ArrayMemoryError in volume splitbyzone

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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

> open D:\\\phiKZ\\\tail-all\\\tail-all-8.cxs

Opened cryosparc_P10_J436_003_volume_map_sharp.mrc as #2, grid size
800,800,800, pixel 3.06, shown at level 0.7, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 0 as #5.1, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 1 as #5.2, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 2 as #5.3, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 3 as #5.4, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 4 as #5.5, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 5 as #5.6, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc as #3, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc as #4, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 0 as #7.1, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 1 as #7.2, grid size
300,300,300, pixel 1.36, shown at level 0.154, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 2 as #7.3, grid size
300,300,300, pixel 1.36, shown at level 0.133, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 3 as #7.4, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 4 as #7.5, grid size
300,300,300, pixel 1.36, shown at level 0.14, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 5 as #7.6, grid size
300,300,300, pixel 1.36, shown at level 0.218, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 6 as #7.7, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 7 as #7.8, grid size
300,300,300, pixel 1.36, shown at level 0.135, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 8 as #7.9, grid size
300,300,300, pixel 1.36, shown at level 0.173, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 9 as #7.10, grid size
300,300,300, pixel 1.36, shown at level 0.17, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 10 as #7.11, grid size
300,300,300, pixel 1.36, shown at level 0.127, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 11 as #7.12, grid size
300,300,300, pixel 1.36, shown at level 0.13, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 0 as #9.1, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 1 as #9.2, grid size
300,300,300, pixel 1.36, shown at level 0.213, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 2 as #9.3, grid size
300,300,300, pixel 1.36, shown at level 0.245, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 3 as #9.4, grid size
300,300,300, pixel 1.36, shown at level 0.251, step 1, values float32  
Log from Tue Feb 25 20:04:42 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open D:\\\phiKZ\\\tail-all\\\tail-all-5.cxs

Opened cryosparc_P10_J436_003_volume_map_sharp.mrc as #2, grid size
800,800,800, pixel 3.06, shown at level 0.7, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 0 as #5.1, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 1 as #5.2, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 2 as #5.3, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 3 as #5.4, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 4 as #5.5, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 5 as #5.6, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc as #3, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc as #4, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Log from Tue Feb 25 11:14:14 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open F:\\\1_study\\\phiKZ\\\tail-all\\\tail-al-5.cxs

Opened cryosparc_P10_J436_003_volume_map_sharp.mrc as #2, grid size
800,800,800, pixel 3.06, shown at level 0.7, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 0 as #5.1, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 1 as #5.2, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 2 as #5.3, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 3 as #5.4, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 4 as #5.5, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 5 as #5.6, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc as #3, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc as #4, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Log from Tue Feb 25 10:58:22 2025UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open F:\\\1_study\\\phiKZ\\\tail-all\\\tail-all-2.cxs

Opened cryosparc_P10_J436_003_volume_map_sharp.mrc as #2, grid size
800,800,800, pixel 3.06, shown at level 0.7, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc as #7, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 0 as #5.1, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 1 as #5.2, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 2 as #5.3, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 3 as #5.4, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 4 as #5.5, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 5 as #5.6, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Log from Mon Feb 24 20:21:26 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open F:\\\1_study\\\phiKZ\\\tail-all\\\PHIKZ034-necklace-tetramer-A.pdb

Chain information for PHIKZ034-necklace-tetramer-A.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open F:\\\1_study\\\phiKZ\\\tail-
> all\\\cryosparc_P10_J436_003_volume_map_sharp.mrc

Opened cryosparc_P10_J436_003_volume_map_sharp.mrc as #2, grid size
800,800,800, pixel 3.06, shown at step 1, values float32  

> open F:\\\1_study\\\phiKZ\\\tail-all\\\PHIKZ144-mat.pdb

Chain information for PHIKZ144-mat.pdb #3  
---  
Chain | Description  
E | No description available  
  

> open F:\\\1_study\\\phiKZ\\\tail-all\\\PHIKZ099-stoper.pdb

Chain information for PHIKZ099-stoper.pdb #4  
---  
Chain | Description  
C | No description available  
  

> open F:\\\1_study\\\phiKZ\\\tail-all\\\PHIKZ098-terminator.pdb

Chain information for PHIKZ098-terminator.pdb #5  
---  
Chain | Description  
C | No description available  
  

> open F:\\\1_study\\\phiKZ\\\tail-all\\\PHIKZ034-necklace-tetramer-B.pdb

Chain information for PHIKZ034-necklace-tetramer-B.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> volume #2 region 0,0,0,799,799,799 step 4

[Repeated 1 time(s)]

> volume #2 step 1

> volume #2 level 0.5

> volume #2 change image level -0.1486,0 level 0.3379,0.8 level 2.288,1

> volume #2 level 0.7

> open
> F:/1_study/phiKZ/EMDB&PDB-241227/2neck/cryosparc_P10_J236_006_volume_map_sharp.mrc

Opened cryosparc_P10_J236_006_volume_map_sharp.mrc as #7, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 2, values float32  

> select add #7

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.87806,-0.27266,0.39328,2.7593,-0.14252,0.63553,0.75881,-77.705,-0.45684,-0.72233,0.51917,538.98

> view matrix models
> #7,0.97288,-0.080462,0.21689,-34.392,-0.011891,0.91893,0.39425,-96.007,-0.23103,-0.38613,0.89304,235.72

> view matrix models
> #7,0.50816,-0.86088,0.025824,433.25,-0.81372,-0.47007,0.34189,635.86,-0.28219,-0.19475,-0.93938,777.21

> view matrix models
> #7,0.4959,-0.86111,-0.11214,481.54,-0.85522,-0.50669,0.10893,736.02,-0.15062,0.041883,-0.9877,672.52

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.4959,-0.86111,-0.11214,1180.7,-0.85522,-0.50669,0.10893,1680.1,-0.15062,0.041883,-0.9877,2462.5

> view matrix models
> #7,0.4959,-0.86111,-0.11214,1392.8,-0.85522,-0.50669,0.10893,1658.9,-0.15062,0.041883,-0.9877,2522.5

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.80966,-0.58062,-0.085654,1190.4,-0.58442,-0.81101,-0.026666,1713.3,-0.053984,0.071648,-0.99597,2483.9

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.80966,-0.58062,-0.085654,1185.2,-0.58442,-0.81101,-0.026666,1692.2,-0.053984,0.071648,-0.99597,2498.7

> view matrix models
> #7,0.80966,-0.58062,-0.085654,1189,-0.58442,-0.81101,-0.026666,1692.5,-0.053984,0.071648,-0.99597,2537

> view matrix models
> #7,0.80966,-0.58062,-0.085654,1191.6,-0.58442,-0.81101,-0.026666,1695.9,-0.053984,0.071648,-0.99597,2553

> view matrix models
> #7,0.80966,-0.58062,-0.085654,1192.3,-0.58442,-0.81101,-0.026666,1697.9,-0.053984,0.071648,-0.99597,2553.5

> view matrix models
> #7,0.80966,-0.58062,-0.085654,1190.1,-0.58442,-0.81101,-0.026666,1693.9,-0.053984,0.071648,-0.99597,2543.9

> view matrix models
> #7,0.80966,-0.58062,-0.085654,1240,-0.58442,-0.81101,-0.026666,1851,-0.053984,0.071648,-0.99597,2548.2

> view matrix models
> #7,0.80966,-0.58062,-0.085654,1183.8,-0.58442,-0.81101,-0.026666,1682.9,-0.053984,0.071648,-0.99597,2513.9

> ui mousemode right zone

> select subtract #7

Nothing selected  

> ui tool show "Fit in Map"

> fitmap #7 inMap #2

Fit map cryosparc_P10_J236_006_volume_map_sharp.mrc in map
cryosparc_P10_J436_003_volume_map_sharp.mrc using 138140 points  
correlation = 0.8596, correlation about mean = 0.07911, overlap = 2.729e+04  
steps = 172, shift = 12, angle = 9.72 degrees  
  
Position of cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.71990283 -0.69407487 0.00003125 1215.56392071  
-0.69407487 -0.71990283 -0.00005903 1685.53413605  
0.00006347 0.00002081 -1.00000000 2511.49045080  
Axis 0.92733560 -0.37423079 0.00002758  
Axis point 0.00000000 1088.01128928 1255.74886739  
Rotation angle (degrees) 179.99753371  
Shift along axis 496.52618386  
  

> volume #7 step 1

> ui tool show "Hide Dust"

> surface dust #7 size 8.16

> surface dust #7 size 10

> set bgColor white

> hide #!7 models

> select add #1

7552 atoms, 7720 bonds, 9 pseudobonds, 913 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel light salmon

> select subtract #1

Nothing selected  

> show #!2 models

> hide #!2 models

> select add #3

1511 atoms, 1542 bonds, 4 pseudobonds, 193 residues, 2 models selected  

> color sel lime

> color sel lime green

> select subtract #3

Nothing selected  

> select add #4

3603 atoms, 3697 bonds, 437 residues, 1 model selected  

> color sel gold

[Repeated 1 time(s)]

> select subtract #4

Nothing selected  

> select add #5

4431 atoms, 4557 bonds, 539 residues, 1 model selected  

> color sel cyan

> select subtract #5

Nothing selected  

> select add #6

7747 atoms, 7923 bonds, 8 pseudobonds, 935 residues, 2 models selected  

> color sel dodger blue

Drag select of 3017 residues, 21 pseudobonds  

> select add #6

24844 atoms, 7923 bonds, 21 pseudobonds, 3017 residues, 8 models selected  

> select add #5

24844 atoms, 12480 bonds, 21 pseudobonds, 3017 residues, 8 models selected  

> select subtract #6

17097 atoms, 4557 bonds, 13 pseudobonds, 2082 residues, 6 models selected  

> select subtract #5

12666 atoms, 13 pseudobonds, 1543 residues, 5 models selected  

> select add #4

12666 atoms, 3697 bonds, 13 pseudobonds, 1543 residues, 5 models selected  

> select add #3

12666 atoms, 5239 bonds, 13 pseudobonds, 1543 residues, 5 models selected  

> select subtract #4

9063 atoms, 1542 bonds, 13 pseudobonds, 1106 residues, 4 models selected  

> select subtract #3

7552 atoms, 9 pseudobonds, 913 residues, 2 models selected  

> select add #1

7552 atoms, 7720 bonds, 9 pseudobonds, 913 residues, 2 models selected  

> sym #1-6 C6 center 1088,1088,1088

Made 6 copies for PHIKZ034-necklace-tetramer-A.pdb, PHIKZ144-mat.pdb,
PHIKZ099-stoper.pdb, PHIKZ098-terminator.pdb, PHIKZ034-necklace-tetramer-B.pdb
symmetry C6  

> close #8

> show #!1 models

> show #!2 models

> show #!3 models

> show #4 models

> show #5 models

> show #!6 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select clear

Drag select of 3017 residues, 21 pseudobonds  

> show #!2 models

> hide #!2 models

> show #!7 models

> ui tool show "Color Zone"

> color zone #7 near sel distance 2.8

> lighting soft

> show #!2 models

> save F:/1_study/phiKZ/tail-all/tail-all.cxs

> hide #!2 models

> select clear

> show #!2 models

> hide #!2 models

> sym #1-6 C6 center 326.4,326.4,326.4

Made 6 copies for PHIKZ034-necklace-tetramer-A.pdb, PHIKZ144-mat.pdb,
PHIKZ099-stoper.pdb, PHIKZ098-terminator.pdb, PHIKZ034-necklace-tetramer-B.pdb
symmetry C6  

> hide #!7 models

> close #8

> show #!7 models

> open F:/1_study/phiKZ/EMDB&PDB-241227/2neck/PHIKZ034-necklace-tetramer-A-
> coot-7.pdb F:/1_study/phiKZ/EMDB&PDB-241227/2neck/PHIKZ034-necklace-
> tetramer-B-coot-1.pdb
> F:/1_study/phiKZ/EMDB&PDB-241227/2neck/PHIKZ098-terminator-coot-4.pdb
> F:/1_study/phiKZ/EMDB&PDB-241227/2neck/PHIKZ099-stoper-coot-2.pdb
> F:/1_study/phiKZ/EMDB&PDB-241227/2neck/PHIKZ144-mat-coot-1.pdb

Chain information for PHIKZ034-necklace-tetramer-A-coot-7.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for PHIKZ034-necklace-tetramer-B-coot-1.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  
Chain information for PHIKZ098-terminator-coot-4.pdb #10  
---  
Chain | Description  
C | No description available  
  
Chain information for PHIKZ099-stoper-coot-2.pdb #11  
---  
Chain | Description  
C | No description available  
  
Chain information for PHIKZ144-mat-coot-1.pdb #12  
---  
Chain | Description  
E | No description available  
  

> sym #8-12 C6 center 326.4,326.4,326.4

Made 6 copies for PHIKZ034-necklace-tetramer-A-coot-7.pdb, PHIKZ034-necklace-
tetramer-B-coot-1.pdb, PHIKZ098-terminator-coot-4.pdb, PHIKZ099-stoper-
coot-2.pdb, PHIKZ144-mat-coot-1.pdb symmetry C6  

> select add #13

149064 atoms, 152634 bonds, 126 pseudobonds, 18102 residues, 55 models
selected  

> ui mousemode right "translate selected models"

> view matrix models #13,1,0,0,432.37,0,1,0,150.09,0,0,1,836.09

> view matrix models #13,1,0,0,857.67,0,1,0,448.81,0,0,1,1422.6

> view matrix models #13,1,0,0,1040.5,0,1,0,640.19,0,0,1,1576.6

> lighting simple

> graphics silhouettes true

> graphics silhouettes false

> view matrix models #13,1,0,0,1051.5,0,1,0,647.99,0,0,1,1591.6

> view matrix models #13,1,0,0,1049.9,0,1,0,465.05,0,0,1,1873.1

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.076664,0.60075,0.79575,859.29,0.68797,0.5458,-0.47833,566.91,-0.72168,0.58412,-0.37145,2418.8

> view matrix models
> #13,-0.3031,0.95226,0.036432,1146.7,0.95101,0.30471,-0.052336,403.58,-0.060939,0.018783,-0.99796,2615.2

> view matrix models
> #13,-0.35076,0.89554,-0.27381,1296.8,0.90309,0.40084,0.15414,310.42,0.24779,-0.19321,-0.94935,2565.8

> ui mousemode right "translate selected models"

> view matrix models
> #13,-0.35076,0.89554,-0.27381,1380.4,0.90309,0.40084,0.15414,588.23,0.24779,-0.19321,-0.94935,2339.1

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.33235,0.93535,-0.12107,1306.2,0.94263,0.3337,-0.0095374,658.53,0.031479,-0.11729,-0.9926,2399.9

> ui mousemode right "translate selected models"

> view matrix models
> #13,-0.33235,0.93535,-0.12107,1128.8,0.94263,0.3337,-0.0095374,852.01,0.031479,-0.11729,-0.9926,2505.4

> view matrix models
> #13,-0.33235,0.93535,-0.12107,1083.8,0.94263,0.3337,-0.0095374,822.28,0.031479,-0.11729,-0.9926,2560.6

> view matrix models
> #13,-0.33235,0.93535,-0.12107,1090.6,0.94263,0.3337,-0.0095374,812.82,0.031479,-0.11729,-0.9926,2542.7

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.23576,0.96527,-0.11259,892.49,0.96874,-0.22423,0.10611,943.94,0.077179,-0.13409,-0.98796,2531.5

> view matrix models
> #13,0.22747,0.96701,-0.11466,895.4,0.96992,-0.21451,0.11508,937,0.086692,-0.13739,-0.98672,2529

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.22747,0.96701,-0.11466,888.5,0.96992,-0.21451,0.11508,945.15,0.086692,-0.13739,-0.98672,2536

> view matrix models
> #13,0.22747,0.96701,-0.11466,882.25,0.96992,-0.21451,0.11508,935.4,0.086692,-0.13739,-0.98672,2530.7

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.2409,0.95497,-0.17321,903.68,0.96632,-0.21936,0.13453,930.75,0.090477,-0.19978,-0.97565,2545.8

> transparency
> (#13.1.3-4#13.2.3-4#13.3.3-4#13.4.3-4#13.5.3-4#13.6.3-4#!13.1.1-2,5#!13.2.1-2,5#!13.3.1-2,5#!13.4.1-2,5#!13.5.1-2,5#!13.6.1-2,5
> & sel) 20

> view matrix models
> #13,0.24093,0.96053,-0.13909,889.08,0.96267,-0.21828,0.16008,922.02,0.1234,-0.17247,-0.97725,2526.7

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.24093,0.96053,-0.13909,884.98,0.96267,-0.21828,0.16008,916.86,0.1234,-0.17247,-0.97725,2545.6

> view matrix models
> #13,0.24093,0.96053,-0.13909,900.94,0.96267,-0.21828,0.16008,918.11,0.1234,-0.17247,-0.97725,2520.3

> hide #!7 models

> show #!1 models

> show #!3 models

> show #4 models

> show #5 models

> show #!6 models

> show #!7 models

> hide #!7 models

> view matrix models
> #13,0.24093,0.96053,-0.13909,886.51,0.96267,-0.21828,0.16008,925.19,0.1234,-0.17247,-0.97725,2522.4

> view matrix models
> #13,0.24093,0.96053,-0.13909,886.02,0.96267,-0.21828,0.16008,923.15,0.1234,-0.17247,-0.97725,2518.2

> view matrix models
> #13,0.24093,0.96053,-0.13909,887.88,0.96267,-0.21828,0.16008,931.66,0.1234,-0.17247,-0.97725,2515.4

> view matrix models
> #13,0.24093,0.96053,-0.13909,882.67,0.96267,-0.21828,0.16008,930.23,0.1234,-0.17247,-0.97725,2500.6

> view matrix models
> #13,0.24093,0.96053,-0.13909,877.42,0.96267,-0.21828,0.16008,925.52,0.1234,-0.17247,-0.97725,2505.3

> view matrix models
> #13,0.24093,0.96053,-0.13909,867.14,0.96267,-0.21828,0.16008,929.29,0.1234,-0.17247,-0.97725,2506.1

> show #!7 models

> hide #!3 models

> hide #!1 models

> hide #4 models

> hide #5 models

> hide #!6 models

> ui tool show "Fit in Map"

> fitmap sel inMap #2

Fit molecules PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.1.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.1.2), PHIKZ098-terminator-
coot-4.pdb (#13.1.3), PHIKZ099-stoper-coot-2.pdb (#13.1.4), PHIKZ144-mat-
coot-1.pdb (#13.1.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.2.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.2.2), PHIKZ098-terminator-
coot-4.pdb (#13.2.3), PHIKZ099-stoper-coot-2.pdb (#13.2.4), PHIKZ144-mat-
coot-1.pdb (#13.2.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.3.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.3.2), PHIKZ098-terminator-
coot-4.pdb (#13.3.3), PHIKZ099-stoper-coot-2.pdb (#13.3.4), PHIKZ144-mat-
coot-1.pdb (#13.3.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.4.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.4.2), PHIKZ098-terminator-
coot-4.pdb (#13.4.3), PHIKZ099-stoper-coot-2.pdb (#13.4.4), PHIKZ144-mat-
coot-1.pdb (#13.4.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.5.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.5.2), PHIKZ098-terminator-
coot-4.pdb (#13.5.3), PHIKZ099-stoper-coot-2.pdb (#13.5.4), PHIKZ144-mat-
coot-1.pdb (#13.5.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.6.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.6.2), PHIKZ098-terminator-
coot-4.pdb (#13.6.3), PHIKZ099-stoper-coot-2.pdb (#13.6.4), PHIKZ144-mat-
coot-1.pdb (#13.6.5) to map cryosparc_P10_J436_003_volume_map_sharp.mrc (#2)
using 149064 atoms  
average map value = 0.4231, steps = 92  
shifted from previous position = 21.6  
rotated from previous position = 12.2 degrees  
atoms outside contour = 141199, contour level = 0.7  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.1.1) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 -0.12321773 45.52596121  
0.01860505 0.98483964 0.17246664 -50.14400721  
0.12183790 -0.17344416 0.97727818 8.33463609  
Axis -0.81542066 -0.57767328 0.03718518  
Axis point 0.00000000 8.11085495 317.73921020  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603138  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.1.2) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 -0.12321773 45.52596121  
0.01860505 0.98483964 0.17246664 -50.14400721  
0.12183790 -0.17344416 0.97727818 8.33463609  
Axis -0.81542066 -0.57767328 0.03718518  
Axis point 0.00000000 8.11085495 317.73921020  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603138  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.1.3) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 -0.12321773 45.52596121  
0.01860505 0.98483964 0.17246664 -50.14400721  
0.12183790 -0.17344416 0.97727818 8.33463609  
Axis -0.81542066 -0.57767328 0.03718518  
Axis point 0.00000000 8.11085495 317.73921020  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603138  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.1.4) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 -0.12321773 45.52596121  
0.01860505 0.98483964 0.17246664 -50.14400721  
0.12183790 -0.17344416 0.97727818 8.33463609  
Axis -0.81542066 -0.57767328 0.03718518  
Axis point 0.00000000 8.11085495 317.73921020  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603138  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.1.5) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 -0.12321773 45.52596121  
0.01860505 0.98483964 0.17246664 -50.14400721  
0.12183790 -0.17344416 0.97727818 8.33463609  
Axis -0.81542066 -0.57767328 0.03718518  
Axis point 0.00000000 8.11085495 317.73921020  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603138  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.2.1) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 0.08775162 -13.77920978  
-0.00073492 0.98120969 0.19294300 -56.20839549  
-0.08928810 -0.19223680 0.97727818 83.38007724  
Axis -0.90799006 0.41733837 0.03718518  
Axis point 0.00000000 398.24247065 313.13415666  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603147  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.2.2) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 0.08775162 -13.77920978  
-0.00073492 0.98120969 0.19294300 -56.20839549  
-0.08928810 -0.19223680 0.97727818 83.38007724  
Axis -0.90799006 0.41733837 0.03718518  
Axis point 0.00000000 398.24247065 313.13415666  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603147  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.2.3) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 0.08775162 -13.77920978  
-0.00073492 0.98120969 0.19294300 -56.20839549  
-0.08928810 -0.19223680 0.97727818 83.38007724  
Axis -0.90799006 0.41733837 0.03718518  
Axis point 0.00000000 398.24247065 313.13415666  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603147  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.2.4) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 0.08775162 -13.77920978  
-0.00073492 0.98120969 0.19294300 -56.20839549  
-0.08928810 -0.19223680 0.97727818 83.38007724  
Axis -0.90799006 0.41733837 0.03718518  
Axis point 0.00000000 398.24247065 313.13415666  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603147  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.2.5) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 0.08775162 -13.77920978  
-0.00073492 0.98120969 0.19294300 -56.20839549  
-0.08928810 -0.19223680 0.97727818 83.38007724  
Axis -0.90799006 0.41733837 0.03718518  
Axis point 0.00000000 398.24247065 313.13415666  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603147  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.3.1) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 0.21096935 -53.81145918  
0.00579144 0.99977356 0.02047637 -15.37818329  
-0.21112600 -0.01879264 0.97727818 66.53579451  
Axis -0.09256940 0.99501164 0.03718518  
Axis point 285.42325358 0.00000000 289.02977739  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603144  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.3.2) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 0.21096935 -53.81145918  
0.00579144 0.99977356 0.02047637 -15.37818329  
-0.21112600 -0.01879264 0.97727818 66.53579451  
Axis -0.09256940 0.99501164 0.03718518  
Axis point 285.42325358 0.00000000 289.02977739  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603144  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.3.3) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 0.21096935 -53.81145918  
0.00579144 0.99977356 0.02047637 -15.37818329  
-0.21112600 -0.01879264 0.97727818 66.53579451  
Axis -0.09256940 0.99501164 0.03718518  
Axis point 285.42325358 0.00000000 289.02977739  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603144  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.3.4) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 0.21096935 -53.81145918  
0.00579144 0.99977356 0.02047637 -15.37818329  
-0.21112600 -0.01879264 0.97727818 66.53579451  
Axis -0.09256940 0.99501164 0.03718518  
Axis point 285.42325358 0.00000000 289.02977739  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603144  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.3.5) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 0.21096935 -53.81145918  
0.00579144 0.99977356 0.02047637 -15.37818329  
-0.21112600 -0.01879264 0.97727818 66.53579451  
Axis -0.09256940 0.99501164 0.03718518  
Axis point 285.42325358 0.00000000 289.02977739  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603144  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.4.1) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 0.12321773 -42.39662816  
0.01860505 0.98483964 -0.17246664 47.89531832  
-0.12183790 0.17344416 0.97727818 -25.35392936  
Axis 0.81542066 0.57767328 0.03718518  
Axis point 0.00000000 182.22218168 287.96993503  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603131  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.4.2) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 0.12321773 -42.39662816  
0.01860505 0.98483964 -0.17246664 47.89531832  
-0.12183790 0.17344416 0.97727818 -25.35392936  
Axis 0.81542066 0.57767328 0.03718518  
Axis point 0.00000000 182.22218168 287.96993503  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603131  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.4.3) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 0.12321773 -42.39662816  
0.01860505 0.98483964 -0.17246664 47.89531832  
-0.12183790 0.17344416 0.97727818 -25.35392936  
Axis 0.81542066 0.57767328 0.03718518  
Axis point 0.00000000 182.22218168 287.96993503  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603131  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.4.4) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 0.12321773 -42.39662816  
0.01860505 0.98483964 -0.17246664 47.89531832  
-0.12183790 0.17344416 0.97727818 -25.35392936  
Axis 0.81542066 0.57767328 0.03718518  
Axis point 0.00000000 182.22218168 287.96993503  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603131  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.4.5) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99237562 0.00283067 0.12321773 -42.39662816  
0.01860505 0.98483964 -0.17246664 47.89531832  
-0.12183790 0.17344416 0.97727818 -25.35392936  
Axis 0.81542066 0.57767328 0.03718518  
Axis point 0.00000000 182.22218168 287.96993503  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603131  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.5.1) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 -0.08775162 27.16404201  
-0.00073492 0.98120969 -0.19294300 68.95446323  
0.08928810 0.19223680 0.97727818 -100.39937051  
Axis 0.90799006 -0.41733837 0.03718518  
Axis point 0.00000000 554.60318275 286.39985416  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603122  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.5.2) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 -0.08775162 27.16404201  
-0.00073492 0.98120969 -0.19294300 68.95446323  
0.08928810 0.19223680 0.97727818 -100.39937051  
Axis 0.90799006 -0.41733837 0.03718518  
Axis point 0.00000000 554.60318275 286.39985416  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603122  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.5.3) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 -0.08775162 27.16404201  
-0.00073492 0.98120969 -0.19294300 68.95446323  
0.08928810 0.19223680 0.97727818 -100.39937051  
Axis 0.90799006 -0.41733837 0.03718518  
Axis point 0.00000000 554.60318275 286.39985416  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603122  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.5.4) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 -0.08775162 27.16404201  
-0.00073492 0.98120969 -0.19294300 68.95446323  
0.08928810 0.19223680 0.97727818 -100.39937051  
Axis 0.90799006 -0.41733837 0.03718518  
Axis point 0.00000000 554.60318275 286.39985416  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603122  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.5.5) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99600557 -0.01650930 -0.08775162 27.16404201  
-0.00073492 0.98120969 -0.19294300 68.95446323  
0.08928810 0.19223680 0.97727818 -100.39937051  
Axis 0.90799006 -0.41733837 0.03718518  
Axis point 0.00000000 554.60318275 286.39985416  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603122  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.6.1) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 -0.21096935 75.05438198  
0.00579144 0.99977356 -0.02047637 11.74534990  
0.21112600 0.01879264 0.97727818 -83.55508779  
Axis 0.09256940 -0.99501164 0.03718518  
Axis point 428.10899362 0.00000000 313.42595841  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603125  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.6.2) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 -0.21096935 75.05438198  
0.00579144 0.99977356 -0.02047637 11.74534990  
0.21112600 0.01879264 0.97727818 -83.55508779  
Axis 0.09256940 -0.99501164 0.03718518  
Axis point 428.10899362 0.00000000 313.42595841  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603125  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.6.3) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 -0.21096935 75.05438198  
0.00579144 0.99977356 -0.02047637 11.74534990  
0.21112600 0.01879264 0.97727818 -83.55508779  
Axis 0.09256940 -0.99501164 0.03718518  
Axis point 428.10899362 0.00000000 313.42595841  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603125  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.6.4) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 -0.21096935 75.05438198  
0.00579144 0.99977356 -0.02047637 11.74534990  
0.21112600 0.01879264 0.97727818 -83.55508779  
Axis 0.09256940 -0.99501164 0.03718518  
Axis point 428.10899362 0.00000000 313.42595841  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603125  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.6.5) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.97744170 -0.00998294 -0.21096935 75.05438198  
0.00579144 0.99977356 -0.02047637 11.74534990  
0.21112600 0.01879264 0.97727818 -83.55508779  
Axis 0.09256940 -0.99501164 0.03718518  
Axis point 428.10899362 0.00000000 313.42595841  
Rotation angle (degrees) 12.24578235  
Shift along axis -7.84603125  
  

> fitmap sel inMap #7

Fit molecules PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.1.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.1.2), PHIKZ098-terminator-
coot-4.pdb (#13.1.3), PHIKZ099-stoper-coot-2.pdb (#13.1.4), PHIKZ144-mat-
coot-1.pdb (#13.1.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.2.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.2.2), PHIKZ098-terminator-
coot-4.pdb (#13.2.3), PHIKZ099-stoper-coot-2.pdb (#13.2.4), PHIKZ144-mat-
coot-1.pdb (#13.2.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.3.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.3.2), PHIKZ098-terminator-
coot-4.pdb (#13.3.3), PHIKZ099-stoper-coot-2.pdb (#13.3.4), PHIKZ144-mat-
coot-1.pdb (#13.3.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.4.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.4.2), PHIKZ098-terminator-
coot-4.pdb (#13.4.3), PHIKZ099-stoper-coot-2.pdb (#13.4.4), PHIKZ144-mat-
coot-1.pdb (#13.4.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.5.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.5.2), PHIKZ098-terminator-
coot-4.pdb (#13.5.3), PHIKZ099-stoper-coot-2.pdb (#13.5.4), PHIKZ144-mat-
coot-1.pdb (#13.5.5), PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.6.1),
PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.6.2), PHIKZ098-terminator-
coot-4.pdb (#13.6.3), PHIKZ099-stoper-coot-2.pdb (#13.6.4), PHIKZ144-mat-
coot-1.pdb (#13.6.5) to map cryosparc_P10_J236_006_volume_map_sharp.mrc (#7)
using 149064 atoms  
average map value = 0.3758, steps = 52  
shifted from previous position = 0.711  
rotated from previous position = 0.0734 degrees  
atoms outside contour = 32005, contour level = 0.23107  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.1.1) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70061043 -0.68240891 -0.20847803 362.71647717  
-0.70308416 -0.71006116 -0.03854617 2061.48971370  
-0.12172790 0.17358345 -0.97726716 2502.42509525  
Axis 0.92184950 -0.37698913 -0.08984819  
Axis point 0.00000000 1028.44660486 1325.54736186  
Rotation angle (degrees) 173.39311428  
Shift along axis -667.62759272  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.1.2) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70061043 -0.68240891 -0.20847803 362.71647717  
-0.70308416 -0.71006116 -0.03854617 2061.48971370  
-0.12172790 0.17358345 -0.97726716 2502.42509525  
Axis 0.92184950 -0.37698913 -0.08984819  
Axis point 0.00000000 1028.44660486 1325.54736186  
Rotation angle (degrees) 173.39311428  
Shift along axis -667.62759272  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.1.3) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70061043 -0.68240891 -0.20847803 362.71647717  
-0.70308416 -0.71006116 -0.03854617 2061.48971370  
-0.12172790 0.17358345 -0.97726716 2502.42509525  
Axis 0.92184950 -0.37698913 -0.08984819  
Axis point 0.00000000 1028.44660486 1325.54736186  
Rotation angle (degrees) 173.39311428  
Shift along axis -667.62759272  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.1.4) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70061043 -0.68240891 -0.20847803 362.71647717  
-0.70308416 -0.71006116 -0.03854617 2061.48971370  
-0.12172790 0.17358345 -0.97726716 2502.42509525  
Axis 0.92184950 -0.37698913 -0.08984819  
Axis point 0.00000000 1028.44660486 1325.54736186  
Rotation angle (degrees) 173.39311428  
Shift along axis -667.62759272  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.1.5) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70061043 -0.68240891 -0.20847803 362.71647717  
-0.70308416 -0.71006116 -0.03854617 2061.48971370  
-0.12172790 0.17358345 -0.97726716 2502.42509525  
Axis 0.92184950 -0.37698913 -0.08984819  
Axis point 0.00000000 1028.44660486 1325.54736186  
Rotation angle (degrees) 173.39311428  
Shift along axis -667.62759272  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.2.1) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71664667 -0.69383262 -0.07080844 324.34599013  
-0.69166602 -0.69401191 -0.19986390 2106.97500581  
0.08953020 0.19220759 -0.97726178 2427.39032581  
Axis 0.92557972 -0.37851818 0.00511479  
Axis point 0.00000000 979.20860078 1324.09469355  
Rotation angle (degrees) 167.77227161  
Shift along axis -484.90469922  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.2.2) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71664667 -0.69383262 -0.07080844 324.34599013  
-0.69166602 -0.69401191 -0.19986390 2106.97500581  
0.08953020 0.19220759 -0.97726178 2427.39032581  
Axis 0.92557972 -0.37851818 0.00511479  
Axis point 0.00000000 979.20860078 1324.09469355  
Rotation angle (degrees) 167.77227161  
Shift along axis -484.90469922  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.2.3) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71664667 -0.69383262 -0.07080844 324.34599013  
-0.69166602 -0.69401191 -0.19986390 2106.97500581  
0.08953020 0.19220759 -0.97726178 2427.39032581  
Axis 0.92557972 -0.37851818 0.00511479  
Axis point 0.00000000 979.20860078 1324.09469355  
Rotation angle (degrees) 167.77227161  
Shift along axis -484.90469922  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.2.4) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71664667 -0.69383262 -0.07080844 324.34599013  
-0.69166602 -0.69401191 -0.19986390 2106.97500581  
0.08953020 0.19220759 -0.97726178 2427.39032581  
Axis 0.92557972 -0.37851818 0.00511479  
Axis point 0.00000000 979.20860078 1324.09469355  
Rotation angle (degrees) 167.77227161  
Shift along axis -484.90469922  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.2.5) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71664667 -0.69383262 -0.07080844 324.34599013  
-0.69166602 -0.69401191 -0.19986390 2106.97500581  
0.08953020 0.19220759 -0.97726178 2427.39032581  
Axis 0.92557972 -0.37851818 0.00511479  
Axis point 0.00000000 979.20860078 1324.09469355  
Rotation angle (degrees) 167.77227161  
Shift along axis -484.90469922  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.3.1) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69872192 -0.70200974 0.13773162 267.27751466  
-0.68348042 -0.71192532 -0.16129740 2105.44949526  
0.21128697 0.01856517 -0.97724774 2444.32154013  
Axis 0.92141223 -0.37681439 0.09492325  
Axis point 0.00000000 1041.69861244 1261.13084776  
Rotation angle (degrees) 174.39892490  
Shift along axis -315.06796238  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.3.2) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69872192 -0.70200974 0.13773162 267.27751466  
-0.68348042 -0.71192532 -0.16129740 2105.44949526  
0.21128697 0.01856517 -0.97724774 2444.32154013  
Axis 0.92141223 -0.37681439 0.09492325  
Axis point 0.00000000 1041.69861244 1261.13084776  
Rotation angle (degrees) 174.39892490  
Shift along axis -315.06796238  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.3.3) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69872192 -0.70200974 0.13773162 267.27751466  
-0.68348042 -0.71192532 -0.16129740 2105.44949526  
0.21128697 0.01856517 -0.97724774 2444.32154013  
Axis 0.92141223 -0.37681439 0.09492325  
Axis point 0.00000000 1041.69861244 1261.13084776  
Rotation angle (degrees) 174.39892490  
Shift along axis -315.06796238  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.3.4) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69872192 -0.70200974 0.13773162 267.27751466  
-0.68348042 -0.71192532 -0.16129740 2105.44949526  
0.21128697 0.01856517 -0.97724774 2444.32154013  
Axis 0.92141223 -0.37681439 0.09492325  
Axis point 0.00000000 1041.69861244 1261.13084776  
Rotation angle (degrees) 174.39892490  
Shift along axis -315.06796238  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.3.5) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69872192 -0.70200974 0.13773162 267.27751466  
-0.68348042 -0.71192532 -0.16129740 2105.44949526  
0.21128697 0.01856517 -0.97724774 2444.32154013  
Axis 0.92141223 -0.37681439 0.09492325  
Axis point 0.00000000 1041.69861244 1261.13084776  
Rotation angle (degrees) 174.39892490  
Shift along axis -315.06796238  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.4.1) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70059498 -0.68238687 0.20860207 231.53808019  
-0.70308922 -0.71005394 0.03858683 2052.08767519  
0.12178758 -0.17369961 -0.97723908 2536.28631019  
Axis -0.92184489 0.37698828 -0.08989908  
Axis point 0.00000000 1153.78547906 1196.48413046  
Rotation angle (degrees) 173.38817473  
Shift along axis 332.16098942  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.4.2) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70059498 -0.68238687 0.20860207 231.53808019  
-0.70308922 -0.71005394 0.03858683 2052.08767519  
0.12178758 -0.17369961 -0.97723908 2536.28631019  
Axis -0.92184489 0.37698828 -0.08989908  
Axis point 0.00000000 1153.78547906 1196.48413046  
Rotation angle (degrees) 173.38817473  
Shift along axis 332.16098942  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.4.3) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70059498 -0.68238687 0.20860207 231.53808019  
-0.70308922 -0.71005394 0.03858683 2052.08767519  
0.12178758 -0.17369961 -0.97723908 2536.28631019  
Axis -0.92184489 0.37698828 -0.08989908  
Axis point 0.00000000 1153.78547906 1196.48413046  
Rotation angle (degrees) 173.38817473  
Shift along axis 332.16098942  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.4.4) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70059498 -0.68238687 0.20860207 231.53808019  
-0.70308922 -0.71005394 0.03858683 2052.08767519  
0.12178758 -0.17369961 -0.97723908 2536.28631019  
Axis -0.92184489 0.37698828 -0.08989908  
Axis point 0.00000000 1153.78547906 1196.48413046  
Rotation angle (degrees) 173.38817473  
Shift along axis 332.16098942  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.4.5) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.70059498 -0.68238687 0.20860207 231.53808019  
-0.70308922 -0.71005394 0.03858683 2052.08767519  
0.12178758 -0.17369961 -0.97723908 2536.28631019  
Axis -0.92184489 0.37698828 -0.08989908  
Axis point 0.00000000 1153.78547906 1196.48413046  
Rotation angle (degrees) 173.38817473  
Shift along axis 332.16098942  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.5.1) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71665803 -0.69380822 0.07093248 266.88798663  
-0.69166230 -0.69400391 0.19990456 1988.66854917  
-0.08946801 -0.19232453 -0.97724446 2611.32051480  
Axis -0.92558211 0.37851303 0.00506394  
Axis point 0.00000000 1199.91412912 1202.64326406  
Rotation angle (degrees) 167.76731205  
Shift along axis 518.93379663  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.5.2) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71665803 -0.69380822 0.07093248 266.88798663  
-0.69166230 -0.69400391 0.19990456 1988.66854917  
-0.08946801 -0.19232453 -0.97724446 2611.32051480  
Axis -0.92558211 0.37851303 0.00506394  
Axis point 0.00000000 1199.91412912 1202.64326406  
Rotation angle (degrees) 167.76731205  
Shift along axis 518.93379663  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.5.3) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71665803 -0.69380822 0.07093248 266.88798663  
-0.69166230 -0.69400391 0.19990456 1988.66854917  
-0.08946801 -0.19232453 -0.97724446 2611.32051480  
Axis -0.92558211 0.37851303 0.00506394  
Axis point 0.00000000 1199.91412912 1202.64326406  
Rotation angle (degrees) 167.76731205  
Shift along axis 518.93379663  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.5.4) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71665803 -0.69380822 0.07093248 266.88798663  
-0.69166230 -0.69400391 0.19990456 1988.66854917  
-0.08946801 -0.19232453 -0.97724446 2611.32051480  
Axis -0.92558211 0.37851303 0.00506394  
Axis point 0.00000000 1199.91412912 1202.64326406  
Rotation angle (degrees) 167.76731205  
Shift along axis 518.93379663  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.5.5) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.71665803 -0.69380822 0.07093248 266.88798663  
-0.69166230 -0.69400391 0.19990456 1988.66854917  
-0.08946801 -0.19232453 -0.97724446 2611.32051480  
Axis -0.92558211 0.37851303 0.00506394  
Axis point 0.00000000 1199.91412912 1202.64326406  
Rotation angle (degrees) 167.76731205  
Shift along axis 518.93379663  
  
Position of PHIKZ034-necklace-tetramer-A-coot-7.pdb (#13.6.1) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69874874 -0.70200737 -0.13760757 340.99790813  
-0.68347163 -0.71192454 0.16133807 1996.54507712  
-0.21122672 -0.01868390 -0.97725850 2594.39051418  
Axis -0.92141917 0.37681011 0.09487281  
Axis point 0.00000000 1135.20065444 1268.55617886  
Rotation angle (degrees) 174.39398767  
Shift along axis 684.25347136  
  
Position of PHIKZ034-necklace-tetramer-B-coot-1.pdb (#13.6.2) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69874874 -0.70200737 -0.13760757 340.99790813  
-0.68347163 -0.71192454 0.16133807 1996.54507712  
-0.21122672 -0.01868390 -0.97725850 2594.39051418  
Axis -0.92141917 0.37681011 0.09487281  
Axis point 0.00000000 1135.20065444 1268.55617886  
Rotation angle (degrees) 174.39398767  
Shift along axis 684.25347136  
  
Position of PHIKZ098-terminator-coot-4.pdb (#13.6.3) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69874874 -0.70200737 -0.13760757 340.99790813  
-0.68347163 -0.71192454 0.16133807 1996.54507712  
-0.21122672 -0.01868390 -0.97725850 2594.39051418  
Axis -0.92141917 0.37681011 0.09487281  
Axis point 0.00000000 1135.20065444 1268.55617886  
Rotation angle (degrees) 174.39398767  
Shift along axis 684.25347136  
  
Position of PHIKZ099-stoper-coot-2.pdb (#13.6.4) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69874874 -0.70200737 -0.13760757 340.99790813  
-0.68347163 -0.71192454 0.16133807 1996.54507712  
-0.21122672 -0.01868390 -0.97725850 2594.39051418  
Axis -0.92141917 0.37681011 0.09487281  
Axis point 0.00000000 1135.20065444 1268.55617886  
Rotation angle (degrees) 174.39398767  
Shift along axis 684.25347136  
  
Position of PHIKZ144-mat-coot-1.pdb (#13.6.5) relative to
cryosparc_P10_J236_006_volume_map_sharp.mrc (#7) coordinates:  
Matrix rotation and translation  
0.69874874 -0.70200737 -0.13760757 340.99790813  
-0.68347163 -0.71192454 0.16133807 1996.54507712  
-0.21122672 -0.01868390 -0.97725850 2594.39051418  
Axis -0.92141917 0.37681011 0.09487281  
Axis point 0.00000000 1135.20065444 1268.55617886  
Rotation angle (degrees) 174.39398767  
Shift along axis 684.25347136  
  

> select clear

> select add #7

2 models selected  

> transparency #7.1 20

> transparency #7.1 30

> hide #!7 models

> select subtract #7

Nothing selected  

> show #!7 models

> select add #1

7552 atoms, 7720 bonds, 9 pseudobonds, 913 residues, 2 models selected  

> close #1

> close #3

> close #4

> close #5

> close #6

> select add #7

2 models selected  

> color #7.1 light gray

> select clear

> hide #!7 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> close #12

> close #11

> close #10

> close #9

> close #8

> select #13.1.1/A

1915 atoms, 1959 bonds, 1 pseudobond, 231 residues, 2 models selected  

> select #13.1.2/A

1915 atoms, 1959 bonds, 1 pseudobond, 231 residues, 2 models selected  

> select #13.1.1/B

2026 atoms, 2073 bonds, 1 pseudobond, 246 residues, 2 models selected  

> save F:/1_study/phiKZ/tail-all/tail-all.cxs

> show #!7 models

> show #!2 models

> hide #!2 models

> hide #!7 models

> show #!7 models

> hide #!13 models

> show #!13 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> select add #13.2.1

9578 atoms, 9793 bonds, 10 pseudobonds, 1159 residues, 4 models selected  

> select subtract #13.2.1

2026 atoms, 2073 bonds, 1 pseudobond, 246 residues, 2 models selected  

> select add #13.1

24844 atoms, 25439 bonds, 21 pseudobonds, 3017 residues, 9 models selected  

> select add #13

149064 atoms, 152634 bonds, 126 pseudobonds, 18102 residues, 55 models
selected  

> select subtract #13

Nothing selected  

> select add #13.1.1

7552 atoms, 7720 bonds, 9 pseudobonds, 913 residues, 2 models selected  

> select add #13.2.1

15104 atoms, 15440 bonds, 18 pseudobonds, 1826 residues, 4 models selected  

> select add #13.3.1

22656 atoms, 23160 bonds, 27 pseudobonds, 2739 residues, 6 models selected  

> select add #13.4.1

30208 atoms, 30880 bonds, 36 pseudobonds, 3652 residues, 8 models selected  

> select add #13.5.1

37760 atoms, 38600 bonds, 45 pseudobonds, 4565 residues, 10 models selected  

> select add #13.6.1

45312 atoms, 46320 bonds, 54 pseudobonds, 5478 residues, 12 models selected  

> ui tool show "Color Actions"

> color sel red

> select #13.1.1,#13.2.1,#13.3.1,#13.4.1,#13.5.1,#13.6.1

Expected an objects specifier or a keyword  

> select #13.1.1,#13.2.1,#13.3.1,#13.4.1,#13.5.1,#13.6.1

Expected an objects specifier or a keyword  

> select #13.1.1#13.2.1#13.3.1#13.4.1#13.5.1#13.6.1

45312 atoms, 46320 bonds, 54 pseudobonds, 5478 residues, 12 models selected  

> select #13.1.2#13.2.2#13.3.2#13.4.2#13.5.2#13.6.2

46482 atoms, 47538 bonds, 48 pseudobonds, 5610 residues, 12 models selected  

> select #13.1.3#13.2.3#13.3.3#13.4.3#13.5.3#13.6.3

26586 atoms, 27342 bonds, 3234 residues, 6 models selected  

> color sel magenta

> select #13.1.4#13.2.4#13.3.4#13.4.4#13.5.4#13.6.4

21618 atoms, 22182 bonds, 2622 residues, 6 models selected  

> color sel orange

> select #13.1.5#13.2.5#13.3.5#13.4.5#13.5.5#13.6.5

9066 atoms, 9252 bonds, 24 pseudobonds, 1158 residues, 12 models selected  

> show #!7 models

> show #!2 models

> hide #!2 models

> hide #!13 models

> show #!13 models

> hide #!7 models

> select add #13.1.1

16618 atoms, 16972 bonds, 33 pseudobonds, 2071 residues, 14 models selected  

> select add #13.2.1

24170 atoms, 24692 bonds, 42 pseudobonds, 2984 residues, 16 models selected  

> select add #13.3.1

31722 atoms, 32412 bonds, 51 pseudobonds, 3897 residues, 18 models selected  

> select subtract #13.3.1

24170 atoms, 24692 bonds, 42 pseudobonds, 2984 residues, 16 models selected  

> select add #13

149064 atoms, 152634 bonds, 126 pseudobonds, 18102 residues, 55 models
selected  

> color zone #7 near sel distance 2.8

> show #!7 models

> volume splitbyzone #7

Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 0 as #1.1, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 1 as #1.2, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 2 as #1.3, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 3 as #1.4, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 4 as #1.5, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 5 as #1.6, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 6 as #1.7, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 7 as #1.8, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 8 as #1.9, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  

> hide #!1 models

> hide #!13 models

> show #!1 models

> volume #!1.1-9 style surface

> volume #!1.1-9 style mesh

> volume #!1.1-9 style image

> volume #!1.1-9 style surface

[Repeated 1 time(s)]

> hide #!1 models

> show #!1 models

> show #!13 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> hide #!1.4 models

> show #!1.4 models

> hide #!1.4 models

> show #!1.4 models

> hide #!1.3 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.4 models

> show #!1.4 models

> hide #!1.6 models

> hide #!1.5 models

> show #!1.5 models

> hide #!1.5 models

> hide #!1.7 models

> show #!1.7 models

> hide #!1.8 models

> show #!1.8 models

> hide #!1.9 models

> show #!1.9 models

> select clear

> hide #!1.7 models

> show #!1.7 models

> hide #!1.7 models

> show #!1.7 models

> hide #!1.8 models

> show #!1.8 models

> hide #!1.9 models

> show #!1.9 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.3 models

> show #!1.3 models

> hide #!1.4 models

> show #!1.4 models

> hide #!1.4 models

> show #!1.4 models

> show #!1.5 models

> hide #!1.5 models

> show #!1.5 models

> show #!1.6 models

> hide #!1.6 models

> show #!1.1 models

> hide #!1.1 models

> close #1.1

> hide #!1.9 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.3 models

> hide #!1.4 models

> hide #!1.5 models

> hide #!1.7 models

> show #!1.7 models

> close #1.3-6

> close #1.9

> show #!2 models

> hide #!2 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> select add #13.1.5

1511 atoms, 1542 bonds, 4 pseudobonds, 193 residues, 2 models selected  

> select add #13.2.5

3022 atoms, 3084 bonds, 8 pseudobonds, 386 residues, 4 models selected  

> select add #13.3.5

4533 atoms, 4626 bonds, 12 pseudobonds, 579 residues, 6 models selected  

> select add #13.4.5

6044 atoms, 6168 bonds, 16 pseudobonds, 772 residues, 8 models selected  

> select add #13.5.5

7555 atoms, 7710 bonds, 20 pseudobonds, 965 residues, 10 models selected  

> select add #13.6.5

9066 atoms, 9252 bonds, 24 pseudobonds, 1158 residues, 12 models selected  

> color zone #7 near sel distance 2.8

> select clear

> select add #13.6.5

1511 atoms, 1542 bonds, 4 pseudobonds, 193 residues, 2 models selected  

> select add #13.5.5

3022 atoms, 3084 bonds, 8 pseudobonds, 386 residues, 4 models selected  

> select add #13.4.5

4533 atoms, 4626 bonds, 12 pseudobonds, 579 residues, 6 models selected  

> select add #13.3.5

6044 atoms, 6168 bonds, 16 pseudobonds, 772 residues, 8 models selected  

> select add #13.2.5

7555 atoms, 7710 bonds, 20 pseudobonds, 965 residues, 10 models selected  

> select add #13.1.5

9066 atoms, 9252 bonds, 24 pseudobonds, 1158 residues, 12 models selected  

> color (#!13.1.5#!13.2.5#!13.3.5#!13.4.5#!13.5.5#!13.6.5 & sel) cyan

> color zone #7 near sel distance 2.8

> volume splitbyzone #7

Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 0 as #3.1, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 1 as #3.2, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  

> hide #!3.1 models

> close #3.1

> select clear

> select add #13.1.2

7747 atoms, 7923 bonds, 8 pseudobonds, 935 residues, 2 models selected  

> select add #13.2.2

15494 atoms, 15846 bonds, 16 pseudobonds, 1870 residues, 4 models selected  

> select add #13.3.2

23241 atoms, 23769 bonds, 24 pseudobonds, 2805 residues, 6 models selected  

> select add #13.4.2

30988 atoms, 31692 bonds, 32 pseudobonds, 3740 residues, 8 models selected  

> select add #13.5.2

38735 atoms, 39615 bonds, 40 pseudobonds, 4675 residues, 10 models selected  

> select add #13.6.2

46482 atoms, 47538 bonds, 48 pseudobonds, 5610 residues, 12 models selected  

> color (#!13.1.2#!13.2.2#!13.3.2#!13.4.2#!13.5.2#!13.6.2 & sel) hot pink

> color zone #7 near sel distance 2.8

> volume splitbyzone #7

Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 0 as #4.1, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 1 as #4.2, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  

> close #4.1

> select clear

> hide #!3 models

> hide #!4 models

> hide #!1 models

> hide #!13 models

> show #!1 models

> show #!13 models

> hide #!1 models

> select add #13

149064 atoms, 152634 bonds, 126 pseudobonds, 18102 residues, 55 models
selected  

> color zone #7 near sel distance 2.8

> volume splitbyzone #7

Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 0 as #5.1, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 1 as #5.2, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 2 as #5.3, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 3 as #5.4, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 4 as #5.5, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  
Opened cryosparc_P10_J236_006_volume_map_sharp.mrc 5 as #5.6, grid size
480,480,480, pixel 1.36, shown at level 0.231, step 1, values float32  

> hide #!5 models

> show #!5 models

> hide #!13 models

> ui tool show "Hide Dust"

> surface dust #7 size 10

> surface dust #7 size 15

[Repeated 2 time(s)]

> show #!13 models

> hide #!13 models

> hide #!5.1 models

> hide #!5 models

> show #!5 models

> show #!5.1 models

> hide #!5.1 models

> show #!5.1 models

> hide #!5.1 models

> save F:/1_study/phiKZ/tail-all/tail-all-1.cxs

> hide #!5 models

> show #!5 models

> close #4

> close #3

> show #!1 models

> hide #!1 models

> hide #!5 models

> show #!1 models

> hide #!1 models

> show #!5 models

> close #1

> save F:/1_study/phiKZ/tail-all/tail-all-2.cxs

——— End of log from Mon Feb 24 20:21:26 2025 ———

opened ChimeraX session  

> color #5.2 red models

> color #5.2 blue models

> color #5.2 #0055ffff models

> color #5.4 #ff8f78ff models

> color #5.5 #aaaaffff models

> color #5.6 #55ffffff models

> color #5.6 springgreen models

> color #5.6 lime models

> color #5.6 #55ff00ff models

> color #5.6 #55ff7fff models

> color #5.6 #aaff7fff models

> color #5.6 #aaff00ff models

> color #5.6 lime models

> color #5.6 springgreen models

> color #5.6 #00aa7fff models

> color #5.3 #aaff00ff models

> color #5.3 lime models

> color #5.3 #aaaa00ff models

> color #5.3 #00aa00ff models

> color #5.3 #aa5500ff models

> color #5.3 #aa557fff models

> color #5.3 #aa55ffff models

> color #5.3 #aa007fff models

> color #5.3 #aa0000ff models

> color #5.3 red models

> color #5.3 #555500ff models

> color #5.3 #55557fff models

> color #5.3 #ffaa00ff models

> color #5.3 #ffaa7fff models

> color #5.3 #ffaa00ff models

> color #5.3 #55ff00ff models

> color #5.3 #ffaa00ff models

> color #5.3 #bc7d00ff models

> show #!2 models

> rename #13 id #1

> rename #7 id #3

> open F:/1_study/phiKZ/tail-all/cryosparc_P10_J379_008_volume_map_sharp.mrc

Opened cryosparc_P10_J379_008_volume_map_sharp.mrc as #4, grid size
300,300,300, pixel 1.36, shown at level 0.341, step 2, values float32  

> color #4 #0055ffff models

> volume #4 step 1

> select add #4

149064 atoms, 152634 bonds, 126 pseudobonds, 18102 residues, 50 models
selected  

> show #!1 models

> select add #1

149064 atoms, 152634 bonds, 126 pseudobonds, 18102 residues, 57 models
selected  

> select subtract #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,-90.588,0,1,0,119.64,0,0,1,-62.76

> view matrix models #4,1,0,0,29.831,0,1,0,225.47,0,0,1,-34.828

> view matrix models #4,1,0,0,240.8,0,1,0,410.87,0,0,1,14.107

> view matrix models #4,1,0,0,464.83,0,1,0,607.76,0,0,1,66.074

> view matrix models #4,1,0,0,681.4,0,1,0,798.08,0,0,1,116.31

> view matrix models #4,1,0,0,911.03,0,1,0,999.89,0,0,1,169.57

> view matrix models #4,1,0,0,953.01,0,1,0,969.02,0,0,1,105.56

> view matrix models #4,1,0,0,955.52,0,1,0,966.19,0,0,1,105.51

> view matrix models #4,1,0,0,1019.9,0,1,0,1022.8,0,0,1,120.45

> view matrix models #4,1,0,0,988.19,0,1,0,994.9,0,0,1,113.09

> ui tool show "Fit in Map"

> fitmap #4 inMap #2

Fit map cryosparc_P10_J379_008_volume_map_sharp.mrc in map
cryosparc_P10_J436_003_volume_map_sharp.mrc using 271118 points  
correlation = 0.9641, correlation about mean = 0.1099, overlap = 1.041e+05  
steps = 104, shift = 41.4, angle = 0.162 degrees  
  
Position of cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) relative to
cryosparc_P10_J436_003_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99999599 0.00282543 0.00020594 1019.33878625  
-0.00282541 0.99999601 -0.00008012 1020.60804615  
-0.00020617 0.00007954 0.99999998 104.48360915  
Axis 0.02816911 0.07270692 -0.99695547  
Axis point 361765.87129634 -360271.73740031 0.00000000  
Rotation angle (degrees) 0.16237927  
Shift along axis -1.24636473  
  

> select subtract #4

Nothing selected  

> hide #!2 models

> open F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ049-other-A-fit-
> coot-0.pdb F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ049-other-B-fit-
> coot-0.pdb F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ062-sheath-init-
> fit-coot-0.pdb
> F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ087-wedge2A-fit-coot-5.pdb
> F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ087-wedge2B-fit-coot-8.pdb
> F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ128-wedge1-fit-coot-5.pdb
> F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ139-docker.pdb
> F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ161-horn-fit-coot-1.pdb
> F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ174-pin-fit-coot-1.pdb

Summary of feedback from opening
F:/1_study/phiKZ/EMDB&PDB-241227/4baseplate/PHIKZ062-sheath-init-fit-
coot-0.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO B 17 ILE B 29 1 13  
Start residue of secondary structure not found: HELIX 2 2 LEU B 46 VAL B 52 1
7  
Start residue of secondary structure not found: HELIX 3 3 TYR B 57 VAL B 75 1
19  
Start residue of secondary structure not found: HELIX 4 4 GLY B 77 GLU B 79 1
3  
Start residue of secondary structure not found: HELIX 5 5 ILE B 115 LEU B 118
1 4  
6 messages similar to the above omitted  
  
Chain information for PHIKZ049-other-A-fit-coot-0.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for PHIKZ049-other-B-fit-coot-0.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for PHIKZ062-sheath-init-fit-coot-0.pdb #8  
---  
Chain | Description  
A | No description available  
  
Chain information for PHIKZ087-wedge2A-fit-coot-5.pdb #9  
---  
Chain | Description  
C | No description available  
  
Chain information for PHIKZ087-wedge2B-fit-coot-8.pdb #10  
---  
Chain | Description  
C | No description available  
  
Chain information for PHIKZ128-wedge1-fit-coot-5.pdb #11  
---  
Chain | Description  
E | No description available  
  
Chain information for PHIKZ139-docker.pdb #12  
---  
Chain | Description  
E | No description available  
  
Chain information for PHIKZ161-horn-fit-coot-1.pdb #13  
---  
Chain | Description  
A | No description available  
F | No description available  
  
Chain information for PHIKZ174-pin-fit-coot-1.pdb #14  
---  
Chain | Description  
G | No description available  
  

> sym #6-14 C6 center 272,272,272

Made 6 copies for PHIKZ049-other-A-fit-coot-0.pdb, PHIKZ049-other-B-fit-
coot-0.pdb, PHIKZ062-sheath-init-fit-coot-0.pdb, PHIKZ087-wedge2A-fit-
coot-5.pdb, PHIKZ087-wedge2B-fit-coot-8.pdb, PHIKZ128-wedge1-fit-coot-5.pdb,
PHIKZ139-docker.pdb, PHIKZ161-horn-fit-coot-1.pdb, PHIKZ174-pin-fit-coot-1.pdb
symmetry C6  

> close #6-8,11,13#9-10,12,14

> rename #15 id #6

> select add #6

193758 atoms, 197562 bonds, 48 pseudobonds, 24270 residues, 85 models selected  

> view matrix models #6,1,0,0,-50.381,0,1,0,99.363,0,0,1,-28.295

> view matrix models #6,1,0,0,70.834,0,1,0,166.6,0,0,1,-7.9991

> view matrix models #6,1,0,0,182.34,0,1,0,228.46,0,0,1,10.67

> view matrix models #6,1,0,0,305.88,0,1,0,296.99,0,0,1,31.356

> view matrix models #6,1,0,0,404.18,0,1,0,351.52,0,0,1,47.814

> view matrix models #6,1,0,0,496.64,0,1,0,402.81,0,0,1,63.296

> view matrix models #6,1,0,0,578.62,0,1,0,448.28,0,0,1,77.021

> view matrix models #6,1,0,0,660.59,0,1,0,493.76,0,0,1,90.747

> view matrix models #6,1,0,0,746.45,0,1,0,541.38,0,0,1,105.12

> view matrix models #6,1,0,0,809,0,1,0,576.08,0,0,1,115.6

> view matrix models #6,1,0,0,874.66,0,1,0,612.5,0,0,1,126.59

> view matrix models #6,1,0,0,775.86,0,1,0,791.28,0,0,1,124.38

> view matrix models #6,1,0,0,841.91,0,1,0,827.92,0,0,1,135.44

> view matrix models #6,1,0,0,918.83,0,1,0,870.59,0,0,1,148.32

> view matrix models #6,1,0,0,982.16,0,1,0,905.72,0,0,1,158.92

> view matrix models #6,1,0,0,986.04,0,1,0,907.87,0,0,1,159.57

> view matrix models #6,1,0,0,963.9,0,1,0,954.04,0,0,1,138.86

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.08795,-0.74553,0.66064,1272.3,-0.42376,0.5722,0.70215,1033.3,-0.90149,-0.34171,-0.2656,755.87

> view matrix models
> #6,-0.59832,-0.79931,0.055822,1605.3,-0.7442,0.58017,0.33101,1199,-0.29697,0.15651,-0.94197,606.59

> view matrix models
> #6,-0.55844,-0.82918,-0.024388,1620.1,-0.79809,0.52902,0.28842,1236.7,-0.22625,0.18053,-0.95719,584.27

> view matrix models
> #6,-0.57096,-0.81475,-0.10092,1636.2,-0.80697,0.53435,0.25153,1245.6,-0.15101,0.22505,-0.96257,552.75

> view matrix models
> #6,-0.61299,-0.13629,-0.77824,1607,0.5629,0.61586,-0.55123,1028.7,0.55442,-0.77598,-0.3008,487.44

> view matrix models
> #6,0.067037,-0.94821,0.31048,1406.7,0.96535,-0.017013,-0.26039,1028.9,0.25219,0.31718,0.91422,5.4176

> view matrix models
> #6,-0.40485,-0.66103,0.63177,1386.2,0.91013,-0.35792,0.20873,1034.3,0.088143,0.65949,0.74653,-6.4758

> view matrix models
> #6,-0.49966,-0.80881,-0.31012,1657.8,0.86132,-0.42587,-0.27706,1171.3,0.092021,-0.40555,0.90943,245.35

> view matrix models
> #6,-0.36742,-0.86531,-0.34093,1644,0.92305,-0.29435,-0.24767,1111.4,0.11396,-0.4057,0.90688,239.95

> view matrix models
> #6,-0.33147,-0.94339,0.011762,1578.6,0.94221,-0.33165,-0.047511,1072.6,0.048723,-0.0046665,0.9988,127.07

> view matrix models
> #6,-0.35519,-0.92942,0.10008,1561.7,0.90911,-0.36837,-0.19448,1124,0.21762,0.021907,0.97579,79.087

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.35519,-0.92942,0.10008,1567.3,0.90911,-0.36837,-0.19448,1110.1,0.21762,0.021907,0.97579,87.776

> view matrix models
> #6,-0.35519,-0.92942,0.10008,1565.2,0.90911,-0.36837,-0.19448,1124,0.21762,0.021907,0.97579,65.202

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.47859,-0.84127,0.25142,1541.6,0.8603,-0.50655,-0.057323,1144.2,0.17558,0.18887,0.96618,33.816

> view matrix models
> #6,-0.17496,-0.96105,-0.21396,1593.1,0.91019,-0.075015,-0.40734,1091.2,0.37543,-0.26601,0.88786,119.72

> view matrix models
> #6,-0.17169,-0.97343,-0.15151,1582.2,0.92069,-0.10383,-0.37624,1089.6,0.35051,-0.20409,0.91405,103.76

> view matrix models
> #6,-0.069334,-0.97569,0.20791,1477.2,0.97767,-0.10791,-0.18035,1032.8,0.1984,0.19076,0.96138,26.279

> view matrix models
> #6,-0.045791,-0.94995,0.30904,1441.8,0.9948,-0.071542,-0.072509,994.73,0.090989,0.30411,0.94828,27.189

> view matrix models
> #6,-0.25622,-0.88139,0.39687,1461.3,0.96557,-0.25252,0.062576,1022.3,0.045063,0.39924,0.91574,20.961

> view matrix models
> #6,-0.25047,-0.85662,0.45107,1441.4,0.96812,-0.22104,0.1178,1001.2,-0.0012031,0.4662,0.88468,22.218

> view matrix models
> #6,-0.27346,-0.8327,0.48149,1434.7,0.9615,-0.22248,0.16133,994.06,-0.027216,0.50707,0.86147,23.309

> view matrix models
> #6,-0.29578,-0.79535,0.52909,1420.3,0.9534,-0.21128,0.21538,981.53,-0.059513,0.56814,0.82078,24.482

> view matrix models
> #6,-0.34397,-0.73782,0.58078,1406.7,0.93455,-0.209,0.28799,970.22,-0.091099,0.64183,0.76142,26.155

> fitmap sel inMap #4

Fit molecules PHIKZ049-other-A-fit-coot-0.pdb (#6.1.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.1.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.1.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.1.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.1.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.1.6), PHIKZ139-docker.pdb
(#6.1.7), PHIKZ161-horn-fit-coot-1.pdb (#6.1.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.1.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.2.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.2.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.2.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.2.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.2.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.2.6), PHIKZ139-docker.pdb
(#6.2.7), PHIKZ161-horn-fit-coot-1.pdb (#6.2.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.2.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.3.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.3.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.3.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.3.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.3.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.3.6), PHIKZ139-docker.pdb
(#6.3.7), PHIKZ161-horn-fit-coot-1.pdb (#6.3.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.3.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.4.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.4.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.4.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.4.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.4.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.4.6), PHIKZ139-docker.pdb
(#6.4.7), PHIKZ161-horn-fit-coot-1.pdb (#6.4.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.4.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.5.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.5.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.5.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.5.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.5.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.5.6), PHIKZ139-docker.pdb
(#6.5.7), PHIKZ161-horn-fit-coot-1.pdb (#6.5.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.5.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.6.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.6.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.6.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.6.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.6.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.6.6), PHIKZ139-docker.pdb
(#6.6.7), PHIKZ161-horn-fit-coot-1.pdb (#6.6.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.6.9) to map cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) using 193758
atoms  
average map value = 0.06057, steps = 128  
shifted from previous position = 15.8  
rotated from previous position = 3.88 degrees  
atoms outside contour = 185167, contour level = 0.34127  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.1.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99869649 -0.02888110 -0.04208559 -1000.82757839  
0.03080974 0.99846977 0.04592255 -1027.65864204  
0.04069490 -0.04715934 0.99805807 -93.11066514  
Axis -0.67387257 -0.59929490 0.43213583  
Axis point 0.00000000 -13660.10064722 5609.40741642  
Rotation angle (degrees) 3.96028037  
Shift along axis 1250.06438396  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.1.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99869649 -0.02888110 -0.04208559 -1000.82757839  
0.03080974 0.99846977 0.04592255 -1027.65864204  
0.04069490 -0.04715934 0.99805807 -93.11066514  
Axis -0.67387257 -0.59929490 0.43213583  
Axis point 0.00000000 -13660.10064722 5609.40741642  
Rotation angle (degrees) 3.96028037  
Shift along axis 1250.06438396  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.1.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99869649 -0.02888110 -0.04208559 -1000.82757839  
0.03080974 0.99846977 0.04592255 -1027.65864204  
0.04069490 -0.04715934 0.99805807 -93.11066514  
Axis -0.67387257 -0.59929490 0.43213583  
Axis point 0.00000000 -13660.10064722 5609.40741642  
Rotation angle (degrees) 3.96028037  
Shift along axis 1250.06438396  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.1.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99869649 -0.02888110 -0.04208559 -1000.82757839  
0.03080974 0.99846977 0.04592255 -1027.65864204  
0.04069490 -0.04715934 0.99805807 -93.11066514  
Axis -0.67387257 -0.59929490 0.43213583  
Axis point 0.00000000 -13660.10064722 5609.40741642  
Rotation angle (degrees) 3.96028037  
Shift along axis 1250.06438396  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.1.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99869649 -0.02888110 -0.04208559 -1000.82757839  
0.03080974 0.99846977 0.04592255 -1027.65864204  
0.04069490 -0.04715934 0.99805807 -93.11066514  
Axis -0.67387257 -0.59929490 0.43213583  
Axis point 0.00000000 -13660.10064722 5609.40741642  
Rotation angle (degrees) 3.96028037  
Shift along axis 1250.06438396  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.1.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99869649 -0.02888110 -0.04208559 -1000.82757839  
0.03080974 0.99846977 0.04592255 -1027.65864204  
0.04069490 -0.04715934 0.99805807 -93.11066514  
Axis -0.67387257 -0.59929490 0.43213583  
Axis point 0.00000000 -13660.10064722 5609.40741642  
Rotation angle (degrees) 3.96028037  
Shift along axis 1250.06438396  
  
Position of PHIKZ139-docker.pdb (#6.1.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99869649 -0.02888110 -0.04208559 -1000.82757839  
0.03080974 0.99846977 0.04592255 -1027.65864204  
0.04069490 -0.04715934 0.99805807 -93.11066514  
Axis -0.67387257 -0.59929490 0.43213583  
Axis point 0.00000000 -13660.10064722 5609.40741642  
Rotation angle (degrees) 3.96028037  
Shift along axis 1250.06438396  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.1.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99869649 -0.02888110 -0.04208559 -1000.82757839  
0.03080974 0.99846977 0.04592255 -1027.65864204  
0.04069490 -0.04715934 0.99805807 -93.11066514  
Axis -0.67387257 -0.59929490 0.43213583  
Axis point 0.00000000 -13660.10064722 5609.40741642  
Rotation angle (degrees) 3.96028037  
Shift along axis 1250.06438396  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.1.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99869649 -0.02888110 -0.04208559 -1000.82757839  
0.03080974 0.99846977 0.04592255 -1027.65864204  
0.04069490 -0.04715934 0.99805807 -93.11066514  
Axis -0.67387257 -0.59929490 0.43213583  
Axis point 0.00000000 -13660.10064722 5609.40741642  
Rotation angle (degrees) 3.96028037  
Shift along axis 1250.06438396  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.2.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99936509 -0.03041567 0.01855566 -1002.05004449  
0.02926794 0.99781284 0.05926996 -1035.64500318  
-0.02031782 -0.05868925 0.99806952 -73.37868975  
Axis -0.85604417 0.28210951 0.43313115  
Axis point 0.00000000 -5841.40260355 19798.78730942  
Rotation angle (degrees) 3.95068597  
Shift along axis 533.85119935  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.2.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99936509 -0.03041567 0.01855566 -1002.05004449  
0.02926794 0.99781284 0.05926996 -1035.64500318  
-0.02031782 -0.05868925 0.99806952 -73.37868975  
Axis -0.85604417 0.28210951 0.43313115  
Axis point 0.00000000 -5841.40260355 19798.78730942  
Rotation angle (degrees) 3.95068597  
Shift along axis 533.85119935  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.2.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99936509 -0.03041567 0.01855566 -1002.05004449  
0.02926794 0.99781284 0.05926996 -1035.64500318  
-0.02031782 -0.05868925 0.99806952 -73.37868975  
Axis -0.85604417 0.28210951 0.43313115  
Axis point 0.00000000 -5841.40260355 19798.78730942  
Rotation angle (degrees) 3.95068597  
Shift along axis 533.85119935  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.2.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99936509 -0.03041567 0.01855566 -1002.05004449  
0.02926794 0.99781284 0.05926996 -1035.64500318  
-0.02031782 -0.05868925 0.99806952 -73.37868975  
Axis -0.85604417 0.28210951 0.43313115  
Axis point 0.00000000 -5841.40260355 19798.78730942  
Rotation angle (degrees) 3.95068597  
Shift along axis 533.85119935  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.2.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99936509 -0.03041567 0.01855566 -1002.05004449  
0.02926794 0.99781284 0.05926996 -1035.64500318  
-0.02031782 -0.05868925 0.99806952 -73.37868975  
Axis -0.85604417 0.28210951 0.43313115  
Axis point 0.00000000 -5841.40260355 19798.78730942  
Rotation angle (degrees) 3.95068597  
Shift along axis 533.85119935  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.2.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99936509 -0.03041567 0.01855566 -1002.05004449  
0.02926794 0.99781284 0.05926996 -1035.64500318  
-0.02031782 -0.05868925 0.99806952 -73.37868975  
Axis -0.85604417 0.28210951 0.43313115  
Axis point 0.00000000 -5841.40260355 19798.78730942  
Rotation angle (degrees) 3.95068597  
Shift along axis 533.85119935  
  
Position of PHIKZ139-docker.pdb (#6.2.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99936509 -0.03041567 0.01855566 -1002.05004449  
0.02926794 0.99781284 0.05926996 -1035.64500318  
-0.02031782 -0.05868925 0.99806952 -73.37868975  
Axis -0.85604417 0.28210951 0.43313115  
Axis point 0.00000000 -5841.40260355 19798.78730942  
Rotation angle (degrees) 3.95068597  
Shift along axis 533.85119935  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.2.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99936509 -0.03041567 0.01855566 -1002.05004449  
0.02926794 0.99781284 0.05926996 -1035.64500318  
-0.02031782 -0.05868925 0.99806952 -73.37868975  
Axis -0.85604417 0.28210951 0.43313115  
Axis point 0.00000000 -5841.40260355 19798.78730942  
Rotation angle (degrees) 3.95068597  
Shift along axis 533.85119935  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.2.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99936509 -0.03041567 0.01855566 -1002.05004449  
0.02926794 0.99781284 0.05926996 -1035.64500318  
-0.02031782 -0.05868925 0.99806952 -73.37868975  
Axis -0.85604417 0.28210951 0.43313115  
Axis point 0.00000000 -5841.40260355 19798.78730942  
Rotation angle (degrees) 3.95068597  
Shift along axis 533.85119935  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.3.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99771439 -0.03022503 0.06043549 -1009.81624009  
0.02946507 0.99947563 0.01342680 -1039.18043368  
-0.06080962 -0.01161537 0.99808180 -75.17045355  
Axis -0.18220130 0.88215259 0.43429194  
Axis point 3625.80626834 0.00000000 19153.56697361  
Rotation angle (degrees) 3.94053857  
Shift along axis -765.37180106  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.3.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99771439 -0.03022503 0.06043549 -1009.81624009  
0.02946507 0.99947563 0.01342680 -1039.18043368  
-0.06080962 -0.01161537 0.99808180 -75.17045355  
Axis -0.18220130 0.88215259 0.43429194  
Axis point 3625.80626834 0.00000000 19153.56697361  
Rotation angle (degrees) 3.94053857  
Shift along axis -765.37180106  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.3.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99771439 -0.03022503 0.06043549 -1009.81624009  
0.02946507 0.99947563 0.01342680 -1039.18043368  
-0.06080962 -0.01161537 0.99808180 -75.17045355  
Axis -0.18220130 0.88215259 0.43429194  
Axis point 3625.80626834 0.00000000 19153.56697361  
Rotation angle (degrees) 3.94053857  
Shift along axis -765.37180106  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.3.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99771439 -0.03022503 0.06043549 -1009.81624009  
0.02946507 0.99947563 0.01342680 -1039.18043368  
-0.06080962 -0.01161537 0.99808180 -75.17045355  
Axis -0.18220130 0.88215259 0.43429194  
Axis point 3625.80626834 0.00000000 19153.56697361  
Rotation angle (degrees) 3.94053857  
Shift along axis -765.37180106  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.3.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99771439 -0.03022503 0.06043549 -1009.81624009  
0.02946507 0.99947563 0.01342680 -1039.18043368  
-0.06080962 -0.01161537 0.99808180 -75.17045355  
Axis -0.18220130 0.88215259 0.43429194  
Axis point 3625.80626834 0.00000000 19153.56697361  
Rotation angle (degrees) 3.94053857  
Shift along axis -765.37180106  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.3.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99771439 -0.03022503 0.06043549 -1009.81624009  
0.02946507 0.99947563 0.01342680 -1039.18043368  
-0.06080962 -0.01161537 0.99808180 -75.17045355  
Axis -0.18220130 0.88215259 0.43429194  
Axis point 3625.80626834 0.00000000 19153.56697361  
Rotation angle (degrees) 3.94053857  
Shift along axis -765.37180106  
  
Position of PHIKZ139-docker.pdb (#6.3.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99771439 -0.03022503 0.06043549 -1009.81624009  
0.02946507 0.99947563 0.01342680 -1039.18043368  
-0.06080962 -0.01161537 0.99808180 -75.17045355  
Axis -0.18220130 0.88215259 0.43429194  
Axis point 3625.80626834 0.00000000 19153.56697361  
Rotation angle (degrees) 3.94053857  
Shift along axis -765.37180106  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.3.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99771439 -0.03022503 0.06043549 -1009.81624009  
0.02946507 0.99947563 0.01342680 -1039.18043368  
-0.06080962 -0.01161537 0.99808180 -75.17045355  
Axis -0.18220130 0.88215259 0.43429194  
Axis point 3625.80626834 0.00000000 19153.56697361  
Rotation angle (degrees) 3.94053857  
Shift along axis -765.37180106  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.3.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99771439 -0.03022503 0.06043549 -1009.81624009  
0.02946507 0.99947563 0.01342680 -1039.18043368  
-0.06080962 -0.01161537 0.99808180 -75.17045355  
Axis -0.18220130 0.88215259 0.43429194  
Axis point 3625.80626834 0.00000000 19153.56697361  
Rotation angle (degrees) 3.94053857  
Shift along axis -765.37180106  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.4.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99871319 -0.02890051 0.04167405 -1017.15349926  
0.03080330 0.99847726 -0.04576378 -1033.71799132  
-0.04028800 0.04698859 0.99808264 -96.69443682  
Axis 0.67493627 0.59641781 0.43445003  
Axis point 0.00000000 -10570.39283837 -4706.99602429  
Rotation angle (degrees) 3.94000883  
Shift along axis -1345.05050933  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.4.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99871319 -0.02890051 0.04167405 -1017.15349926  
0.03080330 0.99847726 -0.04576378 -1033.71799132  
-0.04028800 0.04698859 0.99808264 -96.69443682  
Axis 0.67493627 0.59641781 0.43445003  
Axis point 0.00000000 -10570.39283837 -4706.99602429  
Rotation angle (degrees) 3.94000883  
Shift along axis -1345.05050933  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.4.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99871319 -0.02890051 0.04167405 -1017.15349926  
0.03080330 0.99847726 -0.04576378 -1033.71799132  
-0.04028800 0.04698859 0.99808264 -96.69443682  
Axis 0.67493627 0.59641781 0.43445003  
Axis point 0.00000000 -10570.39283837 -4706.99602429  
Rotation angle (degrees) 3.94000883  
Shift along axis -1345.05050933  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.4.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99871319 -0.02890051 0.04167405 -1017.15349926  
0.03080330 0.99847726 -0.04576378 -1033.71799132  
-0.04028800 0.04698859 0.99808264 -96.69443682  
Axis 0.67493627 0.59641781 0.43445003  
Axis point 0.00000000 -10570.39283837 -4706.99602429  
Rotation angle (degrees) 3.94000883  
Shift along axis -1345.05050933  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.4.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99871319 -0.02890051 0.04167405 -1017.15349926  
0.03080330 0.99847726 -0.04576378 -1033.71799132  
-0.04028800 0.04698859 0.99808264 -96.69443682  
Axis 0.67493627 0.59641781 0.43445003  
Axis point 0.00000000 -10570.39283837 -4706.99602429  
Rotation angle (degrees) 3.94000883  
Shift along axis -1345.05050933  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.4.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99871319 -0.02890051 0.04167405 -1017.15349926  
0.03080330 0.99847726 -0.04576378 -1033.71799132  
-0.04028800 0.04698859 0.99808264 -96.69443682  
Axis 0.67493627 0.59641781 0.43445003  
Axis point 0.00000000 -10570.39283837 -4706.99602429  
Rotation angle (degrees) 3.94000883  
Shift along axis -1345.05050933  
  
Position of PHIKZ139-docker.pdb (#6.4.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99871319 -0.02890051 0.04167405 -1017.15349926  
0.03080330 0.99847726 -0.04576378 -1033.71799132  
-0.04028800 0.04698859 0.99808264 -96.69443682  
Axis 0.67493627 0.59641781 0.43445003  
Axis point 0.00000000 -10570.39283837 -4706.99602429  
Rotation angle (degrees) 3.94000883  
Shift along axis -1345.05050933  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.4.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99871319 -0.02890051 0.04167405 -1017.15349926  
0.03080330 0.99847726 -0.04576378 -1033.71799132  
-0.04028800 0.04698859 0.99808264 -96.69443682  
Axis 0.67493627 0.59641781 0.43445003  
Axis point 0.00000000 -10570.39283837 -4706.99602429  
Rotation angle (degrees) 3.94000883  
Shift along axis -1345.05050933  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.4.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99871319 -0.02890051 0.04167405 -1017.15349926  
0.03080330 0.99847726 -0.04576378 -1033.71799132  
-0.04028800 0.04698859 0.99808264 -96.69443682  
Axis 0.67493627 0.59641781 0.43445003  
Axis point 0.00000000 -10570.39283837 -4706.99602429  
Rotation angle (degrees) 3.94000883  
Shift along axis -1345.05050933  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.5.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99935662 -0.03043984 -0.01896720 -1015.45180316  
0.02927120 0.99782216 -0.05911119 -1024.53865746  
0.02072523 0.05851796 0.99807120 -116.42640831  
Axis 0.85387695 -0.28812973 0.43344597  
Axis point 0.00000000 -3287.37621643 -20244.77353732  
Rotation angle (degrees) 3.94962915  
Shift along axis -622.33540719  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.5.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99935662 -0.03043984 -0.01896720 -1015.45180316  
0.02927120 0.99782216 -0.05911119 -1024.53865746  
0.02072523 0.05851796 0.99807120 -116.42640831  
Axis 0.85387695 -0.28812973 0.43344597  
Axis point 0.00000000 -3287.37621643 -20244.77353732  
Rotation angle (degrees) 3.94962915  
Shift along axis -622.33540719  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.5.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99935662 -0.03043984 -0.01896720 -1015.45180316  
0.02927120 0.99782216 -0.05911119 -1024.53865746  
0.02072523 0.05851796 0.99807120 -116.42640831  
Axis 0.85387695 -0.28812973 0.43344597  
Axis point 0.00000000 -3287.37621643 -20244.77353732  
Rotation angle (degrees) 3.94962915  
Shift along axis -622.33540719  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.5.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99935662 -0.03043984 -0.01896720 -1015.45180316  
0.02927120 0.99782216 -0.05911119 -1024.53865746  
0.02072523 0.05851796 0.99807120 -116.42640831  
Axis 0.85387695 -0.28812973 0.43344597  
Axis point 0.00000000 -3287.37621643 -20244.77353732  
Rotation angle (degrees) 3.94962915  
Shift along axis -622.33540719  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.5.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99935662 -0.03043984 -0.01896720 -1015.45180316  
0.02927120 0.99782216 -0.05911119 -1024.53865746  
0.02072523 0.05851796 0.99807120 -116.42640831  
Axis 0.85387695 -0.28812973 0.43344597  
Axis point 0.00000000 -3287.37621643 -20244.77353732  
Rotation angle (degrees) 3.94962915  
Shift along axis -622.33540719  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.5.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99935662 -0.03043984 -0.01896720 -1015.45180316  
0.02927120 0.99782216 -0.05911119 -1024.53865746  
0.02072523 0.05851796 0.99807120 -116.42640831  
Axis 0.85387695 -0.28812973 0.43344597  
Axis point 0.00000000 -3287.37621643 -20244.77353732  
Rotation angle (degrees) 3.94962915  
Shift along axis -622.33540719  
  
Position of PHIKZ139-docker.pdb (#6.5.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99935662 -0.03043984 -0.01896720 -1015.45180316  
0.02927120 0.99782216 -0.05911119 -1024.53865746  
0.02072523 0.05851796 0.99807120 -116.42640831  
Axis 0.85387695 -0.28812973 0.43344597  
Axis point 0.00000000 -3287.37621643 -20244.77353732  
Rotation angle (degrees) 3.94962915  
Shift along axis -622.33540719  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.5.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99935662 -0.03043984 -0.01896720 -1015.45180316  
0.02927120 0.99782216 -0.05911119 -1024.53865746  
0.02072523 0.05851796 0.99807120 -116.42640831  
Axis 0.85387695 -0.28812973 0.43344597  
Axis point 0.00000000 -3287.37621643 -20244.77353732  
Rotation angle (degrees) 3.94962915  
Shift along axis -622.33540719  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.5.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99935662 -0.03043984 -0.01896720 -1015.45180316  
0.02927120 0.99782216 -0.05911119 -1024.53865746  
0.02072523 0.05851796 0.99807120 -116.42640831  
Axis 0.85387695 -0.28812973 0.43344597  
Axis point 0.00000000 -3287.37621643 -20244.77353732  
Rotation angle (degrees) 3.94962915  
Shift along axis -622.33540719  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.6.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99768923 -0.03022978 -0.06084703 -1006.89207790  
0.02947478 0.99947746 -0.01326802 -1022.01473868  
0.06121632 0.01144391 0.99805892 -114.63440044  
Axis 0.17892746 -0.88380320 0.43229256  
Axis point 6034.20773518 0.00000000 -18757.71486376  
Rotation angle (degrees) 3.95975327  
Shift along axis 673.54365999  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.6.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99768923 -0.03022978 -0.06084703 -1006.89207790  
0.02947478 0.99947746 -0.01326802 -1022.01473868  
0.06121632 0.01144391 0.99805892 -114.63440044  
Axis 0.17892746 -0.88380320 0.43229256  
Axis point 6034.20773518 0.00000000 -18757.71486376  
Rotation angle (degrees) 3.95975327  
Shift along axis 673.54365999  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.6.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99768923 -0.03022978 -0.06084703 -1006.89207790  
0.02947478 0.99947746 -0.01326802 -1022.01473868  
0.06121632 0.01144391 0.99805892 -114.63440044  
Axis 0.17892746 -0.88380320 0.43229256  
Axis point 6034.20773518 0.00000000 -18757.71486376  
Rotation angle (degrees) 3.95975327  
Shift along axis 673.54365999  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.6.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99768923 -0.03022978 -0.06084703 -1006.89207790  
0.02947478 0.99947746 -0.01326802 -1022.01473868  
0.06121632 0.01144391 0.99805892 -114.63440044  
Axis 0.17892746 -0.88380320 0.43229256  
Axis point 6034.20773518 0.00000000 -18757.71486376  
Rotation angle (degrees) 3.95975327  
Shift along axis 673.54365999  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.6.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99768923 -0.03022978 -0.06084703 -1006.89207790  
0.02947478 0.99947746 -0.01326802 -1022.01473868  
0.06121632 0.01144391 0.99805892 -114.63440044  
Axis 0.17892746 -0.88380320 0.43229256  
Axis point 6034.20773518 0.00000000 -18757.71486376  
Rotation angle (degrees) 3.95975327  
Shift along axis 673.54365999  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.6.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99768923 -0.03022978 -0.06084703 -1006.89207790  
0.02947478 0.99947746 -0.01326802 -1022.01473868  
0.06121632 0.01144391 0.99805892 -114.63440044  
Axis 0.17892746 -0.88380320 0.43229256  
Axis point 6034.20773518 0.00000000 -18757.71486376  
Rotation angle (degrees) 3.95975327  
Shift along axis 673.54365999  
  
Position of PHIKZ139-docker.pdb (#6.6.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99768923 -0.03022978 -0.06084703 -1006.89207790  
0.02947478 0.99947746 -0.01326802 -1022.01473868  
0.06121632 0.01144391 0.99805892 -114.63440044  
Axis 0.17892746 -0.88380320 0.43229256  
Axis point 6034.20773518 0.00000000 -18757.71486376  
Rotation angle (degrees) 3.95975327  
Shift along axis 673.54365999  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.6.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99768923 -0.03022978 -0.06084703 -1006.89207790  
0.02947478 0.99947746 -0.01326802 -1022.01473868  
0.06121632 0.01144391 0.99805892 -114.63440044  
Axis 0.17892746 -0.88380320 0.43229256  
Axis point 6034.20773518 0.00000000 -18757.71486376  
Rotation angle (degrees) 3.95975327  
Shift along axis 673.54365999  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.6.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99768923 -0.03022978 -0.06084703 -1006.89207790  
0.02947478 0.99947746 -0.01326802 -1022.01473868  
0.06121632 0.01144391 0.99805892 -114.63440044  
Axis 0.17892746 -0.88380320 0.43229256  
Axis point 6034.20773518 0.00000000 -18757.71486376  
Rotation angle (degrees) 3.95975327  
Shift along axis 673.54365999  
  

> view matrix models
> #6,-0.24546,-0.9313,0.26913,1505,0.85011,-0.073368,0.52147,902.29,-0.4659,0.35679,0.80972,196.26

> view matrix models
> #6,-0.26445,-0.9627,-0.057176,1593,0.72795,-0.23815,0.64293,954.49,-0.63257,0.1284,0.76378,316.75

> view matrix models
> #6,-0.37708,-0.86499,0.33105,1508.2,0.86775,-0.20501,0.45275,949.87,-0.32375,0.45799,0.8279,124.49

> view matrix models
> #6,-0.25987,-0.95736,0.12623,1549.1,0.96538,-0.2545,0.05727,1027.6,-0.022701,0.13675,0.99035,96.091

> fitmap sel inMap #4

Fit molecules PHIKZ049-other-A-fit-coot-0.pdb (#6.1.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.1.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.1.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.1.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.1.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.1.6), PHIKZ139-docker.pdb
(#6.1.7), PHIKZ161-horn-fit-coot-1.pdb (#6.1.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.1.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.2.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.2.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.2.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.2.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.2.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.2.6), PHIKZ139-docker.pdb
(#6.2.7), PHIKZ161-horn-fit-coot-1.pdb (#6.2.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.2.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.3.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.3.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.3.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.3.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.3.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.3.6), PHIKZ139-docker.pdb
(#6.3.7), PHIKZ161-horn-fit-coot-1.pdb (#6.3.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.3.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.4.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.4.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.4.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.4.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.4.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.4.6), PHIKZ139-docker.pdb
(#6.4.7), PHIKZ161-horn-fit-coot-1.pdb (#6.4.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.4.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.5.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.5.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.5.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.5.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.5.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.5.6), PHIKZ139-docker.pdb
(#6.5.7), PHIKZ161-horn-fit-coot-1.pdb (#6.5.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.5.9), PHIKZ049-other-A-fit-coot-0.pdb (#6.6.1), PHIKZ049-other-B-fit-
coot-0.pdb (#6.6.2), PHIKZ062-sheath-init-fit-coot-0.pdb (#6.6.3),
PHIKZ087-wedge2A-fit-coot-5.pdb (#6.6.4), PHIKZ087-wedge2B-fit-coot-8.pdb
(#6.6.5), PHIKZ128-wedge1-fit-coot-5.pdb (#6.6.6), PHIKZ139-docker.pdb
(#6.6.7), PHIKZ161-horn-fit-coot-1.pdb (#6.6.8), PHIKZ174-pin-fit-coot-1.pdb
(#6.6.9) to map cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) using 193758
atoms  
average map value = 0.2803, steps = 160  
shifted from previous position = 11.9  
rotated from previous position = 11.1 degrees  
atoms outside contour = 126717, contour level = 0.34127  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.1.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98947133 0.14282104 -0.02342314 -1051.84115905  
-0.13835384 0.98092091 0.13657376 -985.60632753  
0.04248186 -0.13189513 0.99035295 -73.84231346  
Axis -0.68086192 -0.16714117 -0.71308546  
Axis point -6333.51244376 2447.39245532 0.00000000  
Rotation angle (degrees) 11.37056415  
Shift along axis 933.54987002  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.1.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98947133 0.14282104 -0.02342314 -1051.84115905  
-0.13835384 0.98092091 0.13657376 -985.60632753  
0.04248186 -0.13189513 0.99035295 -73.84231346  
Axis -0.68086192 -0.16714117 -0.71308546  
Axis point -6333.51244376 2447.39245532 0.00000000  
Rotation angle (degrees) 11.37056415  
Shift along axis 933.54987002  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.1.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98947133 0.14282104 -0.02342314 -1051.84115905  
-0.13835384 0.98092091 0.13657376 -985.60632753  
0.04248186 -0.13189513 0.99035295 -73.84231346  
Axis -0.68086192 -0.16714117 -0.71308546  
Axis point -6333.51244376 2447.39245532 0.00000000  
Rotation angle (degrees) 11.37056415  
Shift along axis 933.54987002  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.1.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98947133 0.14282104 -0.02342314 -1051.84115905  
-0.13835384 0.98092091 0.13657376 -985.60632753  
0.04248186 -0.13189513 0.99035295 -73.84231346  
Axis -0.68086192 -0.16714117 -0.71308546  
Axis point -6333.51244376 2447.39245532 0.00000000  
Rotation angle (degrees) 11.37056415  
Shift along axis 933.54987002  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.1.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98947133 0.14282104 -0.02342314 -1051.84115905  
-0.13835384 0.98092091 0.13657376 -985.60632753  
0.04248186 -0.13189513 0.99035295 -73.84231346  
Axis -0.68086192 -0.16714117 -0.71308546  
Axis point -6333.51244376 2447.39245532 0.00000000  
Rotation angle (degrees) 11.37056415  
Shift along axis 933.54987002  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.1.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98947133 0.14282104 -0.02342314 -1051.84115905  
-0.13835384 0.98092091 0.13657376 -985.60632753  
0.04248186 -0.13189513 0.99035295 -73.84231346  
Axis -0.68086192 -0.16714117 -0.71308546  
Axis point -6333.51244376 2447.39245532 0.00000000  
Rotation angle (degrees) 11.37056415  
Shift along axis 933.54987002  
  
Position of PHIKZ139-docker.pdb (#6.1.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98947133 0.14282104 -0.02342314 -1051.84115905  
-0.13835384 0.98092091 0.13657376 -985.60632753  
0.04248186 -0.13189513 0.99035295 -73.84231346  
Axis -0.68086192 -0.16714117 -0.71308546  
Axis point -6333.51244376 2447.39245532 0.00000000  
Rotation angle (degrees) 11.37056415  
Shift along axis 933.54987002  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.1.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98947133 0.14282104 -0.02342314 -1051.84115905  
-0.13835384 0.98092091 0.13657376 -985.60632753  
0.04248186 -0.13189513 0.99035295 -73.84231346  
Axis -0.68086192 -0.16714117 -0.71308546  
Axis point -6333.51244376 2447.39245532 0.00000000  
Rotation angle (degrees) 11.37056415  
Shift along axis 933.54987002  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.1.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98947133 0.14282104 -0.02342314 -1051.84115905  
-0.13835384 0.98092091 0.13657376 -985.60632753  
0.04248186 -0.13189513 0.99035295 -73.84231346  
Axis -0.68086192 -0.16714117 -0.71308546  
Axis point -6333.51244376 2447.39245532 0.00000000  
Rotation angle (degrees) 11.37056415  
Shift along axis 933.54987002  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.2.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98500885 0.13578583 0.10639446 -1054.32471810  
-0.14539376 0.98541362 0.08843448 -983.22455121  
-0.09283440 -0.10257783 0.99038354 -45.01188897  
Axis -0.48479689 0.50565080 -0.71364504  
Axis point -7601.05310055 6760.89008460 0.00000000  
Rotation angle (degrees) 11.36172271  
Shift along axis 46.08757909  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.2.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98500885 0.13578583 0.10639446 -1054.32471810  
-0.14539376 0.98541362 0.08843448 -983.22455121  
-0.09283440 -0.10257783 0.99038354 -45.01188897  
Axis -0.48479689 0.50565080 -0.71364504  
Axis point -7601.05310055 6760.89008460 0.00000000  
Rotation angle (degrees) 11.36172271  
Shift along axis 46.08757909  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.2.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98500885 0.13578583 0.10639446 -1054.32471810  
-0.14539376 0.98541362 0.08843448 -983.22455121  
-0.09283440 -0.10257783 0.99038354 -45.01188897  
Axis -0.48479689 0.50565080 -0.71364504  
Axis point -7601.05310055 6760.89008460 0.00000000  
Rotation angle (degrees) 11.36172271  
Shift along axis 46.08757909  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.2.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98500885 0.13578583 0.10639446 -1054.32471810  
-0.14539376 0.98541362 0.08843448 -983.22455121  
-0.09283440 -0.10257783 0.99038354 -45.01188897  
Axis -0.48479689 0.50565080 -0.71364504  
Axis point -7601.05310055 6760.89008460 0.00000000  
Rotation angle (degrees) 11.36172271  
Shift along axis 46.08757909  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.2.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98500885 0.13578583 0.10639446 -1054.32471810  
-0.14539376 0.98541362 0.08843448 -983.22455121  
-0.09283440 -0.10257783 0.99038354 -45.01188897  
Axis -0.48479689 0.50565080 -0.71364504  
Axis point -7601.05310055 6760.89008460 0.00000000  
Rotation angle (degrees) 11.36172271  
Shift along axis 46.08757909  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.2.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98500885 0.13578583 0.10639446 -1054.32471810  
-0.14539376 0.98541362 0.08843448 -983.22455121  
-0.09283440 -0.10257783 0.99038354 -45.01188897  
Axis -0.48479689 0.50565080 -0.71364504  
Axis point -7601.05310055 6760.89008460 0.00000000  
Rotation angle (degrees) 11.36172271  
Shift along axis 46.08757909  
  
Position of PHIKZ139-docker.pdb (#6.2.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98500885 0.13578583 0.10639446 -1054.32471810  
-0.14539376 0.98541362 0.08843448 -983.22455121  
-0.09283440 -0.10257783 0.99038354 -45.01188897  
Axis -0.48479689 0.50565080 -0.71364504  
Axis point -7601.05310055 6760.89008460 0.00000000  
Rotation angle (degrees) 11.36172271  
Shift along axis 46.08757909  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.2.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98500885 0.13578583 0.10639446 -1054.32471810  
-0.14539376 0.98541362 0.08843448 -983.22455121  
-0.09283440 -0.10257783 0.99038354 -45.01188897  
Axis -0.48479689 0.50565080 -0.71364504  
Axis point -7601.05310055 6760.89008460 0.00000000  
Rotation angle (degrees) 11.36172271  
Shift along axis 46.08757909  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.2.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98500885 0.13578583 0.10639446 -1054.32471810  
-0.14539376 0.98541362 0.08843448 -983.22455121  
-0.09283440 -0.10257783 0.99038354 -45.01188897  
Axis -0.48479689 0.50565080 -0.71364504  
Axis point -7601.05310055 6760.89008460 0.00000000  
Rotation angle (degrees) 11.36172271  
Shift along axis 46.08757909  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.3.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98117532 0.14316201 0.12961342 -1056.63112442  
-0.13799376 0.98926635 -0.04806050 -980.58161972  
-0.13510263 0.02926993 0.99039919 -69.37825297  
Axis 0.19635418 0.67215582 -0.71389886  
Axis point -3576.55938501 5789.75274318 0.00000000  
Rotation angle (degrees) 11.35665439  
Shift along axis -817.04852787  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.3.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98117532 0.14316201 0.12961342 -1056.63112442  
-0.13799376 0.98926635 -0.04806050 -980.58161972  
-0.13510263 0.02926993 0.99039919 -69.37825297  
Axis 0.19635418 0.67215582 -0.71389886  
Axis point -3576.55938501 5789.75274318 0.00000000  
Rotation angle (degrees) 11.35665439  
Shift along axis -817.04852787  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.3.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98117532 0.14316201 0.12961342 -1056.63112442  
-0.13799376 0.98926635 -0.04806050 -980.58161972  
-0.13510263 0.02926993 0.99039919 -69.37825297  
Axis 0.19635418 0.67215582 -0.71389886  
Axis point -3576.55938501 5789.75274318 0.00000000  
Rotation angle (degrees) 11.35665439  
Shift along axis -817.04852787  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.3.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98117532 0.14316201 0.12961342 -1056.63112442  
-0.13799376 0.98926635 -0.04806050 -980.58161972  
-0.13510263 0.02926993 0.99039919 -69.37825297  
Axis 0.19635418 0.67215582 -0.71389886  
Axis point -3576.55938501 5789.75274318 0.00000000  
Rotation angle (degrees) 11.35665439  
Shift along axis -817.04852787  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.3.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98117532 0.14316201 0.12961342 -1056.63112442  
-0.13799376 0.98926635 -0.04806050 -980.58161972  
-0.13510263 0.02926993 0.99039919 -69.37825297  
Axis 0.19635418 0.67215582 -0.71389886  
Axis point -3576.55938501 5789.75274318 0.00000000  
Rotation angle (degrees) 11.35665439  
Shift along axis -817.04852787  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.3.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98117532 0.14316201 0.12961342 -1056.63112442  
-0.13799376 0.98926635 -0.04806050 -980.58161972  
-0.13510263 0.02926993 0.99039919 -69.37825297  
Axis 0.19635418 0.67215582 -0.71389886  
Axis point -3576.55938501 5789.75274318 0.00000000  
Rotation angle (degrees) 11.35665439  
Shift along axis -817.04852787  
  
Position of PHIKZ139-docker.pdb (#6.3.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98117532 0.14316201 0.12961342 -1056.63112442  
-0.13799376 0.98926635 -0.04806050 -980.58161972  
-0.13510263 0.02926993 0.99039919 -69.37825297  
Axis 0.19635418 0.67215582 -0.71389886  
Axis point -3576.55938501 5789.75274318 0.00000000  
Rotation angle (degrees) 11.35665439  
Shift along axis -817.04852787  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.3.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98117532 0.14316201 0.12961342 -1056.63112442  
-0.13799376 0.98926635 -0.04806050 -980.58161972  
-0.13510263 0.02926993 0.99039919 -69.37825297  
Axis 0.19635418 0.67215582 -0.71389886  
Axis point -3576.55938501 5789.75274318 0.00000000  
Rotation angle (degrees) 11.35665439  
Shift along axis -817.04852787  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.3.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98117532 0.14316201 0.12961342 -1056.63112442  
-0.13799376 0.98926635 -0.04806050 -980.58161972  
-0.13510263 0.02926993 0.99039919 -69.37825297  
Axis 0.19635418 0.67215582 -0.71389886  
Axis point -3576.55938501 5789.75274318 0.00000000  
Rotation angle (degrees) 11.35665439  
Shift along axis -817.04852787  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.4.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98948876 0.14276667 0.02301478 -1054.51672348  
-0.13836056 0.98094188 -0.13641621 -974.20285413  
-0.04205185 0.13179796 0.99038424 -122.57512868  
Axis 0.68081455 0.16516021 -0.71359208  
Axis point -6527.79692668 3131.90200120 0.00000000  
Rotation angle (degrees) 11.36043312  
Shift along axis -791.36122733  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.4.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98948876 0.14276667 0.02301478 -1054.51672348  
-0.13836056 0.98094188 -0.13641621 -974.20285413  
-0.04205185 0.13179796 0.99038424 -122.57512868  
Axis 0.68081455 0.16516021 -0.71359208  
Axis point -6527.79692668 3131.90200120 0.00000000  
Rotation angle (degrees) 11.36043312  
Shift along axis -791.36122733  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.4.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98948876 0.14276667 0.02301478 -1054.51672348  
-0.13836056 0.98094188 -0.13641621 -974.20285413  
-0.04205185 0.13179796 0.99038424 -122.57512868  
Axis 0.68081455 0.16516021 -0.71359208  
Axis point -6527.79692668 3131.90200120 0.00000000  
Rotation angle (degrees) 11.36043312  
Shift along axis -791.36122733  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.4.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98948876 0.14276667 0.02301478 -1054.51672348  
-0.13836056 0.98094188 -0.13641621 -974.20285413  
-0.04205185 0.13179796 0.99038424 -122.57512868  
Axis 0.68081455 0.16516021 -0.71359208  
Axis point -6527.79692668 3131.90200120 0.00000000  
Rotation angle (degrees) 11.36043312  
Shift along axis -791.36122733  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.4.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98948876 0.14276667 0.02301478 -1054.51672348  
-0.13836056 0.98094188 -0.13641621 -974.20285413  
-0.04205185 0.13179796 0.99038424 -122.57512868  
Axis 0.68081455 0.16516021 -0.71359208  
Axis point -6527.79692668 3131.90200120 0.00000000  
Rotation angle (degrees) 11.36043312  
Shift along axis -791.36122733  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.4.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98948876 0.14276667 0.02301478 -1054.51672348  
-0.13836056 0.98094188 -0.13641621 -974.20285413  
-0.04205185 0.13179796 0.99038424 -122.57512868  
Axis 0.68081455 0.16516021 -0.71359208  
Axis point -6527.79692668 3131.90200120 0.00000000  
Rotation angle (degrees) 11.36043312  
Shift along axis -791.36122733  
  
Position of PHIKZ139-docker.pdb (#6.4.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98948876 0.14276667 0.02301478 -1054.51672348  
-0.13836056 0.98094188 -0.13641621 -974.20285413  
-0.04205185 0.13179796 0.99038424 -122.57512868  
Axis 0.68081455 0.16516021 -0.71359208  
Axis point -6527.79692668 3131.90200120 0.00000000  
Rotation angle (degrees) 11.36043312  
Shift along axis -791.36122733  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.4.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98948876 0.14276667 0.02301478 -1054.51672348  
-0.13836056 0.98094188 -0.13641621 -974.20285413  
-0.04205185 0.13179796 0.99038424 -122.57512868  
Axis 0.68081455 0.16516021 -0.71359208  
Axis point -6527.79692668 3131.90200120 0.00000000  
Rotation angle (degrees) 11.36043312  
Shift along axis -791.36122733  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.4.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98948876 0.14276667 0.02301478 -1054.51672348  
-0.13836056 0.98094188 -0.13641621 -974.20285413  
-0.04205185 0.13179796 0.99038424 -122.57512868  
Axis 0.68081455 0.16516021 -0.71359208  
Axis point -6527.79692668 3131.90200120 0.00000000  
Rotation angle (degrees) 11.36043312  
Shift along axis -791.36122733  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.5.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98497048 0.13574355 -0.10680282 -1045.76653442  
-0.14537896 0.98542993 -0.08827693 -975.20353136  
0.09326367 0.10247705 0.99035364 -151.40437105  
Axis 0.48382383 -0.50744387 -0.71303241  
Axis point -7097.89273369 7263.30776439 0.00000000  
Rotation angle (degrees) 11.36927556  
Shift along axis 96.85050286  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.5.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98497048 0.13574355 -0.10680282 -1045.76653442  
-0.14537896 0.98542993 -0.08827693 -975.20353136  
0.09326367 0.10247705 0.99035364 -151.40437105  
Axis 0.48382383 -0.50744387 -0.71303241  
Axis point -7097.89273369 7263.30776439 0.00000000  
Rotation angle (degrees) 11.36927556  
Shift along axis 96.85050286  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.5.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98497048 0.13574355 -0.10680282 -1045.76653442  
-0.14537896 0.98542993 -0.08827693 -975.20353136  
0.09326367 0.10247705 0.99035364 -151.40437105  
Axis 0.48382383 -0.50744387 -0.71303241  
Axis point -7097.89273369 7263.30776439 0.00000000  
Rotation angle (degrees) 11.36927556  
Shift along axis 96.85050286  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.5.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98497048 0.13574355 -0.10680282 -1045.76653442  
-0.14537896 0.98542993 -0.08827693 -975.20353136  
0.09326367 0.10247705 0.99035364 -151.40437105  
Axis 0.48382383 -0.50744387 -0.71303241  
Axis point -7097.89273369 7263.30776439 0.00000000  
Rotation angle (degrees) 11.36927556  
Shift along axis 96.85050286  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.5.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98497048 0.13574355 -0.10680282 -1045.76653442  
-0.14537896 0.98542993 -0.08827693 -975.20353136  
0.09326367 0.10247705 0.99035364 -151.40437105  
Axis 0.48382383 -0.50744387 -0.71303241  
Axis point -7097.89273369 7263.30776439 0.00000000  
Rotation angle (degrees) 11.36927556  
Shift along axis 96.85050286  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.5.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98497048 0.13574355 -0.10680282 -1045.76653442  
-0.14537896 0.98542993 -0.08827693 -975.20353136  
0.09326367 0.10247705 0.99035364 -151.40437105  
Axis 0.48382383 -0.50744387 -0.71303241  
Axis point -7097.89273369 7263.30776439 0.00000000  
Rotation angle (degrees) 11.36927556  
Shift along axis 96.85050286  
  
Position of PHIKZ139-docker.pdb (#6.5.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98497048 0.13574355 -0.10680282 -1045.76653442  
-0.14537896 0.98542993 -0.08827693 -975.20353136  
0.09326367 0.10247705 0.99035364 -151.40437105  
Axis 0.48382383 -0.50744387 -0.71303241  
Axis point -7097.89273369 7263.30776439 0.00000000  
Rotation angle (degrees) 11.36927556  
Shift along axis 96.85050286  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.5.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98497048 0.13574355 -0.10680282 -1045.76653442  
-0.14537896 0.98542993 -0.08827693 -975.20353136  
0.09326367 0.10247705 0.99035364 -151.40437105  
Axis 0.48382383 -0.50744387 -0.71303241  
Axis point -7097.89273369 7263.30776439 0.00000000  
Rotation angle (degrees) 11.36927556  
Shift along axis 96.85050286  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.5.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98497048 0.13574355 -0.10680282 -1045.76653442  
-0.14537896 0.98542993 -0.08827693 -975.20353136  
0.09326367 0.10247705 0.99035364 -151.40437105  
Axis 0.48382383 -0.50744387 -0.71303241  
Axis point -7097.89273369 7263.30776439 0.00000000  
Rotation angle (degrees) 11.36927556  
Shift along axis 96.85050286  
  
Position of PHIKZ049-other-A-fit-coot-0.pdb (#6.6.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98111952 0.14317410 -0.13002178 -1045.39737632  
-0.13797223 0.98926169 0.04821805 -983.96407327  
0.13552914 -0.02936828 0.99033800 -127.03791984  
Axis -0.19670167 -0.67324117 -0.71277961  
Axis point -2890.06512833 5603.44449664 0.00000000  
Rotation angle (degrees) 11.37433827  
Shift along axis 958.62657930  
  
Position of PHIKZ049-other-B-fit-coot-0.pdb (#6.6.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98111952 0.14317410 -0.13002178 -1045.39737632  
-0.13797223 0.98926169 0.04821805 -983.96407327  
0.13552914 -0.02936828 0.99033800 -127.03791984  
Axis -0.19670167 -0.67324117 -0.71277961  
Axis point -2890.06512833 5603.44449664 0.00000000  
Rotation angle (degrees) 11.37433827  
Shift along axis 958.62657930  
  
Position of PHIKZ062-sheath-init-fit-coot-0.pdb (#6.6.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98111952 0.14317410 -0.13002178 -1045.39737632  
-0.13797223 0.98926169 0.04821805 -983.96407327  
0.13552914 -0.02936828 0.99033800 -127.03791984  
Axis -0.19670167 -0.67324117 -0.71277961  
Axis point -2890.06512833 5603.44449664 0.00000000  
Rotation angle (degrees) 11.37433827  
Shift along axis 958.62657930  
  
Position of PHIKZ087-wedge2A-fit-coot-5.pdb (#6.6.4) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98111952 0.14317410 -0.13002178 -1045.39737632  
-0.13797223 0.98926169 0.04821805 -983.96407327  
0.13552914 -0.02936828 0.99033800 -127.03791984  
Axis -0.19670167 -0.67324117 -0.71277961  
Axis point -2890.06512833 5603.44449664 0.00000000  
Rotation angle (degrees) 11.37433827  
Shift along axis 958.62657930  
  
Position of PHIKZ087-wedge2B-fit-coot-8.pdb (#6.6.5) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98111952 0.14317410 -0.13002178 -1045.39737632  
-0.13797223 0.98926169 0.04821805 -983.96407327  
0.13552914 -0.02936828 0.99033800 -127.03791984  
Axis -0.19670167 -0.67324117 -0.71277961  
Axis point -2890.06512833 5603.44449664 0.00000000  
Rotation angle (degrees) 11.37433827  
Shift along axis 958.62657930  
  
Position of PHIKZ128-wedge1-fit-coot-5.pdb (#6.6.6) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98111952 0.14317410 -0.13002178 -1045.39737632  
-0.13797223 0.98926169 0.04821805 -983.96407327  
0.13552914 -0.02936828 0.99033800 -127.03791984  
Axis -0.19670167 -0.67324117 -0.71277961  
Axis point -2890.06512833 5603.44449664 0.00000000  
Rotation angle (degrees) 11.37433827  
Shift along axis 958.62657930  
  
Position of PHIKZ139-docker.pdb (#6.6.7) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98111952 0.14317410 -0.13002178 -1045.39737632  
-0.13797223 0.98926169 0.04821805 -983.96407327  
0.13552914 -0.02936828 0.99033800 -127.03791984  
Axis -0.19670167 -0.67324117 -0.71277961  
Axis point -2890.06512833 5603.44449664 0.00000000  
Rotation angle (degrees) 11.37433827  
Shift along axis 958.62657930  
  
Position of PHIKZ161-horn-fit-coot-1.pdb (#6.6.8) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98111952 0.14317410 -0.13002178 -1045.39737632  
-0.13797223 0.98926169 0.04821805 -983.96407327  
0.13552914 -0.02936828 0.99033800 -127.03791984  
Axis -0.19670167 -0.67324117 -0.71277961  
Axis point -2890.06512833 5603.44449664 0.00000000  
Rotation angle (degrees) 11.37433827  
Shift along axis 958.62657930  
  
Position of PHIKZ174-pin-fit-coot-1.pdb (#6.6.9) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.98111952 0.14317410 -0.13002178 -1045.39737632  
-0.13797223 0.98926169 0.04821805 -983.96407327  
0.13552914 -0.02936828 0.99033800 -127.03791984  
Axis -0.19670167 -0.67324117 -0.71277961  
Axis point -2890.06512833 5603.44449664 0.00000000  
Rotation angle (degrees) 11.37433827  
Shift along axis 958.62657930  
  

> select subtract #6

Nothing selected  

> volume #4 level 0.3

> hide #!4 models

> hide #!6.1.7 models

> show #!6.1.7 models

> hide #!6.1.7 models

> show #!6.1.7 models

> hide #!6.1.7 models

> show #!6.1.7 models

> hide #!6.1.7 models

> save F:/1_study/phiKZ/tail-all/tail-al-5.cxs

——— End of log from Tue Feb 25 10:58:22 2025 ———

opened ChimeraX session  

> close #6.1.7#6.2.7#6.3.7#6.4.7#6.5.7#6.6.7

> rename #6.2.9 id #6.2.7

> rename #6.1.9 id #6.1.7

> rename #6.3.9 id #6.3.7

> rename #6.4.9 id #6.4.7

> rename #6.5.9 id #6.5.7

> rename #6.6.9 id #6.6.7

> save F:/1_study/phiKZ/tail-all/tail-all-5.cxs

——— End of log from Tue Feb 25 11:14:14 2025 ———

opened ChimeraX session  

> hide #!6 models

> show #!6 models

> select #6.1.6#6.2.6#6.3.6#6.4.6#6.5.6#6.6.6

30138 atoms, 30828 bonds, 3666 residues, 6 models selected  

> ui tool show "Color Actions"

QWindowsWindow::setGeometry: Unable to set geometry 408x779+1236+468 (frame:
430x835+1225+423) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 402x762+1239+482 (frame:
424x818+1228+437) margins: 11, 45, 11, 11 minimum size: 272x519 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=430, y=835)))  

> color sel seashell

> color sel blanched almond

> color sel peach puff

> color sel pink

> select #6.1.5#6.2.5#6.3.5#6.4.5#6.5.5#6.6.5

46230 atoms, 47106 bonds, 6 pseudobonds, 5778 residues, 12 models selected  

> color sel dark violet

> color sel slate blue

> select #6.1.1#6.2.1#6.3.1#6.4.1#6.5.1#6.6.1

12540 atoms, 12804 bonds, 1614 residues, 6 models selected  

> color sel gold

> color sel tomato

> select #6.1.2#6.2.2#6.3.2#6.4.2#6.5.2#6.6.2

12444 atoms, 12702 bonds, 1602 residues, 6 models selected  

> color sel chartreuse

> color sel pale green

> color sel tan

> color sel medium slate blue

> color sel burly wood

> color sel tan

> color sel burly wood

> color sel tan

> color sel wheat

> ui tool show "Color Zone"

> select add #6

186888 atoms, 190566 bonds, 24 pseudobonds, 23424 residues, 73 models selected  

> select subtract #6

Nothing selected  

> show #!4 models

> select add #4

2 models selected  

> select subtract #4

Nothing selected  

> hide #!4 models

> select add #6

186888 atoms, 190566 bonds, 24 pseudobonds, 23424 residues, 73 models selected  

> color zone #4 near sel distance 8.16

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!6 models

> select subtract #6

Nothing selected  

> volume splitbyzone #4

Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 0 as #7.1, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 1 as #7.2, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 2 as #7.3, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 3 as #7.4, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 4 as #7.5, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 5 as #7.6, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 6 as #7.7, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 7 as #7.8, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 8 as #7.9, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 9 as #7.10, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 10 as #7.11, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 11 as #7.12, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  

> hide #!7.1 models

> hide #!7.6 models

> hide #!7.4 models

> hide #!7.7 models

> volume #7.2 level 0.154

> volume #7.3 level 0.1332

> volume #7.5 level 0.1401

> volume #7.6 level 0.2178

> volume #7.8 level 0.1346

> volume #7.9 level 0.1726

> volume #7.10 level 0.1701

> volume #7.11 level 0.1271

> volume #7.12 level 0.13

> show #!7.1 models

> color #7.1 #ff557fff models

> color #7.1 #aaaa00ff models

> color #7.1 #0055ffff models

> color #7.1 cyan models

> color #7.1 #55aa00ff models

> color #7.1 #ffaa00ff models

> color #7.1 #ff55ffff models

> save D:/phiKZ/tail-all/tail-all-6.cxs

> select add #7.11

2 models selected  

> color sel tan

> color sel papaya whip

> color sel seashell

> color sel cornsilk

> color sel navajo white

> color sel pink

> color sel dark sea green

> color sel wheat

> color sel burly wood

> color sel light sea green

> select subtract #7.11

Nothing selected  

> select add #7.3

2 models selected  

> color sel dark goldenrod

> color sel slate gray

> color sel pale violet red

> hide #!7.1 models

> hide #!7.5 models

> show #!7.5 models

> select add #7.5

4 models selected  

> color sel gold

> color sel orange

> color sel goldenrod

[Repeated 1 time(s)]

> color sel sandy brown

> color sel indian red

> color sel orange

> color sel green yellow

> color sel orange

> color sel dark salmon

> color sel light salmon

> color sel yellow

> color sel gold

> color sel dark orange

> color sel orange

> show #!7.1 models

> open D:/phiKZ/EMDB&PDB-241227/4baseplate/spike-C3/PHIKZ_p51-spike-coot-2.pdb
> D:/phiKZ/EMDB&PDB-241227/4baseplate/spike-C3/PHIKZ101-hub-coot-3.pdb
> D:/phiKZ/EMDB&PDB-241227/4baseplate/spike-C3/PHIKZ174-pin-coot-1.pdb

Summary of feedback from opening
D:/phiKZ/EMDB&PDB-241227/4baseplate/spike-C3/PHIKZ_p51-spike-coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
157 messages similar to the above omitted  
Start residue of secondary structure not found: SHEET 1 1 1 GLY D 27 ALA D 29
0  
Start residue of secondary structure not found: SHEET 2 2 2 LEU D 40 MET D 41
0  
Start residue of secondary structure not found: SHEET 3 3 3 VAL D 42 PRO D 44
0  
Start residue of secondary structure not found: SHEET 4 4 4 VAL D 60 ASP D 68
0  
Start residue of secondary structure not found: SHEET 5 5 5 THR D 75 SER D 81
0  
31 messages similar to the above omitted  
  
Chain information for PHIKZ_p51-spike-coot-2.pdb #8  
---  
Chain | Description  
A | No description available  
  
Chain information for PHIKZ101-hub-coot-3.pdb #9  
---  
Chain | Description  
B | No description available  
  
Chain information for PHIKZ174-pin-coot-1.pdb #10  
---  
Chain | Description  
A | No description available  
D | No description available  
  
Computing secondary structure  
[Repeated 1 time(s)]

> select add #7

25 models selected  

> select subtract #7

Nothing selected  

> select add #8

2138 atoms, 2180 bonds, 1 pseudobond, 274 residues, 2 models selected  

> select add #9

5635 atoms, 5743 bonds, 6 pseudobonds, 711 residues, 4 models selected  

> select add #10

10697 atoms, 10907 bonds, 8 pseudobonds, 1357 residues, 6 models selected  

> hide #!7 models

> hide #!5 models

> show #!4 models

> hide #!4 models

> show #!5 models

> hide #!5 models

> show #!7 models

> hide #!7 models

> show #!4 models

> color single #4

> ui mousemode right "translate selected models"

> view matrix models
> #8,1,0,0,467.28,0,1,0,1112.5,0,0,1,-87.709,#9,1,0,0,467.28,0,1,0,1112.5,0,0,1,-87.709,#10,1,0,0,467.28,0,1,0,1112.5,0,0,1,-87.709

> view matrix models
> #8,1,0,0,503.46,0,1,0,1238.7,0,0,1,-16.892,#9,1,0,0,503.46,0,1,0,1238.7,0,0,1,-16.892,#10,1,0,0,503.46,0,1,0,1238.7,0,0,1,-16.892

> view matrix models
> #8,1,0,0,613.84,0,1,0,1197.4,0,0,1,0.3393,#9,1,0,0,613.84,0,1,0,1197.4,0,0,1,0.3393,#10,1,0,0,613.84,0,1,0,1197.4,0,0,1,0.3393

> view matrix models
> #8,1,0,0,739.78,0,1,0,1150.3,0,0,1,20,#9,1,0,0,739.78,0,1,0,1150.3,0,0,1,20,#10,1,0,0,739.78,0,1,0,1150.3,0,0,1,20

> view matrix models
> #8,1,0,0,808.41,0,1,0,1124.6,0,0,1,30.715,#9,1,0,0,808.41,0,1,0,1124.6,0,0,1,30.715,#10,1,0,0,808.41,0,1,0,1124.6,0,0,1,30.715

> view matrix models
> #8,1,0,0,886.24,0,1,0,1095.5,0,0,1,42.865,#9,1,0,0,886.24,0,1,0,1095.5,0,0,1,42.865,#10,1,0,0,886.24,0,1,0,1095.5,0,0,1,42.865

> view matrix models
> #8,1,0,0,950.62,0,1,0,1071.4,0,0,1,52.916,#9,1,0,0,950.62,0,1,0,1071.4,0,0,1,52.916,#10,1,0,0,950.62,0,1,0,1071.4,0,0,1,52.916

> view matrix models
> #8,1,0,0,1012.9,0,1,0,1048.1,0,0,1,62.636,#9,1,0,0,1012.9,0,1,0,1048.1,0,0,1,62.636,#10,1,0,0,1012.9,0,1,0,1048.1,0,0,1,62.636

> view matrix models
> #8,1,0,0,1004.4,0,1,0,1028.8,0,0,1,70.586,#9,1,0,0,1004.4,0,1,0,1028.8,0,0,1,70.586,#10,1,0,0,1004.4,0,1,0,1028.8,0,0,1,70.586

> view matrix models
> #8,1,0,0,1000.9,0,1,0,1012,0,0,1,53.039,#9,1,0,0,1000.9,0,1,0,1012,0,0,1,53.039,#10,1,0,0,1000.9,0,1,0,1012,0,0,1,53.039

> close #8

> close #9

> close #10

> open D:/phiKZ/EMDB&PDB-241227/4baseplate/spike-C3/PHIKZ_p51-spike-coot-2.pdb
> D:/phiKZ/EMDB&PDB-241227/4baseplate/spike-C3/PHIKZ101-hub-coot-3.pdb
> D:/phiKZ/EMDB&PDB-241227/4baseplate/spike-C3/PHIKZ174-pin-coot-1.pdb

Summary of feedback from opening
D:/phiKZ/EMDB&PDB-241227/4baseplate/spike-C3/PHIKZ_p51-spike-coot-2.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
157 messages similar to the above omitted  
Start residue of secondary structure not found: SHEET 1 1 1 GLY D 27 ALA D 29
0  
Start residue of secondary structure not found: SHEET 2 2 2 LEU D 40 MET D 41
0  
Start residue of secondary structure not found: SHEET 3 3 3 VAL D 42 PRO D 44
0  
Start residue of secondary structure not found: SHEET 4 4 4 VAL D 60 ASP D 68
0  
Start residue of secondary structure not found: SHEET 5 5 5 THR D 75 SER D 81
0  
31 messages similar to the above omitted  
  
Chain information for PHIKZ_p51-spike-coot-2.pdb #8  
---  
Chain | Description  
A | No description available  
  
Chain information for PHIKZ101-hub-coot-3.pdb #9  
---  
Chain | Description  
B | No description available  
  
Chain information for PHIKZ174-pin-coot-1.pdb #10  
---  
Chain | Description  
A | No description available  
D | No description available  
  
Computing secondary structure  
[Repeated 1 time(s)]

> sym #8-10 C3 center 204,204,204

Made 3 copies for PHIKZ_p51-spike-coot-2.pdb, PHIKZ101-hub-coot-3.pdb,
PHIKZ174-pin-coot-1.pdb symmetry C3  

> select add #11

32091 atoms, 32721 bonds, 24 pseudobonds, 4071 residues, 22 models selected  

> view matrix models #11,1,0,0,458.91,0,1,0,1220.8,0,0,1,-12.589

> view matrix models #11,1,0,0,462.17,0,1,0,1250.4,0,0,1,37.403

> view matrix models #11,1,0,0,518.2,0,1,0,1229.4,0,0,1,46.151

> view matrix models #11,1,0,0,572.93,0,1,0,1209,0,0,1,54.695

> view matrix models #11,1,0,0,619.19,0,1,0,1191.6,0,0,1,61.917

> view matrix models #11,1,0,0,690.21,0,1,0,1165.1,0,0,1,73.004

> view matrix models #11,1,0,0,747.55,0,1,0,1143.6,0,0,1,81.955

> view matrix models #11,1,0,0,812.05,0,1,0,1119.5,0,0,1,92.024

> view matrix models #11,1,0,0,875.25,0,1,0,1095.8,0,0,1,101.89

> view matrix models #11,1,0,0,926.08,0,1,0,1076.8,0,0,1,109.82

> view matrix models #11,1,0,0,920.11,0,1,0,1059.2,0,0,1,105.95

> view matrix models #11,1,0,0,950.74,0,1,0,1047.8,0,0,1,110.74

> view matrix models #11,1,0,0,992.46,0,1,0,1031.8,0,0,1,122.14

> view matrix models #11,1,0,0,1039.5,0,1,0,1013.8,0,0,1,135.01

> view matrix models #11,1,0,0,1041.6,0,1,0,1004.8,0,0,1,114.86

> view matrix models #11,1,0,0,1066.7,0,1,0,995.21,0,0,1,121.74

> view matrix models #11,1,0,0,1091.6,0,1,0,985.69,0,0,1,128.54

> view matrix models #11,1,0,0,1093,0,1,0,985.41,0,0,1,123.14

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.95576,-0.18247,0.2307,1090.4,0.19309,0.98089,-0.024122,952.52,-0.22189,0.0676,0.97273,163.06

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.95576,-0.18247,0.2307,1091.8,0.19309,0.98089,-0.024122,946.73,-0.22189,0.0676,0.97273,126.37

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.99957,-0.024996,-0.015359,1102.3,0.026684,0.99218,0.1219,948.73,0.012192,-0.12226,0.99242,116.49

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.99957,-0.024996,-0.015359,1057.6,0.026684,0.99218,0.1219,927.66,0.012192,-0.12226,0.99242,121.72

> view matrix models
> #11,0.99957,-0.024996,-0.015359,1037.1,0.026684,0.99218,0.1219,938.64,0.012192,-0.12226,0.99242,116.81

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.92673,-0.37433,0.032445,1114.7,0.37321,0.92706,0.035747,894.52,-0.04346,-0.021019,0.99883,106.82

> view matrix models
> #11,0.87868,-0.47546,0.043251,1141.6,0.47609,0.87938,-0.0050681,890.47,-0.035624,0.025044,0.99905,96.475

> view matrix models
> #11,0.27219,-0.91177,0.30754,1284.2,0.95874,0.28422,-0.0058919,916.82,-0.082037,0.29645,0.95152,61.545

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.27219,-0.91177,0.30754,1270.4,0.95874,0.28422,-0.0058919,925.77,-0.082037,0.29645,0.95152,62.505

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.13883,-0.92971,0.34112,1294.1,0.98805,0.15332,0.015725,944.4,-0.066919,0.33486,0.93989,53.477

> view matrix models
> #11,0.086695,-0.91295,0.39875,1288.8,0.9849,0.13875,0.10354,929.47,-0.14985,0.38376,0.9112,65.97

> view matrix models
> #11,-0.048714,-0.44625,0.89358,1116.5,0.055527,0.89205,0.44851,886.56,-0.99727,0.071466,-0.018676,491.37

> undo

> view matrix models
> #11,0.05527,-0.95119,0.30363,1324.4,0.97585,0.11582,0.18519,918.85,-0.21132,0.28606,0.93462,95.599

> view matrix models
> #11,0.017873,-0.95432,0.29824,1334.1,0.98273,0.071719,0.17059,930.56,-0.18419,0.29004,0.93912,88.323

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.017873,-0.95432,0.29824,1332.8,0.98273,0.071719,0.17059,936.97,-0.18419,0.29004,0.93912,98.84

> view matrix models
> #11,0.017873,-0.95432,0.29824,1328.8,0.98273,0.071719,0.17059,931.51,-0.18419,0.29004,0.93912,101.68

> view matrix models
> #11,0.017873,-0.95432,0.29824,1322.2,0.98273,0.071719,0.17059,922.45,-0.18419,0.29004,0.93912,106.4

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.72072,-0.64838,0.2453,1432.2,0.6757,-0.73611,0.039602,1178.4,0.15489,0.19429,0.96864,45.408

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.72072,-0.64838,0.2453,1499.2,0.6757,-0.73611,0.039602,1109.2,0.15489,0.19429,0.96864,-25.838

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.68704,-0.70264,0.18514,1516.8,0.72534,-0.64809,0.23207,1039.2,-0.043076,0.29373,0.95492,-3.9645

> view matrix models
> #11,0.3391,-0.76538,-0.547,1470.1,0.9241,0.3799,0.041304,833.58,0.17619,-0.51949,0.83612,131.73

> view matrix models
> #11,0.3783,-0.64528,-0.6637,1462.6,0.87863,0.47599,0.03803,822.76,0.29137,-0.59753,0.74703,145.34

> view matrix models
> #11,0.36151,-0.80681,-0.4673,1454.8,0.61846,0.58257,-0.52737,976.28,0.69772,-0.098358,0.70958,-24.377

> view matrix models
> #11,0.77419,-0.62671,0.088737,1214.6,0.59679,0.67604,-0.43222,941.1,0.21089,0.38757,0.89739,-75.468

> view matrix models
> #11,0.72828,-0.66809,0.15255,1217.6,0.66486,0.63489,-0.39354,926.94,0.16606,0.38803,0.90656,-68.637

> view matrix models
> #11,0.77212,-0.63487,0.027648,1230.5,0.63466,0.76819,-0.084222,838.03,0.032232,0.082576,0.99606,-3.2514

> view matrix models
> #11,0.767,-0.64066,0.035447,1230.9,0.64093,0.76236,-0.089567,839.07,0.030359,0.091417,0.99535,-4.3929

> view matrix models
> #11,0.72763,-0.6579,-0.19422,1292.6,0.67435,0.73793,0.0267,811.21,0.12576,-0.1504,0.98059,25.031

> view matrix models
> #11,0.54447,-0.83072,-0.116,1343.9,0.82576,0.55514,-0.09972,845.97,0.14724,-0.041495,0.98823,-2.01

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.54447,-0.83072,-0.116,1385,0.82576,0.55514,-0.09972,907.11,0.14724,-0.041495,0.98823,30.008

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.45131,-0.88244,-0.13276,1416.8,0.87725,0.46599,-0.11522,919.57,0.16354,-0.064459,0.98443,32.565

> view matrix models
> #11,0.40476,-0.90987,-0.091131,1422,0.89719,0.41441,-0.15268,935.15,0.17668,-0.019964,0.98407,20.676

> view matrix models
> #11,0.43427,-0.895,-0.10188,1415.6,0.88444,0.44511,-0.1402,928.22,0.17082,-0.029223,0.98487,23.581

> view matrix models
> #11,0.533,-0.83976,-0.10352,1386.1,0.83186,0.54245,-0.11732,912.41,0.15467,-0.023583,0.98768,24.748

> view matrix models
> #11,0.61151,-0.78467,-0.10176,1359.8,0.77867,0.61963,-0.098623,902.42,0.14044,-0.01893,0.98991,25.936

> view matrix models
> #11,0.60922,-0.78885,-0.080968,1356.4,0.78661,0.61409,-0.064353,894.34,0.10049,-0.024484,0.99464,33.54

> view matrix models
> #11,0.60585,-0.79339,-0.059017,1353.1,0.79348,0.60797,-0.027656,886.12,0.057823,-0.030073,0.99787,41.921

> view matrix models
> #11,0.6033,-0.79621,-0.045621,1351.1,0.79689,0.6041,-0.0049919,881.07,0.031534,-0.033343,0.99895,47.367

> ui mousemode right "translate selected models"

> view matrix models
> #11,0.6033,-0.79621,-0.045621,1256.9,0.79689,0.6041,-0.0049919,936,0.031534,-0.033343,0.99895,63.665

> view matrix models
> #11,0.6033,-0.79621,-0.045621,1223.9,0.79689,0.6041,-0.0049919,955.23,0.031534,-0.033343,0.99895,69.37

> view matrix models
> #11,0.6033,-0.79621,-0.045621,1234,0.79689,0.6041,-0.0049919,962.22,0.031534,-0.033343,0.99895,104.06

> view matrix models
> #11,0.6033,-0.79621,-0.045621,1262.6,0.79689,0.6041,-0.0049919,945.51,0.031534,-0.033343,0.99895,99.107

> view matrix models
> #11,0.6033,-0.79621,-0.045621,1271.3,0.79689,0.6041,-0.0049919,940.48,0.031534,-0.033343,0.99895,97.613

> view matrix models
> #11,0.6033,-0.79621,-0.045621,1270.8,0.79689,0.6041,-0.0049919,938.73,0.031534,-0.033343,0.99895,100.84

> view matrix models
> #11,0.6033,-0.79621,-0.045621,1271,0.79689,0.6041,-0.0049919,938.66,0.031534,-0.033343,0.99895,102.21

> view matrix models
> #11,0.6033,-0.79621,-0.045621,1266.3,0.79689,0.6041,-0.0049919,941.4,0.031534,-0.033343,0.99895,103.02

> ui tool show "Fit in Map"

> hide #!4 models

> show #!4 models

> fitmap sel inMap #4

Fit molecules PHIKZ_p51-spike-coot-2.pdb (#11.1.1), PHIKZ101-hub-coot-3.pdb
(#11.1.2), PHIKZ174-pin-coot-1.pdb (#11.1.3), PHIKZ_p51-spike-coot-2.pdb
(#11.2.1), PHIKZ101-hub-coot-3.pdb (#11.2.2), PHIKZ174-pin-coot-1.pdb
(#11.2.3), PHIKZ_p51-spike-coot-2.pdb (#11.3.1), PHIKZ101-hub-coot-3.pdb
(#11.3.2), PHIKZ174-pin-coot-1.pdb (#11.3.3) to map
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) using 32091 atoms  
average map value = 0.1989, steps = 104  
shifted from previous position = 7.59  
rotated from previous position = 7.48 degrees  
atoms outside contour = 22537, contour level = 0.29998  
  
Position of PHIKZ_p51-spike-coot-2.pdb (#11.1.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99176379 -0.12411695 0.03161583 -994.31265182  
0.12515598 0.99157720 -0.03332616 -1046.32933535  
-0.02721320 0.03700859 0.99894435 -104.60470218  
Axis 0.26481185 0.22149254 0.93851784  
Axis point 6825.90120608 -7198.34798734 0.00000000  
Rotation angle (degrees) 7.63150343  
Shift along axis -593.23329978  
  
Position of PHIKZ101-hub-coot-3.pdb (#11.1.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99176379 -0.12411695 0.03161583 -994.31265182  
0.12515598 0.99157720 -0.03332616 -1046.32933535  
-0.02721320 0.03700859 0.99894435 -104.60470218  
Axis 0.26481185 0.22149254 0.93851784  
Axis point 6825.90120608 -7198.34798734 0.00000000  
Rotation angle (degrees) 7.63150343  
Shift along axis -593.23329978  
  
Position of PHIKZ174-pin-coot-1.pdb (#11.1.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99176379 -0.12411695 0.03161583 -994.31265182  
0.12515598 0.99157720 -0.03332616 -1046.32933535  
-0.02721320 0.03700859 0.99894435 -104.60470218  
Axis 0.26481185 0.22149254 0.93851784  
Axis point 6825.90120608 -7198.34798734 0.00000000  
Rotation angle (degrees) 7.63150343  
Shift along axis -593.23329978  
  
Position of PHIKZ_p51-spike-coot-2.pdb (#11.2.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99115660 -0.12481736 -0.04504696 -987.24039787  
0.12445481 0.99216676 -0.01077620 -1043.17911337  
0.04603915 0.00507460 0.99892675 -113.03249100  
Axis 0.05961959 -0.34260201 0.93758699  
Axis point 7315.67298832 -8519.77716558 0.00000000  
Rotation angle (degrees) 7.63910194  
Shift along axis 192.55860289  
  
Position of PHIKZ101-hub-coot-3.pdb (#11.2.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99115660 -0.12481736 -0.04504696 -987.24039787  
0.12445481 0.99216676 -0.01077620 -1043.17911337  
0.04603915 0.00507460 0.99892675 -113.03249100  
Axis 0.05961959 -0.34260201 0.93758699  
Axis point 7315.67298832 -8519.77716558 0.00000000  
Rotation angle (degrees) 7.63910194  
Shift along axis 192.55860289  
  
Position of PHIKZ174-pin-coot-1.pdb (#11.2.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99115660 -0.12481736 -0.04504696 -987.24039787  
0.12445481 0.99216676 -0.01077620 -1043.17911337  
0.04603915 0.00507460 0.99892675 -113.03249100  
Axis 0.05961959 -0.34260201 0.93758699  
Axis point 7315.67298832 -8519.77716558 0.00000000  
Rotation angle (degrees) 7.63910194  
Shift along axis 192.55860289  
  
Position of PHIKZ_p51-spike-coot-2.pdb (#11.3.1) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99207818 -0.12496685 0.01281328 -988.09220338  
0.12429042 0.99125465 0.04434074 -1050.41697278  
-0.01824234 -0.04239691 0.99893429 -90.23442886  
Axis -0.32640203 0.11686525 0.93797880  
Axis point 7988.73525612 -8112.56882139 0.00000000  
Rotation angle (degrees) 7.63543278  
Shift along axis 115.12007071  
  
Position of PHIKZ101-hub-coot-3.pdb (#11.3.2) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99207818 -0.12496685 0.01281328 -988.09220338  
0.12429042 0.99125465 0.04434074 -1050.41697278  
-0.01824234 -0.04239691 0.99893429 -90.23442886  
Axis -0.32640203 0.11686525 0.93797880  
Axis point 7988.73525612 -8112.56882139 0.00000000  
Rotation angle (degrees) 7.63543278  
Shift along axis 115.12007071  
  
Position of PHIKZ174-pin-coot-1.pdb (#11.3.3) relative to
cryosparc_P10_J379_008_volume_map_sharp.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99207818 -0.12496685 0.01281328 -988.09220338  
0.12429042 0.99125465 0.04434074 -1050.41697278  
-0.01824234 -0.04239691 0.99893429 -90.23442886  
Axis -0.32640203 0.11686525 0.93797880  
Axis point 7988.73525612 -8112.56882139 0.00000000  
Rotation angle (degrees) 7.63543278  
Shift along axis 115.12007071  
  

> transparency (#!11.1.1-3#!11.2.1-3#!11.3.1-3 & sel) 20

> transparency #4.1 50

> select subtract #11

Nothing selected  

> select add #11

32091 atoms, 32721 bonds, 24 pseudobonds, 4071 residues, 22 models selected  

> hide #!4 models

> show #!4 models

> select subtract #11

Nothing selected  

> hide #!4 models

> close #8

> close #9

> close #10

> select #11.1.1#11.2.1#11.3.1\

Expected an objects specifier or a keyword  

> select #11.1.1#11.2.1#11.3.1

6414 atoms, 6540 bonds, 3 pseudobonds, 822 residues, 6 models selected  

> color sel medium orchid

> rename #11 id #8

> show #!6 models

> hide #!6 models

> color sel orange red

> color sel yellow green

> color sel light salmon

> color sel sandy brown

> color sel goldenrod

> color sel deep pink

> color sel pale violet red

> select #8.1.3#8.2.3#8.3.3

15186 atoms, 15492 bonds, 6 pseudobonds, 1938 residues, 6 models selected  

> color sel khaki

> color sel sky blue

> color sel wheat

> color sel pale goldenrod

> color sel navajo white

> color sel plum

> select #8.1.2#8.2.2#8.3.2

10491 atoms, 10689 bonds, 15 pseudobonds, 1311 residues, 6 models selected  

> color sel dark cyan

> select #8.1.1#8.2.1#8.3.1

6414 atoms, 6540 bonds, 3 pseudobonds, 822 residues, 6 models selected  

> select #8.1.1#8.2.1#8.3.1

6414 atoms, 6540 bonds, 3 pseudobonds, 822 residues, 6 models selected  

> color sel seashell

> color sel bisque

[Repeated 1 time(s)]

> color sel moccasin

> color sel navajo white

> color sel light pink

> color sel light blue

> color sel lemon chiffon

> color sel gold

> color sel sandy brown

> save D:/phiKZ/tail-all/tail-all-7.cxs

> graphics silhouettes true

> lighting soft

> lighting full

> lighting soft

> lighting flat

> lighting full

> lighting soft

> lighting simple

> save D:/phiKZ/tail-all/1.png width 1500 height 1123 supersample 4
> transparentBackground true

> save D:/phiKZ/tail-all/1.png width 1500 height 1123 supersample 4

> lighting soft

> save D:/phiKZ/tail-all/2.png width 1500 height 1123 supersample 4

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting full

> lighting soft

> select clear

> graphics silhouettes false

> graphics silhouettes true

> lighting soft

> select add #8

32091 atoms, 32721 bonds, 24 pseudobonds, 4071 residues, 22 models selected  

> show #!4 models

> hide #!4 models

> color zone #4 near sel distance 8.16

> show #!4 models

> hide #!8 models

> volume #!4 style surface

> transparency #4.1 0

Need to color zone map before it can be split  

[Repeated 1 time(s)]

> hide #!4 models

> show #!7 models

> hide #!7 models

> show #!4 models

> show #!8 models

> hide #!4 models

> hide #!8 models

> select subtract #8

Nothing selected  

> show #!8 models

> show #!4 models

> hide #!8 models

No atoms selected for color zoning  

Need to color zone map before it can be split  

> show #!5 models

> hide #!4 models

> hide #!5 models

> show #!4 models

> hide #4.1 models

> show #4.1 models

> select add #8

32091 atoms, 32721 bonds, 24 pseudobonds, 4071 residues, 22 models selected  

Need to color zone map before it can be split  

> hide #!4 models

> show #!8 models

> show #!4 models

> hide #!4 models

> color zone #4 near sel distance 8.16

> volume splitbyzone #4

Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 0 as #9.1, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 1 as #9.2, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 2 as #9.3, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  
Opened cryosparc_P10_J379_008_volume_map_sharp.mrc 3 as #9.4, grid size
300,300,300, pixel 1.36, shown at level 0.3, step 1, values float32  

> hide #!8 models

> transparency #9.1.1#9.2.1#9.3.1#9.4.1 0

> hide #!9.1 models

> volume #9.2 level 0.2131

> volume #9.3 level 0.2452

> volume #9.4 level 0.2513

> select subtract #8

Nothing selected  

> show #!5 models

> hide #!5 models

> show #!7 models

> hide #!7.1 models

> show #!7.1 models

> hide #!7.1 models

> show #!7.1 models

> hide #!7.1 models

> show #!7.1 models

> hide #!7.1 models

> hide #!7.12 models

> show #!7.12 models

> hide #!7.11 models

> show #!7.11 models

> hide #!9.3 models

> show #!9.3 models

> hide #!9.4 models

> show #!9.4 models

> hide #!9.4 models

> select add #9.3

2 models selected  

> hide #!1 models

> color sel tomato

> select subtract #9.3

Nothing selected  

> select add #9.3

2 models selected  

> color sel magenta

> color sel dark orchid

> color sel pale turquoise

> color sel floral white

> color sel bisque

> color sel peach puff

> color sel plum

> color sel dark sea green

> color sel medium slate blue

> color sel dark goldenrod

> color sel peru

> color sel lime

> color sel tomato

> color sel indian red

> color sel olive drab

> select subtract #9.3

Nothing selected  

> select add #9.2

2 models selected  

> color sel light cyan

> color sel medium violet red

> color sel antique white

> color sel light pink

> color sel cornsilk

> color sel lavender blush

> color sel misty rose

> color sel orchid

> select subtract #9.2

Nothing selected  

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> show #!5 models

> show #!2 models

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!1 models

> hide #!5 models

> show #!5 models

> save D:/phiKZ/tail-all/tail-all-8.cxs

——— End of log from Tue Feb 25 20:04:42 2025 ———

opened ChimeraX session  

> hide #!2 models

> open D:/phiKZ/tail-all/tube-all-1.pdb D:/phiKZ/tail-all/tube-all-2.pdb
> D:/phiKZ/tail-all/tube-all-3.pdb D:/phiKZ/tail-all/tube-all-4.pdb
> D:/phiKZ/tail-all/tube-all-5.pdb D:/phiKZ/tail-all/tube-all-6.pdb

Chain information for tube-all-1.pdb #10  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R | No description available  
  
Chain information for tube-all-2.pdb #11  
---  
Chain | Description  
0 1 2 3 4 5 6 7 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z | No description available  
  
Chain information for tube-all-3.pdb #12  
---  
Chain | Description  
0 1 2 3 4 5 6 7 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z | No description available  
  
Chain information for tube-all-4.pdb #13  
---  
Chain | Description  
0 1 2 3 4 5 6 7 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j k l m n o p q r s t u v w x y z | No description available  
  
Chain information for tube-all-5.pdb #14  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d | No description available  
  
Chain information for tube-all-6.pdb #15  
---  
Chain | Description  
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d e f g h i j | No description available  
  

> hide #!7 models

> hide #!5 models

> select add #9

9 models selected  

> select subtract #9

Nothing selected  

> hide #!9 models

> show #!9 models

> hide #!10 models

> hide #!11 models

> hide #!12 models

> hide #!13 models

> hide #!14 models

> hide #!15 models

> show #!9.1 models

> hide #!9 models

> show #!9 models

> hide #!9.1 models

> show #!9.4 models

> hide #!9.2 models

> show #!9.2 models

> hide #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> select add #10

93348 atoms, 95292 bonds, 36 pseudobonds, 11862 residues, 2 models selected  

> select add #11

404508 atoms, 412932 bonds, 156 pseudobonds, 51402 residues, 4 models selected  

> select add #12

715668 atoms, 730572 bonds, 276 pseudobonds, 90942 residues, 6 models selected  

> select add #13

1026828 atoms, 1048212 bonds, 396 pseudobonds, 130482 residues, 8 models
selected  

> select add #14

1182408 atoms, 1207032 bonds, 456 pseudobonds, 150252 residues, 10 models
selected  

> select add #15

1369104 atoms, 1397616 bonds, 528 pseudobonds, 173976 residues, 12 models
selected  

> style sel stick

Changed 1369104 atom styles  

> select subtract #10

1275756 atoms, 1302324 bonds, 492 pseudobonds, 162114 residues, 10 models
selected  

> select add #10

1369104 atoms, 1397616 bonds, 528 pseudobonds, 173976 residues, 12 models
selected  

> style sel ball

Changed 1369104 atom styles  

> select subtract #10

1275756 atoms, 1302324 bonds, 492 pseudobonds, 162114 residues, 10 models
selected  

> select add #10

1369104 atoms, 1397616 bonds, 528 pseudobonds, 173976 residues, 12 models
selected  

> style sel sphere

Changed 1369104 atom styles  

> style sel stick

Changed 1369104 atom styles  

> show #!8 models

> hide #!8 models

> color sel bychain

> select subtract #10

1275756 atoms, 1302324 bonds, 492 pseudobonds, 162114 residues, 10 models
selected  

> select add #10

1369104 atoms, 1397616 bonds, 528 pseudobonds, 173976 residues, 12 models
selected  

> rainbow sel

> select subtract #10

1275756 atoms, 1302324 bonds, 492 pseudobonds, 162114 residues, 10 models
selected  

> select add #10

1369104 atoms, 1397616 bonds, 528 pseudobonds, 173976 residues, 12 models
selected  

> show sel cartoons

> hide sel atoms

[Repeated 1 time(s)]

> select subtract #10

1275756 atoms, 1302324 bonds, 492 pseudobonds, 162114 residues, 10 models
selected  

> select subtract #11

964596 atoms, 984684 bonds, 372 pseudobonds, 122574 residues, 8 models
selected  

> select subtract #12

653436 atoms, 667044 bonds, 252 pseudobonds, 83034 residues, 6 models selected  

> select subtract #13

342276 atoms, 349404 bonds, 132 pseudobonds, 43494 residues, 4 models selected  

> select subtract #15

155580 atoms, 158820 bonds, 60 pseudobonds, 19770 residues, 2 models selected  

> select subtract #14

Nothing selected  

> save D:/phiKZ/tail-all/tail-all-9.cxs

Traceback (most recent call last):  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\session.py", line
1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\session.py", line
746, in save  
fserialize(stream, data)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\serialize.py",
line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\toolbar\tool.py", line
170, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\info.py", line 397, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1419, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\toolbar\\__init__.py",
line 37, in run_provider  
providers.run_provider(session, name)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\toolbar\providers.py",
line 56, in run_provider  
what(session)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\toolbar\providers.py",
line 38, in _file_save  
show_save_file_dialog(session)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\save_command\dialog.py", line 62, in display  
run(session, cmd)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\run.py",
line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\save_command\cmd.py",
line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\save_command\cmd.py",
line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core_formats\\__init__.py", line 95, in save  
return cxs_save(session, path, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\session.py", line
1051, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\session.py", line
746, in save  
fserialize(stream, data)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\serialize.py",
line 76, in msgpack_serialize  
stream.write(packer.pack(obj))  
^^^^^^^^^^^^^^^^  
File "msgpack\\\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> show #!1 models

> hide #!1 models

> save D:/phiKZ/tail-all/tail-all-9.cxs

Ran out of memory trying to save a session including 22 maps (4.1 Gbytes).  
  
To save the session you will either have to save the maps to separate files
(then only the path to the file is included in the session) or close some of
the maps.  
  
#5.1 "cryosparc_P10_J236_006_volume_map_sharp.mrc 0" (421 MB)  
#5.2 "cryosparc_P10_J236_006_volume_map_sharp.mrc 1" (421 MB)  
#5.3 "cryosparc_P10_J236_006_volume_map_sharp.mrc 2" (421 MB)  
#5.4 "cryosparc_P10_J236_006_volume_map_sharp.mrc 3" (421 MB)  
#5.5 "cryosparc_P10_J236_006_volume_map_sharp.mrc 4" (421 MB)  
#5.6 "cryosparc_P10_J236_006_volume_map_sharp.mrc 5" (421 MB)  
#7.1 "cryosparc_P10_J379_008_volume_map_sharp.mrc 0" (102 MB)  
#7.2 "cryosparc_P10_J379_008_volume_map_sharp.mrc 1" (102 MB)  
#7.3 "cryosparc_P10_J379_008_volume_map_sharp.mrc 2" (102 MB)  
#7.4 "cryosparc_P10_J379_008_volume_map_sharp.mrc 3" (102 MB)  
#7.5 "cryosparc_P10_J379_008_volume_map_sharp.mrc 4" (102 MB)  
#7.6 "cryosparc_P10_J379_008_volume_map_sharp.mrc 5" (102 MB)  
#7.7 "cryosparc_P10_J379_008_volume_map_sharp.mrc 6" (102 MB)  
#7.8 "cryosparc_P10_J379_008_volume_map_sharp.mrc 7" (102 MB)  
#7.9 "cryosparc_P10_J379_008_volume_map_sharp.mrc 8" (102 MB)  
#7.10 "cryosparc_P10_J379_008_volume_map_sharp.mrc 9" (102 MB)  
#7.11 "cryosparc_P10_J379_008_volume_map_sharp.mrc 10" (102 MB)  
#7.12 "cryosparc_P10_J379_008_volume_map_sharp.mrc 11" (102 MB)  
#9.1 "cryosparc_P10_J379_008_volume_map_sharp.mrc 0" (102 MB)  
#9.2 "cryosparc_P10_J379_008_volume_map_sharp.mrc 1" (102 MB)  
#9.3 "cryosparc_P10_J379_008_volume_map_sharp.mrc 2" (102 MB)  
#9.4 "cryosparc_P10_J379_008_volume_map_sharp.mrc 3" (102 MB)  
[Repeated 1 time(s)]

> show #!2 models

> select add #10

93348 atoms, 95292 bonds, 36 pseudobonds, 11862 residues, 2 models selected  

> select add #11

404508 atoms, 412932 bonds, 156 pseudobonds, 51402 residues, 4 models selected  

> hide #!2 models

> select add #12

715668 atoms, 730572 bonds, 276 pseudobonds, 90942 residues, 6 models selected  

> select add #13

1026828 atoms, 1048212 bonds, 396 pseudobonds, 130482 residues, 8 models
selected  

> select add #14

1182408 atoms, 1207032 bonds, 456 pseudobonds, 150252 residues, 10 models
selected  

> select add #15

1369104 atoms, 1397616 bonds, 528 pseudobonds, 173976 residues, 12 models
selected  

> ui tool show "Color Actions"

QWindowsWindow::setGeometry: Unable to set geometry 408x779+1236+468 (frame:
430x835+1225+423) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 402x762+1239+482 (frame:
424x818+1228+437) margins: 11, 45, 11, 11 minimum size: 272x519 maximum size:
524287x524287 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=430, y=835)))  

> show #!5 models

> show #!9 models

> show #!7 models

> color sel pale turquoise

> hide #!9.4 models

> hide #!7.12 models

> show #!7.12 models

> color #7.12 slateblue models

> color #7.9 #00aa7fff models

> color #7.9 #aaaa7fff models

> color #7.9 springgreen models

> color #7.9 cyan models

> color #7.9 #aa55ffff models

> hide #!7.9 models

> show #!7.9 models

> select subtract #10

1275756 atoms, 1302324 bonds, 492 pseudobonds, 162114 residues, 10 models
selected  

> select subtract #11

964596 atoms, 984684 bonds, 372 pseudobonds, 122574 residues, 8 models
selected  

> select subtract #12

653436 atoms, 667044 bonds, 252 pseudobonds, 83034 residues, 6 models selected  

> select subtract #13

342276 atoms, 349404 bonds, 132 pseudobonds, 43494 residues, 4 models selected  

> select subtract #14

186696 atoms, 190584 bonds, 72 pseudobonds, 23724 residues, 2 models selected  

> select subtract #15

Nothing selected  

> select add #5.3

2 models selected  

> color sel medium purple

> select subtract #5.3

Nothing selected  

> select add #5.5

2 models selected  

> color sel azure

> color sel alice blue

> color sel light cyan

> select subtract #5.5

Nothing selected  

> select add #5.5

2 models selected  

> color sel light cyan

> color sel plum

> color sel dark sea green

> color sel moccasin

> select subtract #5.5

Nothing selected  

> select add #7.3

2 models selected  

> color sel yellow

> color sel orange

> select subtract #7.3

Nothing selected  

> select add #7.5

2 models selected  

> select subtract #7.5

Nothing selected  

> select add #7.7

2 models selected  

> select subtract #7.7

Nothing selected  

> select add #7.3

2 models selected  

> select subtract #7.3

Nothing selected  

> show #!3 models

> show #!4 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> hide #!4 models

> show #!2 models

> ui tool show "Color Zone"

> select add #10

93348 atoms, 95292 bonds, 36 pseudobonds, 11862 residues, 2 models selected  

> select subtract #10

Nothing selected  

> select add #11

311160 atoms, 317640 bonds, 120 pseudobonds, 39540 residues, 2 models selected  

> select add #10

404508 atoms, 412932 bonds, 156 pseudobonds, 51402 residues, 4 models selected  

> select add #12

715668 atoms, 730572 bonds, 276 pseudobonds, 90942 residues, 6 models selected  

> select add #13

1026828 atoms, 1048212 bonds, 396 pseudobonds, 130482 residues, 8 models
selected  

> select add #14

1182408 atoms, 1207032 bonds, 456 pseudobonds, 150252 residues, 10 models
selected  

> select subtract #14

1026828 atoms, 1048212 bonds, 396 pseudobonds, 130482 residues, 8 models
selected  

> select add #15

1213524 atoms, 1238796 bonds, 468 pseudobonds, 154206 residues, 10 models
selected  

> select add #14

1369104 atoms, 1397616 bonds, 528 pseudobonds, 173976 residues, 12 models
selected  

> color zone #2 near sel distance 18.36

> color zone #2 near sel distance 4

> color zone #2 near sel distance 8

[Repeated 1 time(s)]

> volume splitbyzone #2

Traceback (most recent call last):  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorzonegui.py", line 253, in _split_map  
run(self.session, cmd)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\run.py",
line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\surface\colorzone.py",
line 378, in split_volumes_by_color_zone  
vlist.extend(split_volume_by_color_zone(v))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\surface\colorzone.py",
line 321, in split_volume_by_color_zone  
grids = split_zones_by_color(volume, zc.points, zc.point_colors, zc.distance)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\surface\colorzone.py",
line 362, in split_zones_by_color  
g = masked_grid_data(sg, mask, m)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 345, in masked_grid_data  
putmask(masked, mask == mask_value, matrix)  
^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 488. MiB for an
array with shape (800, 800, 800) and data type bool  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 488. MiB for an
array with shape (800, 800, 800) and data type bool  
  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\map_data\arrays.py",
line 345, in masked_grid_data  
putmask(masked, mask == mask_value, matrix)  
^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> color zone #2 near sel distance 8.1

Traceback (most recent call last):  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\ui\widgets\slider.py",
line 329, in _entry_changed_cb  
self._value_changed(value, slider_down = self._slider.isSliderDown())  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorzonegui.py", line 140, in _distance_changed  
self._color(log_command = not slider_down)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\surface\colorzonegui.py", line 226, in _color  
run(self.session, cmd, log = log_command)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\run.py",
line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3171, in run  
self._process_keyword_arguments(final, prev_annos)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 3088, in _process_keyword_arguments  
value, text = self._parse_arg(anno, text, session, final)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\core\commands\cli.py",
line 2780, in _parse_arg  
value, replacement, rest = annotation.parse(text, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\args.py", line
36, in parse  
atoms = aspec.evaluate(session, order_implicit_atoms=ordered).atoms  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 1129, in evaluate  
add_implied_bonds(results)  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\commands\atomspec.py", line 1143, in add_implied_bonds  
objects.add_pseudobonds(atoms.intra_pseudobonds)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\pbgroup.py",
line 403, in interatom_pseudobonds  
structures = atoms.unique_structures  
^^^^^^^^^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molarray.py",
line 789, in unique_structures  
return self.structures.unique()  
^^^^^^^^^^^^^^^  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line
207, in get_prop  
values = empty(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 10.4 MiB for an
array with shape (1369104,) and data type object  
  
numpy.core._exceptions._ArrayMemoryError: Unable to allocate 10.4 MiB for an
array with shape (1369104,) and data type object  
  
File "D:\软件\ChimeraX 1.9\bin\Lib\site-packages\chimerax\atomic\molc.py", line
207, in get_prop  
values = empty(shape, value_type)  
^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

QWindowsWindow::setGeometry: Unable to set geometry 900x698+990+509 (frame:
922x754+979+464) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 894x681+993+523 (frame: 916x737+982+478)
margins: 11, 45, 11, 11 minimum size: 600x319 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=786453, y=786487), mintrack=POINT(x=922, y=535)))  




OpenGL version: 3.3.0 NVIDIA 556.13
OpenGL renderer: NVIDIA GeForce RTX 4060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: zh_CN.cp936
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: HP
Model: OMEN by HP Gaming Laptop 16-wf0xxx
OS: Microsoft Windows 11 家庭中文版 (Build 26100)
Memory: 14,710,988,800
MaxProcessMemory: 137,438,953,344
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900HX
OSLanguage: zh-CN

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

[pett]

There were also earlier memory errors saving sessions, supposedly due to including maps -- which I find confusing because the command didn't have "includeMaps true".

[Tom Goddard]

The user had 22 open maps that were not saved in separate map files. It is easy to create a lot of maps in memory with the "volume splitbyzone" command which this user used since it creates a copy of the map for every color in a colorzoned map.

Maps that were created in memory are saved in the session even without the includeMaps option.

I am baffled why the session saving out-of-memory errors are always on Windows and almost always the computer has reasonable amount of memory, 14(?) GB in this case.

The error message ChimeraX gave saving a session seems clear enough but the user did not close or save any maps as it suggested and instead did another "volume splitzone" to create even more maps.

> save D:/phiKZ/tail-all/tail-all-9.cxs

Ran out of memory trying to save a session including 22 maps (4.1 Gbytes).  
  
To save the session you will either have to save the maps to separate files
(then only the path to the file is included in the session) or close some of
the maps.