![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17857 closed defect (nonchimerax)
Cannot save command history: No space left on device
| Reported by: | 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 , 6 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Cannot save command history: No space left on device |
comment:2 by , 6 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
