, 302 bonds, 39 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

296 atoms, 302 bonds, 39 residues, 1 model selected  

> color sel red

> select #21/b:569

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

107 atoms, 106 bonds, 16 residues, 1 model selected  

> select up

296 atoms, 299 bonds, 43 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

296 atoms, 299 bonds, 43 residues, 1 model selected  

> color sel red

> select clear

> select #21/B:625

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

> select #21/B:666

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

45 atoms, 45 bonds, 5 residues, 1 model selected  

> select up

674 atoms, 683 bonds, 84 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

674 atoms, 683 bonds, 84 residues, 1 model selected  

> color sel red

> select #21/H:22

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

62 atoms, 61 bonds, 9 residues, 1 model selected  

> select up

1734 atoms, 1783 bonds, 227 residues, 1 model selected  

> color sel forest green

> select #21/L:19

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select up

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> show #!12 models

> color zone #12 near #21 distance 30

> volume #12 level 0.1

> volume #12 level 0.11

> volume #12 level 0.12

> color zone #12 near #21 distance 2

> color zone #12 near #21 distance 25

[Repeated 1 time(s)]

> select add #21

15702 atoms, 15946 bonds, 4 pseudobonds, 2138 residues, 2 models selected  

> hide #!12 models

> show #!12 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> volume #12 level 0.11

> color zone #12 near #21 distance 2

> color zone #12 near #21 distance 20

[Repeated 1 time(s)]

> color zone #12 near #21 distance 25

[Repeated 1 time(s)]

> color zone #12 near #21 distance 3

> color zone #12 near #21 distance 30

[Repeated 1 time(s)]

> select subtract #21

Nothing selected  

> select add #21

15702 atoms, 15946 bonds, 4 pseudobonds, 2138 residues, 2 models selected  

> hide #!12 models

> show #!12 models

> show #!17 models

> hide #!12 models

> show #!12 models

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 48  
shifted from previous position = 0.0681  
rotated from previous position = 0.418 degrees  
atoms outside contour = 618, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95974100 0.21021955 -0.18629263 360.69372189  
0.22838448 0.97012286 -0.08186667 0.88971904  
0.16351676 -0.12111714 -0.97907758 361.54098690  
Axis -0.11135741 -0.99244325 0.05153567  
Axis point 164.06818466 0.00000000 196.82105777  
Rotation angle (degrees) 169.84937905  
Shift along axis -22.41665958  
  

> color zone #12 near #21 distance 3

> color zone #12 near #21 distance 30

[Repeated 1 time(s)]

> hide #!17 models

> volume #12 level 0.139

> volume #12 level 0.1439

> volume #12 level 0.12

> color zone #12 near #21 distance 1

> color zone #12 near #21 distance 15

[Repeated 1 time(s)]

> color zone #12 near #21 distance 2

> color zone #12 near #21 distance 20

[Repeated 1 time(s)]

> color zone #12 near #21 distance 2

> color zone #12 near #21 distance 22

[Repeated 1 time(s)]

> volume #12 level 0.11

> hide #!12 models

> show #!12 models

> show #!21 models

> hide #!12 models

> color single #12

> show #!12 models

> show #!17 models

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 44  
shifted from previous position = 0.0153  
rotated from previous position = 0.0418 degrees  
atoms outside contour = 614, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95961963 0.21089946 -0.18614936 360.50801404  
0.22900220 0.97000330 -0.08155727 0.73751865  
0.16336511 -0.12089257 -0.97913064 361.53119730  
Axis -0.11168883 -0.99241299 0.05140100  
Axis point 163.99722730 0.00000000 196.79079982  
Rotation angle (degrees) 169.85771465  
Shift along axis -22.41357586  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 44  
shifted from previous position = 0.008  
rotated from previous position = 0.00824 degrees  
atoms outside contour = 615, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95960728 0.21084503 -0.18627461 360.54629056  
0.22897118 0.97000641 -0.08160739 0.75347645  
0.16348106 -0.12096256 -0.97910265 361.52223861  
Axis -0.11166828 -0.99241370 0.05143202  
Axis point 164.00449613 0.00000000 196.79966706  
Rotation angle (degrees) 169.85064877  
Shift along axis -22.41552400  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 80  
shifted from previous position = 0.0134  
rotated from previous position = 0.0214 degrees  
atoms outside contour = 610, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95958246 0.21110236 -0.18611097 360.45194872  
0.22916859 0.96998108 -0.08135395 0.67083132  
0.16335011 -0.12071661 -0.97915486 361.50604045  
Axis -0.11178297 -0.99240737 0.05130487  
Axis point 163.97647346 0.00000000 196.77157215  
Rotation angle (degrees) 169.85922264  
Shift along axis -22.41110365  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 80  
shifted from previous position = 0.0103  
rotated from previous position = 0.0196 degrees  
atoms outside contour = 614, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95964783 0.21079345 -0.18612404 360.52750241  
0.22888918 0.97003133 -0.08154107 0.75113892  
0.16335782 -0.12085249 -0.97913681 361.53376039  
Axis -0.11163224 -0.99242012 0.05138626  
Axis point 164.00789795 0.00000000 196.79160454  
Rotation angle (degrees) 169.85874481  
Shift along axis -22.41407191  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 48  
shifted from previous position = 0.0153  
rotated from previous position = 0.0314 degrees  
atoms outside contour = 610, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95957850 0.21129275 -0.18591521 360.37382819  
0.22936243 0.96992226 -0.08150871 0.67690037  
0.16310110 -0.12085597 -0.97917918 361.57720508  
Axis -0.11187996 -0.99239259 0.05137929  
Axis point 163.95425559 0.00000000 196.78353624  
Rotation angle (degrees) 169.87211260  
Shift along axis -22.41277795  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 48  
shifted from previous position = 0.0162  
rotated from previous position = 0.0343 degrees  
atoms outside contour = 612, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95958311 0.21089382 -0.18634390 360.54478483  
0.22900288 0.97001214 -0.08145010 0.71355509  
0.16357852 -0.12083143 -0.97910256 361.47471908  
Axis -0.11168940 -0.99241509 0.05135911  
Axis point 164.00037708 0.00000000 196.78248769  
Rotation angle (degrees) 169.84577334  
Shift along axis -22.41215583  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 96  
shifted from previous position = 0.00738  
rotated from previous position = 0.0176 degrees  
atoms outside contour = 612, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95957811 0.21110882 -0.18612605 360.45928970  
0.22918514 0.96997307 -0.08140276 0.67971066  
0.16335242 -0.12076963 -0.97914793 361.51745168  
Axis -0.11178913 -0.99240533 0.05133088  
Axis point 163.97821398 0.00000000 196.77870461  
Rotation angle (degrees) 169.85869128  
Shift along axis -22.41297101  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 64  
shifted from previous position = 0.00773  
rotated from previous position = 0.00523 degrees  
atoms outside contour = 612, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95956408 0.21119416 -0.18610155 360.43749216  
0.22926829 0.96995345 -0.08140241 0.67098548  
0.16331813 -0.12077801 -0.97915262 361.53320433  
Axis -0.11183218 -0.99240036 0.05133304  
Axis point 163.96968676 0.00000000 196.78275078  
Rotation angle (degrees) 169.86036429  
Shift along axis -22.41579832  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 44  
shifted from previous position = 0.0121  
rotated from previous position = 0.0387 degrees  
atoms outside contour = 614, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95964202 0.21059688 -0.18637636 360.62043575  
0.22873840 0.97005863 -0.08163941 0.79096944  
0.16360299 -0.12097604 -0.97908062 361.49727976  
Axis -0.11154580 -0.99242688 0.05144341  
Axis point 164.03051104 0.00000000 196.80159120  
Rotation angle (degrees) 169.84422573  
Shift along axis -22.41402439  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 84  
shifted from previous position = 0.00761  
rotated from previous position = 0.0264 degrees  
atoms outside contour = 613, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95958207 0.21101868 -0.18620782 360.49695973  
0.22912300 0.96997830 -0.08151524 0.71425710  
0.16341631 -0.12088506 -0.97912303 361.52773419  
Axis -0.11175106 -0.99240661 0.05138902  
Axis point 163.98776890 0.00000000 196.79320085  
Rotation angle (degrees) 169.85443304  
Shift along axis -22.41619638  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 72  
shifted from previous position = 0.0128  
rotated from previous position = 0.016 degrees  
atoms outside contour = 609, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95954580 0.21126698 -0.18611321 360.41658157  
0.22934204 0.96993667 -0.08139458 0.65677831  
0.16332204 -0.12078542 -0.97915106 361.52499098  
Axis -0.11186996 -0.99239610 0.05133319  
Axis point 163.95951785 0.00000000 196.77817913  
Rotation angle (degrees) 169.85986379  
Shift along axis -22.41334077  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 40  
shifted from previous position = 0.0101  
rotated from previous position = 0.0714 degrees  
atoms outside contour = 615, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95979460 0.21005947 -0.18619704 360.70208368  
0.22819673 0.97017411 -0.08178290 0.89463278  
0.16346428 -0.12098434 -0.97910276 361.53175294  
Axis -0.11126687 -0.99245631 0.05147965  
Axis point 164.08002323 0.00000000 196.80972123  
Rotation angle (degrees) 169.85385591  
Shift along axis -22.41054795  
  

> hide #!21 models

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 44  
shifted from previous position = 0.00678  
rotated from previous position = 0.0504 degrees  
atoms outside contour = 615, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95962794 0.21091572 -0.18608807 360.49719426  
0.22901518 0.96999812 -0.08158240 0.74174563  
0.16329807 -0.12090575 -0.97914020 361.54953831  
Axis -0.11169575 -0.99241172 0.05141049  
Axis point 163.99675182 0.00000000 196.79365817  
Rotation angle (degrees) 169.86146501  
Shift along axis -22.41468177  
  

> fitmap #17 inMap #12

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4017 atoms  
average map value = 0.3293, steps = 124  
shifted from previous position = 0.0125  
rotated from previous position = 0.00852 degrees  
atoms outside contour = 615, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.95962444 0.21102274 -0.18598477 360.44560145  
0.22910763 0.96997772 -0.08156540 0.72522072  
0.16318893 -0.12088268 -0.97916124 361.57201046  
Axis -0.11174590 -0.99240661 0.05140010  
Axis point 163.98072134 0.00000000 196.79239867  
Rotation angle (degrees) 169.86764198  
Shift along axis -22.41319629  
  

> combine #9, 10, 13, 14, 15, 17, 18, 19

Remapping chain ID 'C' in calf1 #13 to 'D'  
Remapping chain ID 'I' in calf1 #13 to 'K'  
Remapping chain ID 'J' in calf1 #13 to 'M'  
Remapping chain ID 'A' in propeller_thigh #14 to 'E'  
Remapping chain ID 'C' in propeller_thigh #14 to 'F'  
Remapping chain ID 'I' in propeller_thigh #14 to 'N'  
Remapping chain ID 'J' in propeller_thigh #14 to 'O'  
Remapping chain ID 'C' in calf2 #15 to 'G'  
Remapping chain ID 'F' in calf2 #15 to 'P'  
Remapping chain ID 'I' in calf2 #15 to 'Q'  
Remapping chain ID 'J' in calf2 #15 to 'R'  
Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S'  
Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T'  
Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U'  
Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V'  
Remapping chain ID 'C' in I-EGF3 #18 to 'W'  
Remapping chain ID 'E' in I-EGF3 #18 to 'X'  
Remapping chain ID 'I' in I-EGF3 #18 to 'Y'  
Remapping chain ID 'J' in I-EGF3 #18 to 'Z'  
Remapping chain ID 'C' in I-EGF4 #19 to 'a'  
Remapping chain ID 'D' in I-EGF4 #19 to 'b'  
Remapping chain ID 'I' in I-EGF4 #19 to 'c'  
Remapping chain ID 'J' in I-EGF4 #19 to 'd'  

> close #21

> hide #!12 models

Drag select of 55 residues  

> select #17/B:63

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

49 atoms, 48 bonds, 6 residues, 1 model selected  

> select up

548 atoms, 557 bonds, 74 residues, 1 model selected  

> select up

609 atoms, 618 bonds, 82 residues, 1 model selected  

> select up

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> select up

4017 atoms, 4076 bonds, 534 residues, 1 model selected  

> select up

31404 atoms, 31892 bonds, 4276 residues, 33 models selected  

> select up

31404 atoms, 31892 bonds, 4276 residues, 33 models selected  

> color (#!17,22 & sel) red

> select #22/E:459

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

> select up

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select up

31404 atoms, 31892 bonds, 4276 residues, 33 models selected  

> select down

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> color sel blue

> hide #!17 models

> select #22/S:99

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

> select up

75 atoms, 75 bonds, 9 residues, 1 model selected  

> select up

3455 atoms, 3519 bonds, 446 residues, 1 model selected  

> select up

3522 atoms, 3586 bonds, 455 residues, 1 model selected  

> select up

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select up

31404 atoms, 31892 bonds, 4276 residues, 33 models selected  

> color (#!22 & sel) red

> select #22/E:489

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

> select up

79 atoms, 79 bonds, 11 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select up

31404 atoms, 31892 bonds, 4276 residues, 33 models selected  

> select down

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> color sel blue

> select #22/A:631

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

> select up

83 atoms, 82 bonds, 11 residues, 1 model selected  

> select up

426 atoms, 432 bonds, 59 residues, 1 model selected  

> select up

475 atoms, 481 bonds, 65 residues, 1 model selected  

> select up

1011 atoms, 1021 bonds, 135 residues, 1 model selected  

> color sel blue

> select #22/P:949

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

102 atoms, 103 bonds, 12 residues, 1 model selected  

> select up

675 atoms, 694 bonds, 86 residues, 1 model selected  

> color sel blue

> select #22/P:827

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

42 atoms, 43 bonds, 5 residues, 1 model selected  

> select up

496 atoms, 513 bonds, 65 residues, 1 model selected  

> select up

514 atoms, 529 bonds, 68 residues, 1 model selected  

> select down

496 atoms, 513 bonds, 65 residues, 1 model selected  

> color sel cornflower blue

> color sel blue

> select #22/P:752

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

64 atoms, 64 bonds, 8 residues, 1 model selected  

> select up

142 atoms, 143 bonds, 20 residues, 1 model selected  

> color sel blue

> select #22/H:210

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

43 atoms, 43 bonds, 6 residues, 1 model selected  

> select up

1734 atoms, 1783 bonds, 227 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

1734 atoms, 1783 bonds, 227 residues, 1 model selected  

> color sel forest green

> select #22/L:19

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

23 atoms, 22 bonds, 3 residues, 1 model selected  

> select up

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> show #!12 models

> color zone #12 near #22 distance 22

> hide #!12 models

> show #!12 models

> hide #!22 models

> volume #12 level 0.1439

> volume #12 level 0.12

> volume #12 level 0.11

> color zone #12 near #22 distance 22

> color zone #12 near #22 distance 2

> color zone #12 near #22 distance 25

[Repeated 1 time(s)]

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> show #!14 models

> fitmap #14 inMap #12

Fit molecule propeller_thigh (#14) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 4655 atoms  
average map value = 0.3683, steps = 48  
shifted from previous position = 0.00438  
rotated from previous position = 0.0101 degrees  
atoms outside contour = 706, contour level = 0.11  
  
Position of propeller_thigh (#14) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
-0.94946112 0.24514462 -0.19602982 354.78067515  
0.26064686 0.96373629 -0.05723256 -1.63223903  
0.17489080 -0.10543465 -0.97892632 353.83996994  
Axis -0.12875844 -0.99081102 0.04140990  
Axis point 160.57782997 0.00000000 193.61078246  
Rotation angle (degrees) 169.21172439  
Shift along axis -29.41128727  
  

> close #22

> combine #9, 10, 13, 14, 15, 17, 18, 19

Remapping chain ID 'C' in calf1 #13 to 'D'  
Remapping chain ID 'I' in calf1 #13 to 'K'  
Remapping chain ID 'J' in calf1 #13 to 'M'  
Remapping chain ID 'A' in propeller_thigh #14 to 'E'  
Remapping chain ID 'C' in propeller_thigh #14 to 'F'  
Remapping chain ID 'I' in propeller_thigh #14 to 'N'  
Remapping chain ID 'J' in propeller_thigh #14 to 'O'  
Remapping chain ID 'C' in calf2 #15 to 'G'  
Remapping chain ID 'F' in calf2 #15 to 'P'  
Remapping chain ID 'I' in calf2 #15 to 'Q'  
Remapping chain ID 'J' in calf2 #15 to 'R'  
Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S'  
Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T'  
Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U'  
Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V'  
Remapping chain ID 'C' in I-EGF3 #18 to 'W'  
Remapping chain ID 'E' in I-EGF3 #18 to 'X'  
Remapping chain ID 'I' in I-EGF3 #18 to 'Y'  
Remapping chain ID 'J' in I-EGF3 #18 to 'Z'  
Remapping chain ID 'C' in I-EGF4 #19 to 'a'  
Remapping chain ID 'D' in I-EGF4 #19 to 'b'  
Remapping chain ID 'I' in I-EGF4 #19 to 'c'  
Remapping chain ID 'J' in I-EGF4 #19 to 'd'  

> hide #!12 models

> select #21/S:380

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

> select up

22 atoms, 22 bonds, 3 residues, 1 model selected  

> select up

3455 atoms, 3519 bonds, 446 residues, 1 model selected  

> select up

3522 atoms, 3586 bonds, 455 residues, 1 model selected  

> select up

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select up

31404 atoms, 31892 bonds, 4276 residues, 33 models selected  

> select up

31404 atoms, 31892 bonds, 4276 residues, 33 models selected  

> color (#!14,21 & sel) red

> select #14/A:460

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

> select up

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

4655 atoms, 4755 bonds, 622 residues, 1 model selected  

> color sel blue

> hide #!14 models

> select #21/E:458

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> color sel blue

> select #21/A:631

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

> select up

83 atoms, 82 bonds, 11 residues, 1 model selected  

> select up

426 atoms, 432 bonds, 59 residues, 1 model selected  

> select up

475 atoms, 481 bonds, 65 residues, 1 model selected  

> select up

1011 atoms, 1021 bonds, 135 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

1011 atoms, 1021 bonds, 135 residues, 1 model selected  

> color sel blue

> select #21/P:930

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

105 atoms, 109 bonds, 12 residues, 1 model selected  

> select up

675 atoms, 694 bonds, 86 residues, 1 model selected  

> select up

745 atoms, 766 bonds, 96 residues, 1 model selected  

> select up

1171 atoms, 1207 bonds, 151 residues, 1 model selected  

> select up

1181 atoms, 1216 bonds, 153 residues, 1 model selected  

> select down

1171 atoms, 1207 bonds, 151 residues, 1 model selected  

> color sel blue

> select clear

> select #21/P:752

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

64 atoms, 64 bonds, 8 residues, 1 model selected  

> select up

142 atoms, 143 bonds, 20 residues, 1 model selected  

> select up

173 atoms, 176 bonds, 24 residues, 1 model selected  

> select down

142 atoms, 143 bonds, 20 residues, 1 model selected  

> color sel blue

> select #21/H:207

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

43 atoms, 43 bonds, 6 residues, 1 model selected  

> select up

1734 atoms, 1783 bonds, 227 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

1734 atoms, 1783 bonds, 227 residues, 1 model selected  

> color sel forest green

> select clear

> select #21/L:122

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

> select up

45 atoms, 44 bonds, 6 residues, 1 model selected  

> select up

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> select #21/B:679

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

> select up

28 atoms, 28 bonds, 3 residues, 1 model selected  

> select up

674 atoms, 683 bonds, 84 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

674 atoms, 683 bonds, 84 residues, 1 model selected  

> color sel blue

> show #!12 models

> color zone #12 near #21 distance 25

> hide #!21 models

> show #!21 models

> hide #!12 models

> show #!12 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> volume #12 level 0.1

> show #!21 models

> color zone #12 near #21 distance 1

> color zone #12 near #21 distance 15

> color zone #12 near #21 distance 2

> color zone #12 near #21 distance 20

[Repeated 2 time(s)]

> color zone #12 near #21 distance 2

> color zone #12 near #21 distance 25

[Repeated 1 time(s)]

> hide #!21 models

> save
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation1.cxs
> includeMaps true

> show #!11 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!12 models

> hide #!11 models

> show #!11 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!11 models

> hide #!6 models

> show #!11 models

> show #!12 models

> hide #!11 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!12 models

> select #21/E:309

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

40 atoms, 39 bonds, 6 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark blue

> show #!12 models

> color zone #12 near #21 distance 25

[Repeated 1 time(s)]

> hide #!12 models

> select #21/E:458

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> color sel blue

> show #!12 models

> fitmap #21 inMap #12

Fit molecule combination (#21) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 15702 atoms  
average map value = 0.2298, steps = 2000  
shifted from previous position = 0.219  
rotated from previous position = 0.0977 degrees  
atoms outside contour = 5836, contour level = 0.1  
  
Position of combination (#21) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.71825256 0.55816695 -0.41540693 -18.37414359  
-0.68346231 0.45413509 -0.57152479 330.03831857  
-0.13035538 0.69441412 0.70766977 129.05569312  
Axis 0.70487855 -0.15871755 -0.69134287  
Axis point 0.00000000 137.69258986 403.03762522  
Rotation angle (degrees) 63.89428697  
Shift along axis -154.55614618  
  

> fitmap #21 inMap #12

Fit molecule combination (#21) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 15702 atoms  
average map value = 0.2304, steps = 184  
shifted from previous position = 0.356  
rotated from previous position = 0.222 degrees  
atoms outside contour = 5784, contour level = 0.1  
  
Position of combination (#21) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.71931590 0.55516676 -0.41758172 -18.45715539  
-0.68280504 0.45433929 -0.57214778 329.95179623  
-0.12791365 0.69668190 0.70588414 128.40160768  
Axis 0.70638833 -0.16126526 -0.68920900  
Axis point 0.00000000 138.18749460 401.28374388  
Rotation angle (degrees) 63.91081405  
Shift along axis -154.74322329  
  

> fitmap #21 inMap #12

Fit molecule combination (#21) to map
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) using 15702 atoms  
average map value = 0.2304, steps = 252  
shifted from previous position = 0.0272  
rotated from previous position = 0.0277 degrees  
atoms outside contour = 5780, contour level = 0.1  
  
Position of combination (#21) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.71928919 0.55489943 -0.41798288 -18.42114133  
-0.68289991 0.45429114 -0.57207278 329.97883918  
-0.12755693 0.69692624 0.70570748 128.30043184  
Axis 0.70643417 -0.16167610 -0.68906574  
Axis point 0.00000000 138.31627114 401.13032877  
Rotation angle (degrees) 63.91883695  
Shift along axis -154.77044903  
  

> color zone #12 near #21 distance 25

[Repeated 1 time(s)]

> hide #!21 models

> hide #!12 models

> show #!11 models

> volume #11 color #b2ffff7f

> volume #11 color #b2ffff91

> show #9 models

> show #!10 models

> show #!13 models

> show #!14 models

> show #!15 models

> show #!17 models

> show #!18 models

> show #!19 models

> fitmap #14 inMap #11

Fit molecule propeller_thigh (#14) to map
cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) using 4655 atoms  
average map value = 0.3795, steps = 104  
shifted from previous position = 0.368  
rotated from previous position = 1.22 degrees  
atoms outside contour = 788, contour level = 0.11  
  
Position of propeller_thigh (#14) relative to
cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.95535955 0.23579762 -0.17801013 353.39435096  
0.25000471 0.96627070 -0.06179453 0.37538213  
0.15743497 -0.10353937 -0.98208646 357.18725485  
Axis -0.12338459 -0.99147009 0.04199168  
Axis point 161.27504695 0.00000000 193.63149625  
Rotation angle (degrees) 170.26069577  
Shift along axis -28.97670604  
  

> fitmap #13 inMap #11

Fit molecule calf1 (#13) to map cryosparc_P91_J558_009_volume_map_sharp.mrc
(#11) using 1025 atoms  
average map value = 0.2012, steps = 172  
shifted from previous position = 1.1  
rotated from previous position = 19.9 degrees  
atoms outside contour = 171, contour level = 0.11  
  
Position of calf1 (#13) relative to
cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.48543806 0.42982238 0.76131636 99.53778763  
0.75489325 0.64532616 0.11700561 -84.52017329  
-0.44100574 0.63151156 -0.63773590 316.56695185  
Axis 0.38180056 0.89220980 0.24122605  
Axis point 134.55284379 0.00000000 151.32517876  
Rotation angle (degrees) 137.63982897  
Shift along axis 38.95805253  
  

> fitmap #15 inMap #11

Fit molecule calf2 (#15) to map cryosparc_P91_J558_009_volume_map_sharp.mrc
(#11) using 1327 atoms  
average map value = 0.1289, steps = 216  
shifted from previous position = 19.2  
rotated from previous position = 5.82 degrees  
atoms outside contour = 597, contour level = 0.11  
  
Position of calf2 (#15) relative to
cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.92993056 0.27975594 -0.23867502 360.83130959  
0.31017179 0.94536206 -0.10041925 -26.91312653  
0.19754143 -0.16741319 -0.96589347 359.49105011  
Axis -0.15144056 -0.98607224 0.06875536  
Axis point 162.05664276 0.00000000 199.26663712  
Rotation angle (degrees) 167.22112794  
Shift along axis -3.38927214  
  

> show #!21 models

> select add #21

15702 atoms, 15946 bonds, 4 pseudobonds, 2138 residues, 2 models selected  

> hide #!21 models

> select subtract #21

Nothing selected  

> select add #15

1327 atoms, 1350 bonds, 2 pseudobonds, 185 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15,-0.64782,-0.46146,0.60612,327.89,0.46645,-0.86934,-0.16333,310.66,0.6023,0.17692,0.77842,-30.526

> ui mousemode right "translate selected models"

> view matrix models
> #15,-0.64782,-0.46146,0.60612,315.32,0.46645,-0.86934,-0.16333,309.85,0.6023,0.17692,0.77842,-30.758

> view matrix models
> #15,-0.64782,-0.46146,0.60612,314.46,0.46645,-0.86934,-0.16333,312.88,0.6023,0.17692,0.77842,-32.019

> view matrix models
> #15,-0.64782,-0.46146,0.60612,312.54,0.46645,-0.86934,-0.16333,311.18,0.6023,0.17692,0.77842,-32.804

> fitmap #15 inMap #11

Fit molecule calf2 (#15) to map cryosparc_P91_J558_009_volume_map_sharp.mrc
(#11) using 1327 atoms  
average map value = 0.1065, steps = 448  
shifted from previous position = 4.66  
rotated from previous position = 11.9 degrees  
atoms outside contour = 742, contour level = 0.11  
  
Position of calf2 (#15) relative to
cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.78904840 0.56096248 -0.25044702 278.09886634  
0.58511067 0.81046619 -0.02810780 -64.43248189  
0.18721142 -0.16871764 -0.96772219 376.04023242  
Axis -0.30545770 -0.95075951 0.05245899  
Axis point 126.31916183 0.00000000 203.22808361  
Rotation angle (degrees) 166.69335882  
Shift along axis -3.96095490  
  

> fitmap #17 inMap #11

Fit molecule PSI_hybrid_BI_I-EGF-2 (#17) to map
cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) using 4017 atoms  
average map value = 0.3528, steps = 104  
shifted from previous position = 0.731  
rotated from previous position = 1.23 degrees  
atoms outside contour = 666, contour level = 0.11  
  
Position of PSI_hybrid_BI_I-EGF-2 (#17) relative to
cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.96384812 0.19986036 -0.17621758 361.25432493  
0.21467272 0.97422824 -0.06924558 -0.55078014  
0.15783670 -0.10457133 -0.98191263 360.04241355  
Axis -0.10506008 -0.99348969 0.04405250  
Axis point 165.27476559 0.00000000 195.30526299  
Rotation angle (degrees) 170.32137342  
Shift along axis -21.54544606  
  

> fitmap #18 inMap #11

Fit molecule I-EGF3 (#18) to map cryosparc_P91_J558_009_volume_map_sharp.mrc
(#11) using 310 atoms  
average map value = 0.2097, steps = 240  
shifted from previous position = 16.4  
rotated from previous position = 10.3 degrees  
atoms outside contour = 60, contour level = 0.11  
  
Position of I-EGF3 (#18) relative to
cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) coordinates:  
Matrix rotation and translation  
-0.95150098 -0.02774992 -0.30639162 421.86579542  
-0.04658311 0.99743605 0.05432623 19.58686766  
0.30409850 0.06596413 -0.95035405 295.37727295  
Axis 0.01905069 -0.99934311 -0.03082903  
Axis point 188.04663111 0.00000000 180.44188194  
Rotation angle (degrees) 162.21501936  
Shift along axis -20.64335842  
  

> select add #19

1637 atoms, 1649 bonds, 2 pseudobonds, 242 residues, 3 models selected  

> select subtract #15

310 atoms, 299 bonds, 57 residues, 1 model selected  

> view matrix models
> #19,-0.55276,-0.83257,-0.035838,425.27,0.53511,-0.32165,-0.78115,268.5,0.63884,-0.45097,0.62331,96.671

> hide #!11 models

> show #!11 models

> hide #!10 models

> show #!10 models

> select add #11

310 atoms, 299 bonds, 57 residues, 3 models selected  

> select subtract #19

2 models selected  

> view matrix models
> #11,0.19113,-0.77654,-0.60038,451.77,-0.69033,-0.54117,0.48019,338.33,-0.69779,0.32268,-0.6395,449.52

> fitmap #11 inMap #12

Fit map cryosparc_P91_J558_009_volume_map_sharp.mrc in map
cryosparc_P91_J556_008_volume_map_sharp.mrc using 389830 points  
correlation = 0.6822, correlation about mean = 0.3325, overlap = 2.291e+04  
steps = 116, shift = 4.96, angle = 2.16 degrees  
  
Position of cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.99930359 -0.03560552 -0.01116185 9.27365006  
0.03567823 0.99934294 0.00638341 -8.92862256  
0.01092723 -0.00677720 0.99991733 -5.51109902  
Axis -0.17367024 -0.29149227 0.94067577  
Axis point 288.81962012 234.35889751 0.00000000  
Rotation angle (degrees) 2.17143674  
Shift along axis -4.19208985  
  

> fitmap #11 inMap #12

Fit map cryosparc_P91_J558_009_volume_map_sharp.mrc in map
cryosparc_P91_J556_008_volume_map_sharp.mrc using 389830 points  
correlation = 0.6823, correlation about mean = 0.3329, overlap = 2.291e+04  
steps = 40, shift = 0.0161, angle = 0.00976 degrees  
  
Position of cryosparc_P91_J558_009_volume_map_sharp.mrc (#11) relative to
cryosparc_P91_J556_008_volume_map_sharp.mrc (#12) coordinates:  
Matrix rotation and translation  
0.99929895 -0.03575863 -0.01108736 9.29073645  
0.03583081 0.99933750 0.00638144 -8.96341199  
0.01085183 -0.00677424 0.99991817 -5.51184549  
Axis -0.17304946 -0.28858747 0.94168527  
Axis point 288.40170845 233.78310259 0.00000000  
Rotation angle (degrees) 2.17841411  
Shift along axis -4.21145226  
  

> select subtract #11

Nothing selected  

> hide #!11 models

> show #!11 models

> select add #10

3384 atoms, 3460 bonds, 454 residues, 1 model selected  

> view matrix models
> #10,0.22685,0.78149,-0.58122,42.25,-0.81155,-0.17826,-0.55643,452.34,-0.53845,0.59791,0.59378,84.971

> view matrix models
> #10,0.22685,0.78149,-0.58122,40.013,-0.81155,-0.17826,-0.55643,450.17,-0.53845,0.59791,0.59378,86.566

> view matrix models
> #10,0.22685,0.78149,-0.58122,42.621,-0.81155,-0.17826,-0.55643,451.64,-0.53845,0.59791,0.59378,82.587

> fitmap #10 inMap #11

Fit molecule Fab (#10) to map cryosparc_P91_J558_009_volume_map_sharp.mrc
(#11) using 3384 atoms  
average map value = 0.05102, steps = 164  
shifted from previous position = 7.29  
rotated from previous position = 10.5 degrees  
atoms outside contour = 2912, contour level = 0.11  
  
Position of Fab (#10) relative to cryosparc_P91_J558_009_volume_map_sharp.mrc
(#11) coordinates:  
Matrix rotation and translation  
0.93247940 -0.33984058 -0.12243588 147.60775306  
0.00582998 -0.32474496 0.94578365 155.97567602  
-0.36117610 -0.88263757 -0.30083673 549.39252651  
Axis -0.97460589 0.12725603 0.18425326  
Axis point 0.00000000 285.46900361 231.86978513  
Rotation angle (degrees) 110.27651223  
Shift along axis -22.78317865  
  

> view matrix models
> #10,0.36101,0.73569,-0.57308,37.183,-0.83434,-0.019722,-0.5509,426.19,-0.4166,0.67703,0.6067,43.741

> select add #9

4058 atoms, 4143 bonds, 538 residues, 2 models selected  

> select subtract #10

674 atoms, 683 bonds, 84 residues, 1 model selected  

> view matrix models
> #9,0.7454,-0.66392,-0.060001,113.26,-0.18864,-0.29641,0.93625,222.91,-0.63937,-0.68656,-0.34618,478.49

> view matrix models
> #9,0.7454,-0.66392,-0.060001,115.85,-0.18864,-0.29641,0.93625,224.9,-0.63937,-0.68656,-0.34618,482.77

> view matrix models
> #9,0.7454,-0.66392,-0.060001,119.49,-0.18864,-0.29641,0.93625,220.74,-0.63937,-0.68656,-0.34618,485.08

> view matrix models
> #9,0.7454,-0.66392,-0.060001,120.83,-0.18864,-0.29641,0.93625,221.87,-0.63937,-0.68656,-0.34618,485.58

> combine #9, 10, 13, 14, 15, 17, 18, 19

Remapping chain ID 'C' in calf1 #13 to 'D'  
Remapping chain ID 'I' in calf1 #13 to 'K'  
Remapping chain ID 'J' in calf1 #13 to 'M'  
Remapping chain ID 'A' in propeller_thigh #14 to 'E'  
Remapping chain ID 'C' in propeller_thigh #14 to 'F'  
Remapping chain ID 'I' in propeller_thigh #14 to 'N'  
Remapping chain ID 'J' in propeller_thigh #14 to 'O'  
Remapping chain ID 'C' in calf2 #15 to 'G'  
Remapping chain ID 'F' in calf2 #15 to 'P'  
Remapping chain ID 'I' in calf2 #15 to 'Q'  
Remapping chain ID 'J' in calf2 #15 to 'R'  
Remapping chain ID 'B' in PSI_hybrid_BI_I-EGF-2 #17 to 'S'  
Remapping chain ID 'C' in PSI_hybrid_BI_I-EGF-2 #17 to 'T'  
Remapping chain ID 'I' in PSI_hybrid_BI_I-EGF-2 #17 to 'U'  
Remapping chain ID 'J' in PSI_hybrid_BI_I-EGF-2 #17 to 'V'  
Remapping chain ID 'C' in I-EGF3 #18 to 'W'  
Remapping chain ID 'E' in I-EGF3 #18 to 'X'  
Remapping chain ID 'I' in I-EGF3 #18 to 'Y'  
Remapping chain ID 'J' in I-EGF3 #18 to 'Z'  
Remapping chain ID 'C' in I-EGF4 #19 to 'a'  
Remapping chain ID 'D' in I-EGF4 #19 to 'b'  
Remapping chain ID 'I' in I-EGF4 #19 to 'c'  
Remapping chain ID 'J' in I-EGF4 #19 to 'd'  

> volume #11 color #b2fffffb

> color zone #11 near #22 distance 15

> volume #11 color #b2fffffc

> hide #!11 models

> select #22/S:100

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

75 atoms, 75 bonds, 9 residues, 1 model selected  

> select up

3455 atoms, 3519 bonds, 446 residues, 1 model selected  

> select up

3522 atoms, 3586 bonds, 455 residues, 1 model selected  

> select up

4003 atoms, 4076 bonds, 520 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select up

47106 atoms, 47838 bonds, 6414 residues, 34 models selected  

> select down

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select up

47106 atoms, 47838 bonds, 6414 residues, 34 models selected  

> select down

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> color sel red

> select clear

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!10 models

> hide #9 models

> select #22/E:460

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

> select up

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> color sel blue

> select #22/A:704

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

> select up

75 atoms, 74 bonds, 11 residues, 1 model selected  

> select up

585 atoms, 589 bonds, 76 residues, 1 model selected  

> select up

602 atoms, 605 bonds, 79 residues, 1 model selected  

> select up

1011 atoms, 1021 bonds, 135 residues, 1 model selected  

> select down

602 atoms, 605 bonds, 79 residues, 1 model selected  

> select up

1011 atoms, 1021 bonds, 135 residues, 1 model selected  

> color sel blue

> select #22/P:928

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select up

105 atoms, 109 bonds, 12 residues, 1 model selected  

> select up

675 atoms, 694 bonds, 86 residues, 1 model selected  

> select up

745 atoms, 766 bonds, 96 residues, 1 model selected  

> color sel blue

> select #22/P:814

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

77 atoms, 78 bonds, 9 residues, 1 model selected  

> select up

496 atoms, 513 bonds, 65 residues, 1 model selected  

> select up

514 atoms, 529 bonds, 68 residues, 1 model selected  

> color sel blue

> select up

1313 atoms, 1350 bonds, 171 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

1313 atoms, 1350 bonds, 171 residues, 1 model selected  

> select down

514 atoms, 529 bonds, 68 residues, 1 model selected  

> select down

496 atoms, 513 bonds, 65 residues, 1 model selected  

> select down

77 atoms, 78 bonds, 9 residues, 1 model selected  

> select down

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select down

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select clear

> select #22/P:752

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

64 atoms, 64 bonds, 8 residues, 1 model selected  

> select up

142 atoms, 143 bonds, 20 residues, 1 model selected  

> color sel blue

> select #22/B:656

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

42 atoms, 42 bonds, 5 residues, 1 model selected  

> select up

674 atoms, 683 bonds, 84 residues, 1 model selected  

> select up

15702 atoms, 15946 bonds, 2138 residues, 1 model selected  

> select down

674 atoms, 683 bonds, 84 residues, 1 model selected  

> color sel blue

> select #22/H:21

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

62 atoms, 61 bonds, 9 residues, 1 model selected  

> select up

1734 atoms, 1783 bonds, 227 residues, 1 model selected  

> color sel forest green

> select #22/L:36

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

> select up

54 atoms, 57 bonds, 5 residues, 1 model selected  

> select up

1636 atoms, 1677 bonds, 213 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse

> show #!11 models

> color zone #11 near #22 distance 15

> color zone #11 near #22 distance 2

> color zone #11 near #22 distance 25

> hide #!22 models

> volume #11 level 0.1

> color zone #11 near #22 distance 20

[Repeated 1 time(s)]

> color zone #11 near #22 distance 22

[Repeated 1 time(s)]

> color zone #11 near #22 distance 23

[Repeated 1 time(s)]

> volume #11 level 0.105

> volume #11 level 0.11

> save
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation2.cxs
> includeMaps true

——— End of log from Fri Jan 31 04:00:50 2025 ———

opened ChimeraX session  

> save
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/conformation2_structure.pdb
> models #22

> hide #!11 models

> show #!11 models

> show #!22 models

> hide #!11 models

> style sel stick

Changed 1636 atom styles  

> show sel target ab

> cartoon hide sel

> show sel target ab

> select add #22

15702 atoms, 15946 bonds, 4 pseudobonds, 2138 residues, 2 models selected  

> show (#!22 & sel) target ab

Drag select of 24 atoms  

> delete sel

Drag select of 14 atoms  

> delete sel

Drag select of 4 atoms  

> delete sel

> select #22/T:9@CA

1 atom, 1 residue, 1 model selected  

> select add #22/T:8@CA

2 atoms, 2 residues, 1 model selected  

> select add #22/W:8@CA

3 atoms, 3 residues, 1 model selected  

> select add #22/W:7@CA

4 atoms, 4 residues, 1 model selected  

> select add #22/T:7@CA

5 atoms, 5 residues, 1 model selected  

> select add #22/T:10@CA

6 atoms, 6 residues, 1 model selected  

> delete sel

> select #22/W:9@CA

1 atom, 1 residue, 1 model selected  

> select #22/W:9@CA

1 atom, 1 residue, 1 model selected  

> select up

4 atoms, 4 residues, 1 model selected  

> select up

15654 atoms, 15946 bonds, 2090 residues, 1 model selected  

> select down

4 atoms, 4 residues, 1 model selected  

> color sel blue

> select #22/G:2@CA

1 atom, 1 residue, 1 model selected  

> color sel blue

> select #22/F:8@CA

1 atom, 1 residue, 1 model selected  

> color sel blue

> select #22/E:369@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

67 atoms, 67 bonds, 8 residues, 1 model selected  

> select up

4641 atoms, 4755 bonds, 608 residues, 1 model selected  

> select up

15654 atoms, 15946 bonds, 2090 residues, 1 model selected  

> select up

47058 atoms, 47838 bonds, 6366 residues, 34 models selected  

> select down

15654 atoms, 15946 bonds, 2090 residues, 1 model selected  
Drag select of 2 atoms  

> delete sel

> select #22/a:9@CA

1 atom, 1 residue, 1 model selected  

> select add #22/a:8@CA

2 atoms, 2 residues, 1 model selected  

> delete sel

> select #22/O:1@O

1 atom, 1 residue, 1 model selected  

> delete sel

> select add #22

15649 atoms, 15946 bonds, 4 pseudobonds, 2085 residues, 2 models selected  

> hide (#!22 & sel) target a

> cartoon (#!22 & sel)

> show #!21 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> show #!22 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!21 models

> hide #!21 models

> show #!11 models

> ui tool show "Color Zone"

> color zone #11 near #22 distance 25

> volume #11 level 0.1

> hide #!22 models

> volume #11 level 0.105

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> save
> /Users/walz/Desktop/aIIbb3_21C11/partially_extension/21C11_extended_new_conformation2.cxs

——— End of log from Mon Feb 3 13:09:17 2025 ———

opened ChimeraX session  

> open
> /Users/walz/Desktop/aIIbb3_21D/21D_extend_local_resolution_evaluation/cryosparc_P67_J376_011_volume_map_sharp.mrc

Opened cryosparc_P67_J376_011_volume_map_sharp.mrc as #23, grid size
400,400,400, pixel 0.86, shown at level 0.137, step 2, values float32  

> volume #23 step 1

> volume #23 level 0.3047

> surface dust #11 size 8.6

> surface dust #23 size 8.6

> surface dust #11 size 8.6

> surface dust #23 size 8.6

> select add #23

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 138, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 351, in _command_started_cb  
self.history_dialog.add(self._just_typed_command or cmd_text,  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 456, in add  
self._history.enqueue((item, typed))  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 171, in enqueue  
self.save()  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 201, in save  
self._history.save(self._queue)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/history.py", line 108, in save  
with SaveTextFile(self._filename) as f:  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 180, in __init__  
SaveFile.__init__(self, filename, open=open_text, critical=critical)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 74, in __init__  
self._f = open(self._tmp_filename)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
OSError: [Errno 28] No space left on device: '/Users/walz/Library/Application
Support/ChimeraX/commands.33359.tmp'  
  
Error processing trigger "command started":  
OSError: [Errno 28] No space left on device: '/Users/walz/Library/Application
Support/ChimeraX/commands.33359.tmp'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/safesave.py", line 179, in open_text  
return open(filename, 'w', newline=newline, encoding=encoding)  
  
See log for complete Python traceback.  
  
15649 atoms, 15946 bonds, 4 pseudobonds, 2085 residues, 4 models selected  




OpenGL version: 4.1 ATI-6.1.13
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

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

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac20,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 12 MB
      Hyper-Threading Technology: Enabled
      Memory: 8 GB
      System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
      OS Loader Version: 582~2132

Software:

    System Software Overview:

      System Version: macOS 15.1 (24B83)
      Kernel Version: Darwin 24.1.0
      Time since boot: 41 days, 23 hours, 15 minutes

Graphics/Displays:

    AMD Radeon Pro 5300:

      Chipset Model: AMD Radeon Pro 5300
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0047
      ROM Revision: 113-D3220I-231
      VBIOS Version: 113-D322A1XL-012
      Option ROM Version: 113-D322A1XL-012
      EFI Driver Version: 01.01.231
      Metal Support: Metal 3
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 5 months ago

Component: UnassignedInput/Output
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionCannot save command history: No space left on device

comment:2 by Eric Pettersen, 5 months ago

Resolution: nonchimerax
Status: acceptedclosed
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