Opened 17 months ago

Closed 17 months ago

#15564 closed defect (fixed)

Fitmap: Tried to get the position of deleted drawing

Reported by: um18fa@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-13.3-arm64-arm-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
RNA structure not fitting within the 3D model with error


Log:
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
> /Volumes/astbury/Users/um18fa/240607_RNA_MSI2_1/Class3D/job006/run_it025_class001.mrc

Opened run_it025_class001.mrc as #1, grid size 128,128,128, pixel 2.92, shown
at level 0.00301, step 1, values float32  

> open
> /Volumes/astbury/Users/um18fa/240607_RNA_MSI2_1/Class3D/job006/run_it025_class002.mrc

Opened run_it025_class002.mrc as #2, grid size 128,128,128, pixel 2.92, shown
at level 0.0248, step 1, values float32  

> tile

2 models tiled  

> surface dust #1 size 29.2

> surface dust #2 size 29.2

> volume #1 level 0.006823

> tile

2 models tiled  

> set bgColor white

> tile

2 models tiled  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2741_004_volume_map_sharp.mrc

Opened cryosparc_P12_J2741_004_volume_map_sharp.mrc as #3, grid size
128,128,128, pixel 2.92, shown at level 0.0695, step 1, values float32  

> tile

3 models tiled  

> surface dust #1 size 29.2

> surface dust #2 size 29.2

> surface dust #3 size 29.2

> volume #3 level 0.2305

> tile

3 models tiled  

> open
> /Volumes/astbury/Users/um18fa/240607_RNA_MSI2_1/Class3D/job008/run_it002_class006.mrc

Opened run_it002_class006.mrc as #4, grid size 128,128,128, pixel 2.92, shown
at level 0.00432, step 1, values float32  

> open
> /Volumes/astbury/Users/um18fa/240607_RNA_MSI2_1/Class3D/job008/run_it002_class005.mrc

Opened run_it002_class005.mrc as #5, grid size 128,128,128, pixel 2.92, shown
at level 0.00434, step 1, values float32  

> open
> /Volumes/astbury/Users/um18fa/240607_RNA_MSI2_1/Class3D/job008/run_it002_class004.mrc

Opened run_it002_class004.mrc as #6, grid size 128,128,128, pixel 2.92, shown
at level 0.0002, step 1, values float32  

> open
> /Volumes/astbury/Users/um18fa/240607_RNA_MSI2_1/Class3D/job008/run_it002_class001.mrc

Opened run_it002_class001.mrc as #7, grid size 128,128,128, pixel 2.92, shown
at level 0.00436, step 1, values float32  

> open
> /Volumes/astbury/Users/um18fa/240607_RNA_MSI2_1/Class3D/job008/run_it002_class002.mrc

Opened run_it002_class002.mrc as #8, grid size 128,128,128, pixel 2.92, shown
at level 0.00434, step 1, values float32  

> open
> /Volumes/astbury/Users/um18fa/240607_RNA_MSI2_1/Class3D/job008/run_it002_class003.mrc

Opened run_it002_class003.mrc as #9, grid size 128,128,128, pixel 2.92, shown
at level 0.00433, step 1, values float32  

> hide #!1 models

> hide #!2 models

> hide #!3 models

> tile

5 models tiled  

> surface dust #4 size 29.2

> surface dust #5 size 29.2

> surface dust #6 size 29.2

> surface dust #7 size 29.2

> surface dust #8 size 29.2

> surface dust #9 size 29.2

> tile

6 models tiled  

> volume #4 level 0.1

> volume #4 level 0.002558

> volume #3 level 0.1794

> tile

6 models tiled  

> volume #4 level 0.008048

> tile

6 models tiled  

> select add #4

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.037521,-0.097135,-0.99456,712.31,0.10616,-0.99002,0.092686,-96.935,-0.99364,-0.10211,0.047458,381.13

> select subtract #4

Nothing selected  

> select add #5

2 models selected  

> view matrix models
> #5,-0.94795,-0.092382,-0.30472,1057,0.063043,-0.9925,0.10477,-55.729,-0.31211,0.080109,0.94666,43.382

> view matrix models
> #5,0.092403,-0.052419,-0.99434,975.2,0.13595,-0.9886,0.06475,-63.25,-0.9864,-0.14116,-0.084223,414.91

> tile

6 models tiled  

> select subtract #5

Nothing selected  

> volume #5 level 0.007077

> tile

6 models tiled  

> select add #6

2 models selected  

> select subtract #6

Nothing selected  

> close #6

> select add #7

2 models selected  

> view matrix models
> #7,-0.91072,0.2585,-0.32214,330.01,-0.27052,-0.96268,-0.0077252,-320.96,-0.31211,0.080109,0.94666,43.208

> view matrix models
> #7,-0.9156,0.2405,-0.32223,335.14,-0.25348,-0.96734,-0.0017141,-324.27,-0.31211,0.080109,0.94666,43.208

> view matrix models
> #7,-0.16419,0.046176,-0.98535,358.55,-0.21191,-0.97723,-0.010485,-328.33,-0.9634,0.20709,0.17023,282.49

> volume #7 level 0.00708

> volume #8 level 0.00708

> select subtract #7

Nothing selected  

> select add #8

2 models selected  

> view matrix models
> #8,-0.014468,-0.081304,-0.99658,717.39,-0.026281,-0.99631,0.081663,-361.3,-0.99955,0.027373,0.012278,384.49

> select subtract #8

Nothing selected  

> select add #9

2 models selected  

> view matrix models
> #9,-0.92176,0.21581,-0.32217,1031.2,-0.2301,-0.97314,0.0064844,-334.64,-0.31211,0.080109,0.94666,43.659

> view matrix models
> #9,-0.043425,-0.0010768,-0.99906,1037.5,-0.2004,-0.97967,0.0097663,-339.45,-0.97875,0.20063,0.042326,310.68

> volume #9 level 0.00708

> select subtract #9

Nothing selected  

> close #8

> close

> open /Users/francescappadoo/CHIKV_apoSHAPE/test1_CHIKV_337.map

Failed opening file /Users/francescappadoo/CHIKV_apoSHAPE/test1_CHIKV_337.map:  
MRC header value nsymbt (774976816) is invalid  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2761_class_02_00800_volume.mrc

Opened cryosparc_P12_J2761_class_02_00800_volume.mrc as #1, grid size
64,64,64, pixel 5.92, shown at level 0.414, step 1, values float32  

> surface dust #1 size 59.2

> volume #1 level 1

> ui tool show "Scale Bar"

> scalebar

> scalebar 50

> save /Users/francescappadoo/Desktop/image19.png supersample 3

> volume #1 level 1.091

> open "/Users/francescappadoo/Downloads/cryosparc_P12_J2701_005_volume_map
> (1).mrc" format mrc

Opened cryosparc_P12_J2701_005_volume_map (1).mrc as #3, grid size
128,128,128, pixel 2.92, shown at level 0.00523, step 1, values float32  

> tile

3 models tiled  

> surface dust #1 size 59.2

> surface dust #3 size 29.2

> volume #3 level 0.2201

> tile

3 models tiled  

> close #3

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2741_004_volume_map_sharp.mrc

Opened cryosparc_P12_J2741_004_volume_map_sharp.mrc as #3, grid size
128,128,128, pixel 2.92, shown at level 0.0695, step 1, values float32  

> tile

3 models tiled  

> surface dust #1 size 59.2

> surface dust #3 size 29.2

> volume #3 level 0.2754

> tile

3 models tiled  

> select add #1

2 models selected  

> view matrix models
> #1,-0.12624,-0.51981,-0.8449,470.31,0.45438,0.72681,-0.51505,64.512,0.88182,-0.44893,0.14444,82.424

> select subtract #1

Nothing selected  

> volume #1 level 1.243

> select add #1

2 models selected  

> view matrix models
> #1,0.11017,-0.73417,-0.66997,434.46,0.25557,0.67233,-0.69473,145.65,0.96049,-0.094684,0.2617,-21.937

> select subtract #1

Nothing selected  

> select add #3

2 models selected  

> view matrix models
> #3,-0.46448,-0.22699,-0.856,452.31,0.42557,-0.90488,0.0090332,190.9,-0.77663,-0.3601,0.5169,215.82

> hide #!1 models

> close #1

> select subtract #3

Nothing selected  

> hide #!3 models

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2761_class_00_final_volume.mrc

Opened cryosparc_P12_J2761_class_00_final_volume.mrc as #1, grid size
128,128,128, pixel 2.96, shown at level 0.147, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2761_class_05_final_volume.mrc

Opened cryosparc_P12_J2761_class_05_final_volume.mrc as #4, grid size
128,128,128, pixel 2.96, shown at level 0.13, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2761_class_04_final_volume.mrc

Opened cryosparc_P12_J2761_class_04_final_volume.mrc as #5, grid size
128,128,128, pixel 2.96, shown at level 0.121, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2761_class_03_final_volume.mrc

Opened cryosparc_P12_J2761_class_03_final_volume.mrc as #6, grid size
128,128,128, pixel 2.96, shown at level 0.117, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2761_class_02_final_volume.mrc

Opened cryosparc_P12_J2761_class_02_final_volume.mrc as #7, grid size
128,128,128, pixel 2.96, shown at level 0.113, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2761_class_01_final_volume.mrc

Opened cryosparc_P12_J2761_class_01_final_volume.mrc as #8, grid size
128,128,128, pixel 2.96, shown at level 0.12, step 1, values float32  

> tile

7 models tiled  

> surface dust #1 size 29.6

> surface dust #4 size 29.6

> surface dust #5 size 29.6

> surface dust #6 size 29.6

> surface dust #7 size 29.6

> surface dust #8 size 29.6

> show #!3 models

> hide #!3 models

> volume #1 level 1

> volume #4 level 1

> tile

7 models tiled  

> volume #1 level 0.5

> volume #4 level 0.5

> volume #5 level 0.5

> volume #6 level 0.5

> volume #7 level 0.5

> volume #8 level 0.5

> tile

7 models tiled  

> tile

7 models tiled  

> tile

7 models tiled  

> tile

7 models tiled  

> tile

7 models tiled  

> hide #!1 models

> hide #!8 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> tile

2 models tiled  

> scalebar off

> scalebar 50

> volume #7 color silver

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/francescappadoo/Desktop/movie6.mp4

Movie saved to /Users/francescappadoo/Desktop/movie6.mp4  
  

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2768_004_volume_map.mrc

Opened cryosparc_P12_J2768_004_volume_map.mrc as #10, grid size 128,128,128,
pixel 2.96, shown at level 0.0253, step 1, values float32  

> tile

3 models tiled  

> surface dust #7 size 29.6

> surface dust #10 size 29.6

> hide #!9 models

> show #!9 models

> hide #!10 models

> show #!10 models

> hide #!7 models

> tile

2 models tiled  

> surface dust #10 size 29.6

> volume #10 level 0.4142

> tile

2 models tiled  

> tile

2 models tiled  

> open
> /Users/francescappadoo/Downloads/rnacomposer-2024-07-03-103043/Kendall_Fran_SHAPE_MaP.pdb

Chain information for Kendall_Fran_SHAPE_MaP.pdb #11  
---  
Chain | Description  
A | No description available  
  

> tile

3 models tiled  

> select add #10

2 models selected  

> view matrix models
> #10,0.67809,-0.17616,-0.71356,987.33,-0.066781,0.95207,-0.29851,279.27,0.73194,0.25007,0.63382,-457.13

> view matrix models
> #10,0.23493,-0.97138,0.034938,1072.8,-0.95966,-0.23751,-0.15046,643.52,0.15445,0.0018186,-0.988,20.963

> view matrix models
> #10,-0.48445,-0.76934,0.41643,1096.1,0.8724,-0.38953,0.29526,235.17,-0.06494,0.50634,0.85989,-398.53

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 10778, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.23506652 0.08984099 -0.96781833 175.87204389  
0.95697267 0.19568578 -0.21426709 424.41690107  
0.17013831 -0.97654272 -0.13197455 -72.42220883  
Axis -0.47022466 -0.70197086 0.53490717  
Axis point -109.52048406 0.00000000 117.72922446  
Rotation angle (degrees) 125.85087667  
Shift along axis -419.36682757  
  

> transparency sel 50

> view matrix models
> #10,-0.49161,-0.77029,0.40618,1099.6,0.82449,-0.26162,0.50177,179.29,-0.28024,0.58156,0.76371,-352.65

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.49161,-0.77029,0.40618,858.51,0.82449,-0.26162,0.50177,10.893,-0.28024,0.58156,0.76371,-453.63

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.4161, steps = 100  
shifted from previous position = 14.5  
rotated from previous position = 16.6 degrees  
atoms outside contour = 8312, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.10586532 0.41122890 -0.90536364 205.95863976  
0.99296797 0.09223083 -0.07421646 226.16213244  
0.05298248 -0.90685405 -0.41810118 157.76482325  
Axis -0.59624383 -0.68626251 0.41657780  
Axis point -68.26209582 0.00000000 171.06121612  
Rotation angle (degrees) 135.71436659  
Shift along axis -212.28683912  
  

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.5355, steps = 176  
shifted from previous position = 11.4  
rotated from previous position = 21.1 degrees  
atoms outside contour = 7782, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.14830951 0.54940412 -0.82228912 234.12524268  
0.92511514 0.37094826 0.08098992 221.66146353  
0.34952291 -0.74870055 -0.56327723 187.13226297  
Axis -0.55903572 -0.78955323 0.25314969  
Axis point -32.47098043 0.00000000 154.30950999  
Rotation angle (degrees) 132.09170865  
Shift along axis -258.52542322  
  

> select subtract #10

Nothing selected  

> fitmap #11 inMap #10 search 100

Found 85 unique fits from 100 random placements having fraction of points
inside contour >= 0.100 (100 of 100).  
  
Average map values and times found:  
0.5647 (1), 0.5444 (1), 0.544 (2), 0.5431 (1), 0.5307 (2), 0.5238 (2), 0.519
(2), 0.5081 (1), 0.504 (1), 0.5031 (1), 0.5029 (1), 0.4996 (1), 0.497 (1),
0.4963 (1), 0.4893 (1), 0.4868 (1), 0.4831 (1), 0.4819 (1), 0.481 (1), 0.4797
(1), 0.4797 (1), 0.4764 (1), 0.4712 (2), 0.4712 (1), 0.4693 (1), 0.4692 (2),
0.4617 (1), 0.4598 (1), 0.4585 (1), 0.4581 (3), 0.4574 (1), 0.456 (1), 0.4551
(1), 0.4524 (1), 0.4517 (1), 0.45 (1), 0.4488 (2), 0.4485 (1), 0.4484 (2),
0.4481 (1), 0.4472 (1), 0.4445 (1), 0.4444 (1), 0.4435 (2), 0.4411 (1), 0.4389
(1), 0.4313 (1), 0.4302 (1), 0.4298 (1), 0.4296 (1), 0.4295 (1), 0.4247 (1),
0.4243 (1), 0.4213 (1), 0.4188 (1), 0.4188 (1), 0.4162 (1), 0.4131 (2), 0.4125
(1), 0.4117 (1), 0.4102 (1), 0.4099 (1), 0.4027 (1), 0.4009 (1), 0.3977 (1),
0.3955 (1), 0.3931 (1), 0.3929 (1), 0.3929 (2), 0.3856 (1), 0.3846 (2), 0.3842
(1), 0.3813 (1), 0.3543 (2), 0.3509 (1), 0.3508 (1), 0.345 (1), 0.3427 (1),
0.341 (1), 0.3297 (1), 0.3065 (1), 0.2982 (1), 0.2929 (1), 0.2773 (1), 0.2568
(1)  
  
Best fit found:  
Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.5647, steps = 244  
shifted from previous position = 39.1  
rotated from previous position = 36.4 degrees  
atoms outside contour = 7438, contour level = 0.41421  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.42316901 0.04439904 0.90496228 186.28849191  
0.68061827 -0.67486759 -0.28515344 174.19949031  
0.59806913 0.73660196 -0.31580183 231.94892009  
Axis 0.82256852 0.24706564 0.51219098  
Axis point 0.00000000 44.18726940 78.36918025  
Rotation angle (degrees) 141.60523538  
Shift along axis 315.07590191  
  
Found 85 fits.  

Populating font family aliases took 148 ms. Replace uses of missing font
family "Courier" with one that exists to avoid this cost.  

> ui tool show "Fit in Map"

Opened Kendall_Fran_SHAPE_MaP.pdb map 15 as #12, grid size 44,50,38, pixel 5,
shown at level 0.0344, step 1, values float32  
Opened Kendall_Fran_SHAPE_MaP.pdb map 15 as #13, grid size 44,50,38, pixel 5,
shown at level 0.0344, step 1, values float32  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4821, correlation about mean = 0.2308, overlap = 224.8  
steps = 48, shift = 0.221, angle = 0.674 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#13) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.41339839 0.04036046 0.90965533 185.75840527  
0.68412919 -0.67303872 -0.28104467 174.44740525  
0.60089012 0.73850518 -0.30584488 231.81517777  
Axis 0.81911875 0.24806573 0.51721163  
Axis point 0.00000000 44.45149585 77.76607486  
Rotation angle (degrees) 141.51237645  
Shift along axis 315.33012039  
  
Average map value = 0.5642 for 10778 atoms, 7420 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4679, correlation about mean = 0.2177, overlap = 213.6  
steps = 52, shift = 1.45, angle = 2.33 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.65753580 0.23882220 0.71457025 205.11366464  
0.73717051 -0.00799717 -0.67565943 222.84277340  
-0.15564795 0.97103035 -0.18131108 217.02479160  
Axis 0.85408830 0.45135593 0.25847824  
Axis point 0.00000000 -1.28711772 110.04354088  
Rotation angle (degrees) 105.41961923  
Shift along axis 331.86277369  
  
Average map value = 0.5427 for 10778 atoms, 7590 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4598, correlation about mean = 0.1822, overlap = 214.4  
steps = 60, shift = 0.857, angle = 1.91 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.82632079 0.27913890 -0.48915790 225.24165691  
-0.54648750 0.18738571 -0.81623403 185.00230901  
-0.13618145 0.94178978 0.30738665 235.73162750  
Axis 0.89056408 -0.17880767 -0.41823849  
Axis point 0.00000000 -59.53199906 301.01946737  
Rotation angle (degrees) 80.76137705  
Shift along axis 68.92025746  
  
Average map value = 0.5426 for 10778 atoms, 7566 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4682, correlation about mean = 0.2215, overlap = 216.2  
steps = 48, shift = 0.901, angle = 1.84 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.67965545 -0.18686234 -0.70933133 174.32359731  
-0.70946594 -0.07820685 0.70038684 144.43435266  
-0.18635046 0.97926813 -0.07941877 209.30303203  
Axis 0.35292996 -0.66184296 -0.66136551  
Axis point 110.85843508 0.00000000 69.07653093  
Rotation angle (degrees) 156.72813938  
Shift along axis -172.49464704  
  
Average map value = 0.5407 for 10778 atoms, 7651 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4647, correlation about mean = 0.1901, overlap = 214.2  
steps = 84, shift = 2.71, angle = 5.69 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.46920511 -0.06557822 -0.88065093 189.25283215  
-0.55282044 0.79947599 0.23500570 200.85016590  
0.68864802 0.59710766 -0.41137119 229.59734151  
Axis 0.21520082 -0.93265006 -0.28957292  
Axis point 68.64336258 0.00000000 152.45177745  
Rotation angle (degrees) 122.72109870  
Shift along axis -213.08072801  
  
Average map value = 0.5268 for 10778 atoms, 7396 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4614, correlation about mean = 0.2179, overlap = 204.6  
steps = 100, shift = 3.78, angle = 9.84 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.22367034 0.09270357 0.97024618 187.24938902  
-0.66366074 -0.71455954 0.22126696 145.13813742  
0.71381089 -0.69340510 -0.09830205 204.07096161  
Axis -0.75326414 0.21118335 -0.62289223  
Axis point 0.00000000 111.42163595 -19.24204134  
Rotation angle (degrees) 142.61707962  
Shift along axis -237.51170792  
  
Average map value = 0.5187 for 10778 atoms, 7672 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4629, correlation about mean = 0.2173, overlap = 202.8  
steps = 64, shift = 5.56, angle = 7.69 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.59980921 0.37270396 0.70804004 208.92867119  
-0.53717555 -0.46826191 0.70155057 141.36911332  
0.59301885 -0.80113823 -0.08066036 176.44737222  
Axis -0.85358221 0.06533625 -0.51684484  
Axis point 0.00000000 93.33669203 -30.40870462  
Rotation angle (degrees) 118.33048036  
Shift along axis -260.29718333  
  
Average map value = 0.5065 for 10778 atoms, 7568 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4479, correlation about mean = 0.1784, overlap = 203.5  
steps = 76, shift = 0.62, angle = 2.36 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.82312182 -0.40685671 0.39615414 144.58905413  
0.44770493 -0.03580152 0.89346434 191.64848304  
-0.34932904 0.91279011 0.21162074 231.57242697  
Axis 0.01703922 0.65728059 0.75345331  
Axis point 71.21303636 23.58980597 0.00000000  
Rotation angle (degrees) 145.45198999  
Shift along axis 302.90952451  
  
Average map value = 0.5062 for 10778 atoms, 7834 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4359, correlation about mean = 0.1949, overlap = 194.1  
steps = 80, shift = 1.58, angle = 3.89 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.36353153 -0.71735404 0.59434671 154.06453562  
-0.79368787 -0.57253760 -0.20557294 152.74816550  
0.48775442 -0.39699350 -0.77749062 208.36200830  
Axis -0.82503803 0.45942136 -0.32900495  
Axis point 0.00000000 125.16238233 66.04141985  
Rotation angle (degrees) 173.33828260  
Shift along axis -125.48546394  
  
Average map value = 0.4988 for 10778 atoms, 7951 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4386, correlation about mean = 0.1922, overlap = 197.9  
steps = 44, shift = 0.542, angle = 1.43 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.05232323 0.82466901 0.56319030 196.81072162  
0.57705195 -0.43530913 0.69102603 180.17878481  
0.81502958 0.36114678 -0.45310007 228.87880940  
Axis -0.68258705 -0.52110654 -0.51236988  
Axis point 0.00000000 19.62200970 40.56135103  
Rotation angle (degrees) 166.01670639  
Shift along axis -345.50340098  
  
Average map value = 0.5019 for 10778 atoms, 7778 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4386, correlation about mean = 0.1922, overlap = 197.9  
steps = 64, shift = 2.88, angle = 0.0181 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.05217555 0.82482000 0.56298285 196.81521140  
0.57695561 -0.43524677 0.69114575 180.17741117  
0.81510726 0.36087702 -0.45317527 228.87378791  
Axis -0.68262857 -0.52111299 -0.51230801  
Axis point 0.00000000 19.63004395 40.57064140  
Rotation angle (degrees) 166.00072942  
Shift along axis -345.49834880  
  
Average map value = 0.5019 for 10778 atoms, 7778 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4347, correlation about mean = 0.1578, overlap = 199.9  
steps = 64, shift = 2.89, angle = 2.16 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.25166472 -0.01011752 -0.96776159 192.93639065  
-0.40071161 -0.90912071 0.11370883 136.43966382  
-0.88096252 0.41640981 0.22473938 169.37895957  
Axis 0.60332323 -0.17300206 -0.77850586  
Axis point 172.71720403 31.67517226 0.00000000  
Rotation angle (degrees) 165.47151041  
Shift along axis -39.06384986  
  
Average map value = 0.4978 for 10778 atoms, 7804 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4437, correlation about mean = 0.2137, overlap = 192  
steps = 76, shift = 3.05, angle = 9.85 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.63263019 -0.26112694 -0.72910339 173.76229965  
0.11950404 -0.96308095 0.24123401 142.50878167  
-0.76517825 0.06548112 0.64047978 161.79096271  
Axis -0.41766632 0.08572977 0.90454699  
Axis point 116.28670561 75.91821700 0.00000000  
Rotation angle (degrees) 167.85428320  
Shift along axis 85.99011375  
  
Average map value = 0.486 for 10778 atoms, 7926 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4532, correlation about mean = 0.2158, overlap = 194.9  
steps = 52, shift = 5.32, angle = 5.4 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.30706124 0.21120131 0.92795873 192.90050762  
-0.94760676 -0.02237298 0.31865478 173.33675647  
0.08806151 -0.97718645 0.19326590 159.46873960  
Axis -0.67118901 0.43502998 -0.60021183  
Axis point 0.00000000 188.85508180 -142.52310767  
Rotation angle (degrees) 105.13076742  
Shift along axis -149.78103829  
  
Average map value = 0.4921 for 10778 atoms, 7716 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.43, correlation about mean = 0.1676, overlap = 193.5  
steps = 192, shift = 1.36, angle = 4.2 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.55179149 0.21630710 0.80544236 148.90126246  
0.80973835 -0.09221595 0.57949979 205.54120225  
0.19962454 0.97196057 -0.12426818 209.07834647  
Axis 0.41999012 0.64831317 0.63505774  
Axis point 7.95375966 0.00000000 1.78414441  
Rotation angle (degrees) 152.14560571  
Shift along axis 328.56894954  
  
Average map value = 0.4796 for 10778 atoms, 7739 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.43, correlation about mean = 0.1676, overlap = 193.5  
steps = 72, shift = 7.98, angle = 0.0324 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.55142554 0.21622208 0.80571576 148.91630853  
0.80992918 -0.09262910 0.57916712 205.57745047  
0.19986143 0.97194020 -0.12404652 209.09304960  
Axis 0.42017591 0.64812332 0.63512862  
Axis point 7.89380241 0.00000000 1.74379564  
Rotation angle (degrees) 152.13491096  
Shift along axis 328.61156568  
  
Average map value = 0.4796 for 10778 atoms, 7740 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4479, correlation about mean = 0.1784, overlap = 203.5  
steps = 204, shift = 37.3, angle = 47 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.82375411 -0.40452584 0.39722534 144.72149249  
0.44857145 -0.03656342 0.89299874 191.60793671  
-0.34671721 0.91379530 0.21157803 231.65932529  
Axis 0.01836984 0.65713307 0.75355072  
Axis point 71.10043081 23.44275430 -0.00000000  
Rotation angle (degrees) 145.52464598  
Shift along axis 303.13747257  
  
Average map value = 0.5063 for 10778 atoms, 7839 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4479, correlation about mean = 0.1785, overlap = 203.5  
steps = 92, shift = 18.1, angle = 0.241 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.82285637 -0.40793076 0.39560062 144.54125754  
0.44723575 -0.03544007 0.89371369 191.66296642  
-0.35055325 0.91232472 0.21160333 231.53651610  
Axis 0.01639625 0.65735920 0.75339899  
Axis point 71.27687477 23.65340794 0.00000000  
Rotation angle (degrees) 145.42121443  
Shift along axis 302.80072791  
  
Average map value = 0.5062 for 10778 atoms, 7836 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4479, correlation about mean = 0.1786, overlap = 203.5  
steps = 56, shift = 0.0691, angle = 0.0984 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.82226646 -0.40947702 0.39522956 144.45674031  
0.44712960 -0.03519815 0.89377636 191.65858668  
-0.35206959 0.91164113 0.21203157 231.51380256  
Axis 0.01571352 0.65731085 0.75345573  
Axis point 71.32488894 23.75601866 -0.00000000  
Rotation angle (degrees) 145.35766002  
Shift along axis 302.68459337  
  
Average map value = 0.5062 for 10778 atoms, 7828 outside contour  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4821, correlation about mean = 0.2308, overlap = 224.8  
steps = 48, shift = 0.221, angle = 0.676 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.41335908 0.04038356 0.90967219 185.75919669  
0.68414742 -0.67303842 -0.28100110 174.44716022  
0.60089650 0.73850422 -0.30583477 231.81482107  
Axis 0.81910693 0.24808140 0.51722284  
Axis point 0.00000000 44.45062499 77.76176663  
Rotation angle (degrees) 141.51370793  
Shift along axis 315.33365968  
  
Average map value = 0.5642 for 10778 atoms, 7421 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4821, correlation about mean = 0.2307, overlap = 224.8  
steps = 40, shift = 0.0593, angle = 0.0266 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.41299959 0.04063261 0.90982437 185.80483468  
0.68435969 -0.67299078 -0.28059802 174.46884142  
0.60090197 0.73853397 -0.30575215 231.84400683  
Axis 0.81899675 0.24825679 0.51731315  
Axis point 0.00000000 44.44288826 77.72863619  
Rotation angle (degrees) 141.52426169  
Shift along axis 315.42258296  
  
Average map value = 0.5642 for 10778 atoms, 7416 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4821, correlation about mean = 0.2308, overlap = 224.8  
steps = 48, shift = 0.221, angle = 0.676 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.41335852 0.04038413 0.90967242 185.75918195  
0.68414850 -0.67303749 -0.28100072 174.44700851  
0.60089566 0.73850504 -0.30583443 231.81474916  
Axis 0.81910669 0.24808208 0.51722288  
Axis point 0.00000000 44.45046638 77.76166056  
Rotation angle (degrees) 141.51367521  
Shift along axis 315.33365809  
  
Average map value = 0.5642 for 10778 atoms, 7421 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4821, correlation about mean = 0.2307, overlap = 224.8  
steps = 40, shift = 0.0612, angle = 0.0256 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.41302088 0.04063533 0.90981459 185.80662577  
0.68436013 -0.67298301 -0.28061559 174.46994045  
0.60088684 0.73854091 -0.30576515 231.84551053  
Axis 0.81900313 0.24825705 0.51730291  
Axis point 0.00000000 44.44230980 77.73085019  
Rotation angle (degrees) 141.52352174  
Shift along axis 315.42395986  
  
Average map value = 0.5642 for 10778 atoms, 7416 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4679, correlation about mean = 0.2177, overlap = 213.6  
steps = 52, shift = 1.45, angle = 2.33 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.65753575 0.23882258 0.71457020 205.11371650  
0.73717064 -0.00799786 -0.67565931 222.84266646  
-0.15564762 0.97103030 -0.18131180 217.02477720  
Axis 0.85408839 0.45135582 0.25847816  
Axis point 0.00000000 -1.28712380 110.04348520  
Rotation angle (degrees) 105.41966244  
Shift along axis 331.86274089  
  
Average map value = 0.5427 for 10778 atoms, 7590 outside contour  

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4821, correlation about mean = 0.2308, overlap = 224.8  
steps = 48, shift = 0.221, angle = 0.676 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.41335852 0.04038413 0.90967242 185.75918189  
0.68414850 -0.67303749 -0.28100072 174.44700859  
0.60089566 0.73850504 -0.30583443 231.81474914  
Axis 0.81910669 0.24808208 0.51722288  
Axis point 0.00000000 44.45046648 77.76166076  
Rotation angle (degrees) 141.51367513  
Shift along axis 315.33365792  
  
Average map value = 0.5642 for 10778 atoms, 7421 outside contour  

> select add #11

10778 atoms, 11624 bonds, 336 residues, 1 model selected  

> view matrix models
> #11,-0.38793,0.91305,-0.1259,728.47,0.62568,0.36118,0.69143,236.27,0.67678,0.18945,-0.71139,-224.95

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.5647, steps = 72  
shifted from previous position = 7.72  
rotated from previous position = 0.667 degrees  
atoms outside contour = 7438, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.42292110 0.04466869 0.90506492 186.29739972  
0.68082200 -0.67479776 -0.28483226 174.19915113  
0.59801269 0.73664967 -0.31579755 231.95076990  
Axis 0.82249362 0.24723737 0.51222839  
Axis point 0.00000000 44.17143209 78.34183502  
Rotation angle (degrees) 141.61325353  
Shift along axis 315.10873289  
  

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.5647, steps = 60  
shifted from previous position = 0.0372  
rotated from previous position = 0.0139 degrees  
atoms outside contour = 7436, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.42310812 0.04476503 0.90497275 186.27491163  
0.68073803 -0.67485901 -0.28488784 174.18896164  
0.59797599 0.73658770 -0.31601150 231.93243929  
Axis 0.82256221 0.24721486 0.51212911  
Axis point 0.00000000 44.16998163 78.35339865  
Rotation angle (degrees) 141.61732201  
Shift along axis 315.06415537  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.11727,0.67466,-0.72876,735.61,-0.99212,-0.047,0.11614,183.46,0.044102,0.73663,0.67485,-240.81

> view matrix models
> #11,0.52545,-0.46045,-0.71546,711.63,0.70504,0.70634,0.063218,251.11,0.47625,-0.53765,0.69578,-274.38

> view matrix models
> #11,0.30175,0.12682,-0.94492,729.18,0.85581,-0.47283,0.20983,212.88,-0.42017,-0.87198,-0.25121,-294.36

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.4893, steps = 116  
shifted from previous position = 15.6  
rotated from previous position = 15.2 degrees  
atoms outside contour = 7873, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.74073576 -0.30490870 0.59861611 188.66284851  
-0.67030849 -0.39472847 0.62839153 150.13178504  
0.04468876 -0.86672958 -0.49677243 154.62121679  
Axis -0.91401736 0.33863425 -0.22338107  
Axis point 0.00000000 144.02179935 -3.39773314  
Rotation angle (degrees) 125.12642766  
Shift along axis -156.14080745  
  

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.4893, steps = 92  
shifted from previous position = 15  
rotated from previous position = 0.00571 degrees  
atoms outside contour = 7874, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.74070087 -0.30487315 0.59867739 188.65872983  
-0.67034123 -0.39476658 0.62833267 150.12620526  
0.04477604 -0.86672473 -0.49677304 154.62500428  
Axis -0.91400735 0.33862908 -0.22342989  
Axis point 0.00000000 144.01516420 -3.39679145  
Rotation angle (degrees) 125.12900639  
Shift along axis -156.14621460  
  

> view matrix models
> #11,-0.74637,0.66317,0.056075,708.56,0.37754,0.3525,0.85628,219.76,0.54809,0.66027,-0.51347,-224.07

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.74637,0.66317,0.056075,694.78,0.37754,0.3525,0.85628,214.34,0.54809,0.66027,-0.51347,-217.45

> view matrix models
> #11,-0.74637,0.66317,0.056075,711.71,0.37754,0.3525,0.85628,225.88,0.54809,0.66027,-0.51347,-211.21

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.531, steps = 88  
shifted from previous position = 3.66  
rotated from previous position = 19.2 degrees  
atoms outside contour = 7603, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.54800315 -0.06028954 -0.83430078 190.11685703  
-0.66257367 0.64008870 0.38895066 197.47222773  
0.51057681 0.76593190 -0.39071682 235.15918283  
Axis 0.24784471 -0.88418405 -0.39596914  
Axis point 84.19298631 -0.00000000 137.19264567  
Rotation angle (degrees) 130.49002382  
Shift along axis -220.59811600  
  

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.531, steps = 80  
shifted from previous position = 8.92  
rotated from previous position = 0.0389 degrees  
atoms outside contour = 7602, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.54842793 -0.05989584 -0.83404998 190.16832146  
-0.66209942 0.64031907 0.38937883 197.46745280  
0.51073591 0.76577021 -0.39082580 235.14431123  
Axis 0.24749907 -0.88427438 -0.39598363  
Axis point 84.20200110 -0.00000000 137.16359351  
Rotation angle (degrees) 130.50145299  
Shift along axis -220.66222421  
  

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.5307, steps = 96  
shifted from previous position = 20  
rotated from previous position = 19.5 degrees  
atoms outside contour = 7465, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.40698735 -0.11135563 -0.90662081 188.12675488  
-0.54580230 0.82551385 0.14362020 201.17040243  
0.73243509 0.55328731 -0.39675179 227.73751892  
Axis 0.23484145 -0.93958790 -0.24904632  
Axis point 63.86485894 0.00000000 160.59973782  
Rotation angle (degrees) 119.28227503  
Shift along axis -201.55450715  
  

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.5307, steps = 48  
shifted from previous position = 2.65  
rotated from previous position = 0.00715 degrees  
atoms outside contour = 7467, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.40688771 -0.11142070 -0.90665754 188.11225684  
-0.54584266 0.82550559 0.14351427 201.17691441  
0.73246037 0.55328653 -0.39670619 227.73767873  
Axis 0.23489138 -0.93958208 -0.24902118  
Axis point 63.85644929 0.00000000 160.60666793  
Rotation angle (degrees) 119.27777596  
Shift along axis -201.54778211  
  

> fitmap #11 inMap #10

Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.5307, steps = 60  
shifted from previous position = 6.08  
rotated from previous position = 0.00453 degrees  
atoms outside contour = 7467, contour level = 0.41421  
  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.40695690 -0.11141842 -0.90662676 188.11638376  
-0.54584142 0.82549788 0.14356327 201.16900880  
0.73242286 0.55329849 -0.39675878 227.73847552  
Axis 0.23487992 -0.93958204 -0.24903215  
Axis point 63.86117089 0.00000000 160.60100235  
Rotation angle (degrees) 119.28202887  
Shift along axis -201.54422840  
  

> fitmap #11 inMap #10 search 500

Found 236 unique fits from 500 random placements having fraction of points
inside contour >= 0.100 (497 of 500).  
  
Average map values and times found:  
0.5647 (8), 0.5477 (4), 0.5444 (10), 0.544 (11), 0.543 (5), 0.5394 (2), 0.5354
(3), 0.5327 (6), 0.5316 (2), 0.531 (1), 0.5307 (8), 0.5246 (2), 0.5246 (2),
0.5238 (5), 0.5215 (1), 0.519 (3), 0.5148 (3), 0.5146 (2), 0.5081 (3), 0.5077
(1), 0.507 (3), 0.5069 (1), 0.5064 (2), 0.5041 (3), 0.504 (2), 0.503 (6),
0.503 (2), 0.5029 (5), 0.502 (1), 0.4996 (3), 0.4989 (1), 0.497 (6), 0.4963
(2), 0.4907 (2), 0.4903 (7), 0.4893 (5), 0.4868 (2), 0.486 (2), 0.4848 (6),
0.4848 (4), 0.4831 (1), 0.4831 (4), 0.4825 (3), 0.4819 (2), 0.481 (4), 0.4797
(2), 0.4797 (1), 0.4787 (1), 0.4767 (5), 0.4764 (4), 0.4762 (5), 0.4744 (1),
0.4716 (4), 0.4712 (2), 0.4698 (2), 0.4693 (3), 0.4691 (1), 0.4682 (3), 0.4664
(3), 0.4646 (2), 0.4641 (2), 0.4628 (2), 0.4617 (1), 0.4603 (3), 0.4603 (1),
0.46 (1), 0.4598 (1), 0.4596 (3), 0.4596 (1), 0.4585 (2), 0.4581 (4), 0.4573
(6), 0.456 (2), 0.4554 (2), 0.4552 (4), 0.4545 (1), 0.4524 (2), 0.4522 (1),
0.4518 (7), 0.4517 (2), 0.4515 (4), 0.4511 (1), 0.4501 (1), 0.45 (3), 0.45
(2), 0.4498 (3), 0.4488 (2), 0.4485 (1), 0.4484 (4), 0.4481 (1), 0.4474 (1),
0.4472 (3), 0.4468 (1), 0.4455 (1), 0.4446 (1), 0.4444 (4), 0.4443 (3), 0.4435
(2), 0.4418 (1), 0.4404 (2), 0.4402 (1), 0.4399 (1), 0.4389 (2), 0.4388 (1),
0.4379 (1), 0.4371 (1), 0.437 (2), 0.435 (2), 0.4337 (2), 0.4331 (1), 0.432
(2), 0.4313 (1), 0.4308 (1), 0.4307 (2), 0.4299 (3), 0.4298 (2), 0.4298 (2),
0.4295 (3), 0.429 (1), 0.4286 (1), 0.4278 (1), 0.4265 (2), 0.4251 (1), 0.4247
(2), 0.4244 (1), 0.4243 (2), 0.4243 (5), 0.423 (2), 0.4223 (2), 0.4217 (1),
0.4216 (2), 0.4213 (1), 0.4199 (1), 0.419 (3), 0.4188 (2), 0.4187 (1), 0.4183
(2), 0.418 (1), 0.4157 (1), 0.4147 (1), 0.4133 (1), 0.4131 (6), 0.4125 (3),
0.4111 (4), 0.4104 (2), 0.4101 (1), 0.4099 (1), 0.4099 (1), 0.4067 (3), 0.4066
(1), 0.4045 (1), 0.404 (1), 0.4027 (1), 0.4027 (1), 0.4008 (1), 0.4007 (1),
0.4004 (1), 0.4004 (1), 0.3994 (1), 0.3989 (1), 0.3988 (2), 0.3978 (1), 0.3972
(1), 0.3964 (4), 0.3962 (2), 0.3955 (3), 0.3955 (1), 0.3929 (1), 0.3929 (3),
0.3915 (1), 0.3894 (1), 0.3887 (1), 0.3846 (2), 0.3841 (1), 0.3833 (1), 0.3822
(1), 0.3812 (1), 0.3805 (3), 0.3805 (2), 0.3801 (2), 0.3795 (1), 0.3785 (1),
0.3779 (1), 0.3776 (2), 0.3775 (1), 0.3753 (1), 0.3693 (2), 0.3692 (1), 0.3681
(2), 0.3675 (1), 0.3669 (1), 0.3662 (1), 0.3643 (2), 0.3643 (2), 0.3631 (2),
0.3613 (1), 0.3609 (1), 0.3564 (2), 0.3561 (1), 0.3555 (1), 0.3549 (1), 0.3536
(1), 0.3517 (2), 0.3478 (1), 0.3462 (1), 0.3458 (2), 0.345 (2), 0.3445 (1),
0.3395 (1), 0.3383 (1), 0.3381 (2), 0.338 (1), 0.3355 (1), 0.3332 (1), 0.3305
(1), 0.3292 (3), 0.3267 (1), 0.3252 (2), 0.3244 (1), 0.3215 (1), 0.3202 (1),
0.3174 (1), 0.3096 (1), 0.3065 (1), 0.3059 (3), 0.3018 (4), 0.3006 (1), 0.2811
(1), 0.2737 (1), 0.2728 (1), 0.2711 (1), 0.27 (1), 0.2239 (1), 0.1624 (1),
0.1622 (1), 0.1472 (1)  
  
Best fit found:  
Fit molecule Kendall_Fran_SHAPE_MaP.pdb (#11) to map
cryosparc_P12_J2768_004_volume_map.mrc (#10) using 10778 atoms  
average map value = 0.5647, steps = 816  
shifted from previous position = 57.8  
rotated from previous position = 120 degrees  
atoms outside contour = 7436, contour level = 0.41421  
Position of Kendall_Fran_SHAPE_MaP.pdb (#11) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.42333157 0.04459045 0.90487679 186.26507354  
0.68059512 -0.67489332 -0.28514777 174.18755058  
0.59798047 0.73656683 -0.31605164 231.92860829  
Axis 0.82263015 0.24709656 0.51207707  
Axis point 0.00000000 44.17885179 78.37665724  
Rotation angle (degrees) 141.61044861  
Shift along axis 315.03373283  
  
Found 236 fits.  

> open
> /Users/francescappadoo/Downloads/rnacomposer-2024-07-03-104300/Madden_Fran_SHAPE_MaP.pdb

Chain information for Madden_Fran_SHAPE_MaP.pdb #14  
---  
Chain | Description  
A | No description available  
  

> hide #14 models

> fitmap #11 inMap #10 resolution 15 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 15 in map
cryosparc_P12_J2768_004_volume_map.mrc using 2552 points  
correlation = 0.4821, correlation about mean = 0.2306, overlap = 224.8  
steps = 48, shift = 0.201, angle = 0.693 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 15 (#12) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.41326798 0.04055328 0.90970596 185.81741383  
0.68428186 -0.67296012 -0.28086112 174.47961561  
0.60080603 0.73856624 -0.30586269 231.85935760  
Axis 0.81907803 0.24819144 0.51721580  
Axis point 0.00000000 44.44487915 77.75873830  
Rotation angle (degrees) 141.51558367  
Shift along axis 315.42463234  
  
Average map value = 0.5642 for 10778 atoms, 7417 outside contour  

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

Opened Kendall_Fran_SHAPE_MaP.pdb map 17 as #2, grid size 41,46,36, pixel
5.67, shown at level 0.0302, step 1, values float32  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4941, correlation about mean = 0.2787, overlap = 151  
steps = 48, shift = 0.573, angle = 1.07 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.40749195 0.04013276 0.91232648 185.78112146  
0.68195412 -0.67781637 -0.27477900 174.29417412  
0.60736222 0.73413508 -0.30357336 231.49336686  
Axis 0.81757248 0.24712747 0.52009927  
Axis point 0.00000000 44.82071122 77.00241812  
Rotation angle (degrees) 141.90129072  
Shift along axis 315.36194184  
  
Average map value = 0.5639 for 10778 atoms, 7388 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4767, correlation about mean = 0.2553, overlap = 142.4  
steps = 144, shift = 2.82, angle = 7.85 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.64530535 0.25593873 0.71977518 205.43426075  
0.75783254 -0.09571767 -0.64538977 218.71028989  
-0.09628501 0.96194257 -0.25572577 220.23369404  
Axis 0.85898731 0.43611724 0.26822108  
Axis point 0.00000000 4.28793128 107.98432079  
Rotation angle (degrees) 110.67514711  
Shift along axis 330.92007111  
  
Average map value = 0.5355 for 10778 atoms, 7677 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4941, correlation about mean = 0.2787, overlap = 151  
steps = 48, shift = 0.573, angle = 1.07 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.40749194 0.04013277 0.91232648 185.78112155  
0.68195413 -0.67781638 -0.27477901 174.29417425  
0.60736222 0.73413508 -0.30357336 231.49336680  
Axis 0.81757248 0.24712747 0.52009927  
Axis point 0.00000000 44.82071099 77.00241827  
Rotation angle (degrees) 141.90129069  
Shift along axis 315.36194187  
  
Average map value = 0.5639 for 10778 atoms, 7388 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.472, correlation about mean = 0.2549, overlap = 142.8  
steps = 40, shift = 0.795, angle = 1.8 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.71518149 -0.55429252 0.42576423 174.67263670  
-0.10917616 -0.69027484 -0.71526302 180.63190162  
0.69035935 0.46505956 -0.55418729 227.70922626  
Axis 0.91574934 -0.20528524 0.34534204  
Axis point 0.00000000 78.36504798 125.18618163  
Rotation angle (degrees) 139.87500560  
Shift along axis 201.51285617  
  
Average map value = 0.5459 for 10778 atoms, 7725 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4767, correlation about mean = 0.2553, overlap = 142.4  
steps = 144, shift = 2.82, angle = 7.85 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.64530508 0.25593865 0.71977544 205.43427073  
0.75783287 -0.09571859 -0.64538923 218.71028158  
-0.09628413 0.96194249 -0.25572636 220.23373868  
Axis 0.85898730 0.43611707 0.26822140  
Axis point 0.00000000 4.28802708 107.98428322  
Rotation angle (degrees) 110.67520204  
Shift along axis 330.92011881  
  
Average map value = 0.5355 for 10778 atoms, 7677 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4693, correlation about mean = 0.2224, overlap = 144.1  
steps = 52, shift = 1.05, angle = 2.48 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.82795091 0.28612236 -0.48231857 225.65959641  
-0.54168561 0.18539190 -0.81988201 184.94066124  
-0.14516856 0.94008713 0.30848374 235.30891458  
Axis 0.89160347 -0.17080079 -0.41936898  
Axis point 0.00000000 -60.75100565 300.70638437  
Rotation angle (degrees) 80.74008983  
Shift along axis 70.92960961  
  
Average map value = 0.5419 for 10778 atoms, 7575 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4715, correlation about mean = 0.2471, overlap = 134.6  
steps = 44, shift = 1.24, angle = 2 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.36474454 -0.10009390 -0.92571194 187.08307082  
-0.83368873 -0.40762861 0.37256143 150.28768069  
-0.41463782 0.90764535 0.06523308 211.65304535  
Axis 0.51353778 -0.49049477 -0.70405527  
Axis point 188.32931190 -48.90828995 0.00000000  
Rotation angle (degrees) 148.60211384  
Shift along axis -126.65654071  
  
Average map value = 0.5007 for 10778 atoms, 7698 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4373, correlation about mean = 0.2079, overlap = 131.5  
steps = 76, shift = 1.14, angle = 2.7 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.71919371 0.61078503 -0.33121298 202.95135417  
0.25249389 0.67385475 0.69438219 192.72739407  
0.64730762 0.41576609 -0.63885161 225.45506156  
Axis -0.25829894 -0.90716524 -0.33216395  
Axis point 53.85146595 0.00000000 97.59980776  
Rotation angle (degrees) 147.36204335  
Shift along axis -302.14575567  
  
Average map value = 0.4993 for 10778 atoms, 7846 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4432, correlation about mean = 0.1923, overlap = 134.9  
steps = 52, shift = 3.14, angle = 1.87 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.25106383 -0.00238102 -0.96796760 193.19529413  
-0.39324827 -0.91350361 0.10424472 137.06526864  
-0.88449011 0.40682366 0.22841130 168.91826967  
Axis 0.60359092 -0.16652267 -0.77971033  
Axis point 172.65766900 32.84721311 0.00000000  
Rotation angle (degrees) 165.48407978  
Shift along axis -37.92086754  
  
Average map value = 0.4983 for 10778 atoms, 7780 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4691, correlation about mean = 0.2251, overlap = 143.6  
steps = 120, shift = 10.5, angle = 19.8 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.62072430 0.76072526 -0.18973255 254.80279160  
-0.63188242 0.34213816 -0.69546108 195.29761084  
-0.46414002 0.55157827 0.69306233 199.67520836  
Axis 0.66002514 0.14523666 -0.73707064  
Axis point 396.19796357 -94.58315656 0.00000000  
Rotation angle (degrees) 70.85485225  
Shift along axis 49.36588857  
  
Average map value = 0.5379 for 10778 atoms, 7592 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4452, correlation about mean = 0.2296, overlap = 129.4  
steps = 208, shift = 3.08, angle = 9.25 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.62655937 -0.25978325 -0.73480341 173.68342014  
0.10743607 -0.96260121 0.24870955 142.86580175  
-0.77193320 0.07688688 0.63103683 162.13925297  
Axis -0.42203794 0.09119973 0.90197926  
Axis point 117.07548329 75.20787850 0.00000000  
Rotation angle (degrees) 168.25460533  
Shift along axis 85.97457219  
  
Average map value = 0.4856 for 10778 atoms, 7893 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4452, correlation about mean = 0.2296, overlap = 129.4  
steps = 40, shift = 0.0293, angle = 0.0684 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.62680685 -0.26072498 -0.73425859 173.66052480  
0.10839826 -0.96236937 0.24918878 142.89599198  
-0.77159770 0.07660085 0.63148178 162.11573639  
Axis -0.42178408 0.09125227 0.90209269  
Axis point 116.99099326 75.27973809 0.00000000  
Rotation angle (degrees) 168.19434066  
Shift along axis 86.03575896  
  
Average map value = 0.4856 for 10778 atoms, 7893 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.458, correlation about mean = 0.2431, overlap = 131.6  
steps = 48, shift = 4.81, angle = 5.19 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.30355771 0.21101185 0.92915377 192.75246677  
-0.94809551 -0.03002596 0.31656493 172.80989698  
0.09469768 -0.97702219 0.19094481 159.20852706  
Axis -0.67130621 0.43304046 -0.60151803  
Axis point 0.00000000 187.50923390 -141.42149668  
Rotation angle (degrees) 105.53111974  
Shift along axis -150.32905021  
  
Average map value = 0.4928 for 10778 atoms, 7717 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4339, correlation about mean = 0.1906, overlap = 130.9  
steps = 236, shift = 9.94, angle = 9.39 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.55068331 0.23938759 0.79965085 148.66399645  
0.81055502 -0.07545596 0.58078135 205.03370108  
0.19937026 0.96798758 -0.15248442 210.18877044  
Axis 0.42336014 0.65632950 0.62449802  
Axis point 9.10272480 0.00000000 5.80227101  
Rotation angle (degrees) 152.78690184  
Shift along axis 328.77054812  
  
Average map value = 0.4781 for 10778 atoms, 7721 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.3795, correlation about mean = 0.1984, overlap = 66.17  
steps = 216, shift = 27.9, angle = 49.3 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.87487175 0.02611014 0.48365040 152.45735182  
0.38767418 0.63635168 0.66690725 202.75840175  
-0.29035875 0.77095705 -0.56684829 238.79416782  
Axis 0.12090275 0.89937544 0.42012659  
Axis point 76.71833744 0.00000000 57.44849463  
Rotation angle (degrees) 154.51316504  
Shift along axis 301.11221790  
  
Average map value = 0.2488 for 10778 atoms, 8810 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.458, correlation about mean = 0.2431, overlap = 131.6  
steps = 48, shift = 4.81, angle = 5.19 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.30355928 0.21101187 0.92915326 192.75246814  
-0.94809513 -0.03002433 0.31656623 172.81002707  
0.09469646 -0.97702224 0.19094522 159.20868945  
Axis -0.67130657 0.43304060 -0.60151752  
Axis point -0.00000000 187.50947455 -141.42157580  
Rotation angle (degrees) 105.53101252  
Shift along axis -150.32905639  
  
Average map value = 0.4928 for 10778 atoms, 7717 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.458, correlation about mean = 0.2431, overlap = 131.6  
steps = 44, shift = 0.0144, angle = 0.0169 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.30342164 0.21092236 0.92921854 192.74389011  
-0.94816423 -0.02982523 0.31637804 172.82156097  
0.09444538 -0.97704767 0.19093947 159.21495997  
Axis -0.67121670 0.43320129 -0.60150210  
Axis point 0.00000000 187.57368201 -141.45284770  
Rotation angle (degrees) 105.52935586  
Shift along axis -150.27452828  
  
Average map value = 0.4928 for 10778 atoms, 7715 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4339, correlation about mean = 0.1906, overlap = 130.9  
steps = 1044, shift = 9.96, angle = 9.37 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.55099842 0.23895555 0.79956301 148.66916474  
0.81048619 -0.07499138 0.58093757 205.04969246  
0.19877854 0.96813044 -0.15234998 210.19891188  
Axis 0.42309022 0.65648427 0.62451827  
Axis point 9.15722111 0.00000000 5.80263202  
Rotation angle (degrees) 152.76912100  
Shift along axis 328.78542805  
  
Average map value = 0.4781 for 10778 atoms, 7725 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4467, correlation about mean = 0.243, overlap = 129.7  
steps = 84, shift = 1.75, angle = 3.25 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
-0.17696403 -0.26523090 -0.94780605 192.48805866  
0.03428629 -0.96408164 0.26338387 155.56083858  
-0.98361994 0.01411270 0.17970149 135.84373625  
Axis -0.63700511 0.09152134 0.76540730  
Axis point 142.70715205 81.89919261 0.00000000  
Rotation angle (degrees) 168.71679517  
Shift along axis -4.40295254  
  
Average map value = 0.4859 for 10778 atoms, 8024 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4421, correlation about mean = 0.1912, overlap = 131.2  
steps = 88, shift = 1.44, angle = 2.62 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76671035 -0.30066663 0.56723438 190.31321237  
-0.64161790 -0.38907396 0.66102039 150.47576012  
0.02194940 -0.87075890 -0.49122006 152.45240422  
Axis -0.92203426 0.32822707 -0.20523110  
Axis point 0.00000000 143.87762959 -3.43890756  
Rotation angle (degrees) 123.83422163  
Shift along axis -157.37305904  
  
Average map value = 0.4845 for 10778 atoms, 7876 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1912, overlap = 131.2  
steps = 52, shift = 2.59, angle = 0.0884 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76768254 -0.29986970 0.56634063 190.40063820  
-0.64044728 -0.38956819 0.66186399 150.47842322  
0.02215539 -0.87081274 -0.49111537 152.45197222  
Axis -0.92235771 0.32748814 -0.20495800  
Axis point 0.00000000 143.80866205 -3.40450713  
Rotation angle (degrees) 123.81412893  
Shift along axis -157.58384858  
  
Average map value = 0.4844 for 10778 atoms, 7874 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.1  
steps = 60, shift = 0.0571, angle = 0.232 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77020598 -0.29763653 0.56408799 190.62438654  
-0.63739328 -0.39059747 0.66420136 150.46871032  
0.02264080 -0.87111775 -0.49055198 152.44008539  
Axis -0.92318325 0.32557074 -0.20429482  
Axis point 0.00000000 143.63015183 -3.34440174  
Rotation angle (degrees) 123.74321333  
Shift along axis -158.13575220  
  
Average map value = 0.4842 for 10778 atoms, 7873 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.1  
steps = 48, shift = 0.0191, angle = 0.0705 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77097385 -0.29733698 0.56319629 190.64768431  
-0.63646513 -0.39112562 0.66478035 150.46358391  
0.02261676 -0.87098307 -0.49079218 152.44876422  
Axis -0.92345059 0.32504908 -0.20391688  
Axis point 0.00000000 143.57213219 -3.26431754  
Rotation angle (degrees) 123.74323001  
Shift along axis -158.23254493  
  
Average map value = 0.4842 for 10778 atoms, 7873 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1914, overlap = 131.1  
steps = 64, shift = 0.0479, angle = 0.215 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77328790 -0.29521981 0.56113378 190.85337500  
-0.63363172 -0.39214322 0.66688422 150.46625255  
0.02316742 -0.87124566 -0.49030018 152.43262314  
Axis -0.92421039 0.32324584 -0.20334031  
Axis point 0.00000000 143.40368065 -3.21199020  
Rotation angle (degrees) 123.68163678  
Shift along axis -158.74677782  
  
Average map value = 0.4839 for 10778 atoms, 7874 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1915, overlap = 131  
steps = 48, shift = 0.0797, angle = 0.122 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77450156 -0.29397805 0.56011093 191.00081645  
-0.63214830 -0.39210079 0.66831544 150.53896310  
0.02314992 -0.87168452 -0.48952034 152.38289330  
Axis -0.92458126 0.32237929 -0.20302979  
Axis point 0.00000000 143.38485479 -3.28017807  
Rotation angle (degrees) 123.61157396  
Shift along axis -159.00339854  
  
Average map value = 0.4836 for 10778 atoms, 7875 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1914, overlap = 131.1  
steps = 48, shift = 0.0419, angle = 0.203 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77232322 -0.29560350 0.56225922 190.83354764  
-0.63480042 -0.39169544 0.66603539 150.48956528  
0.02335203 -0.87131698 -0.49016465 152.43581830  
Axis -0.92388434 0.32386063 -0.20384313  
Axis point 0.00000000 143.47374196 -3.29740225  
Rotation angle (degrees) 123.69476729  
Shift along axis -158.64347499  
  
Average map value = 0.4839 for 10778 atoms, 7874 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.2  
steps = 40, shift = 0.0657, angle = 0.267 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76943958 -0.29818650 0.56484296 190.57083836  
-0.63831448 -0.39047920 0.66338575 150.46079550  
0.02274680 -0.87098268 -0.49078685 152.45619272  
Axis -0.92293915 0.32607668 -0.20459065  
Axis point 0.00000000 143.66315170 -3.35409583  
Rotation angle (degrees) 123.77363987  
Shift along axis -158.01464071  
  
Average map value = 0.4842 for 10778 atoms, 7874 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.2  
steps = 44, shift = 0.0114, angle = 0.0324 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76908311 -0.29846031 0.56518371 190.54489325  
-0.63874666 -0.39027362 0.66309068 150.47102035  
0.02267009 -0.87098104 -0.49079332 152.45232762  
Axis -0.92281909 0.32634845 -0.20469886  
Axis point 0.00000000 143.69507712 -3.37629279  
Rotation angle (degrees) 123.77906296  
Shift along axis -157.93929855  
  
Average map value = 0.4842 for 10778 atoms, 7873 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1912, overlap = 131.2  
steps = 44, shift = 0.02, angle = 0.00676 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76912141 -0.29844461 0.56513988 190.54597049  
-0.63869848 -0.39037977 0.66307460 150.44923041  
0.02272819 -0.87093885 -0.49086550 152.46060612  
Axis -0.92283604 0.32630552 -0.20469086  
Axis point 0.00000000 143.67683946 -3.35751589  
Rotation angle (degrees) 123.78388974  
Shift along axis -157.95756634  
  
Average map value = 0.4843 for 10778 atoms, 7871 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1912, overlap = 131.2  
steps = 44, shift = 0.0191, angle = 0.0222 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76888755 -0.29868669 0.56533018 190.51163324  
-0.63898372 -0.39024341 0.66288002 150.44101765  
0.02262299 -0.87091697 -0.49090917 152.46204970  
Axis -0.92275826 0.32650185 -0.20472846  
Axis point 0.00000000 143.69183378 -3.35783754  
Rotation angle (degrees) 123.78875584  
Shift along axis -157.89023338  
  
Average map value = 0.4843 for 10778 atoms, 7875 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.2  
steps = 44, shift = 0.0117, angle = 0.18 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77086646 -0.29713737 0.56344858 190.65098568  
-0.63658121 -0.39129598 0.66456892 150.44698832  
0.02300695 -0.87097467 -0.49078895 152.46118719  
Axis -0.92342025 0.32500200 -0.20412922  
Axis point 0.00000000 143.54612980 -3.26864156  
Rotation angle (degrees) 123.75268811  
Shift along axis -158.27719162  
  
Average map value = 0.4842 for 10778 atoms, 7875 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1914, overlap = 131.1  
steps = 44, shift = 0.0746, angle = 0.109 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77198733 -0.29599052 0.56251683 190.79870682  
-0.63521584 -0.39149046 0.66575978 150.49518745  
0.02316144 -0.87127772 -0.49024349 152.43474482  
Axis -0.92377276 0.32415723 -0.20387733  
Axis point 0.00000000 143.50777057 -3.30471503  
Rotation angle (degrees) 123.70198949  
Shift along axis -158.54853434  
  
Average map value = 0.484 for 10778 atoms, 7874 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.2  
steps = 40, shift = 0.0966, angle = 0.23 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76951535 -0.29823391 0.56471469 190.53764475  
-0.63822377 -0.39060016 0.66340181 150.44009849  
0.02272879 -0.87091221 -0.49091273 152.46094067  
Axis -0.92296994 0.32603280 -0.20452164  
Axis point 0.00000000 143.64159304 -3.32105454  
Rotation angle (degrees) 123.77953592  
Shift along axis -157.99367442  
  
Average map value = 0.4843 for 10778 atoms, 7875 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1914, overlap = 131.1  
steps = 60, shift = 0.0926, angle = 0.242 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77211219 -0.29586704 0.56241042 190.80394643  
-0.63506355 -0.39151291 0.66589185 150.49423207  
0.02317554 -0.87130957 -0.49018620 152.43098007  
Axis -0.92381215 0.32406406 -0.20384698  
Axis point 0.00000000 143.49873852 -3.30483810  
Rotation angle (degrees) 123.69649078  
Shift along axis -158.56982750  
  
Average map value = 0.4839 for 10778 atoms, 7875 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.1  
steps = 44, shift = 0.0462, angle = 0.236 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76955187 -0.29809366 0.56473897 190.58503967  
-0.63818335 -0.39034007 0.66359376 150.49209431  
0.02262721 -0.87107682 -0.49062528 152.44052106  
Axis -0.92296759 0.32603192 -0.20453364  
Axis point 0.00000000 143.68285202 -3.37994893  
Rotation angle (degrees) 123.75940793  
Shift along axis -158.01780422  
  
Average map value = 0.4842 for 10778 atoms, 7872 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1912, overlap = 131.2  
steps = 44, shift = 0.0447, angle = 0.128 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76818028 -0.29940286 0.56591255 190.44882940  
-0.63984975 -0.38962675 0.66240722 150.46585586  
0.02216810 -0.87094716 -0.49087637 152.44276626  
Axis -0.92251345 0.32713349 -0.20482338  
Axis point 0.00000000 143.77682524 -3.40636604  
Rotation angle (degrees) 123.79074874  
Shift along axis -157.69302973  
  
Average map value = 0.4843 for 10778 atoms, 7872 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1912, overlap = 131.2  
steps = 44, shift = 0.0211, angle = 0.00781 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76818548 -0.29936920 0.56592329 190.45035230  
-0.63983965 -0.38974410 0.66234793 150.48375581  
0.02227874 -0.87090622 -0.49094399 152.44720531  
Axis -0.92251992 0.32709706 -0.20485239  
Axis point 0.00000000 143.77678966 -3.40337714  
Rotation angle (degrees) 123.79694522  
Shift along axis -157.70062436  
  
Average map value = 0.4843 for 10778 atoms, 7873 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.1  
steps = 60, shift = 0.0413, angle = 0.17 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77002922 -0.29773877 0.56427533 190.61800095  
-0.63760474 -0.39058765 0.66400415 150.48886664  
0.02269924 -0.87108722 -0.49060349 152.44198636  
Axis -0.92312733 0.32567683 -0.20437843  
Axis point 0.00000000 143.64696351 -3.35520551  
Rotation angle (degrees) 123.75073992  
Shift along axis -158.10980341  
  
Average map value = 0.4842 for 10778 atoms, 7872 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.2  
steps = 48, shift = 0.0571, angle = 0.0285 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76990111 -0.29789409 0.56436815 190.57447040  
-0.63775166 -0.39091474 0.66367049 150.43255822  
0.02291636 -0.87088737 -0.49094808 152.47121463  
Axis -0.92310331 0.32570680 -0.20443911  
Axis point 0.00000000 143.60249648 -3.29387895  
Rotation angle (degrees) 123.77830079  
Shift along axis -158.09409712  
  
Average map value = 0.4843 for 10778 atoms, 7876 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1914, overlap = 131.1  
steps = 76, shift = 0.0951, angle = 0.256 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77264165 -0.29543569 0.56190982 190.84883175  
-0.63441683 -0.39172753 0.66638191 150.49643877  
0.02324259 -0.87135947 -0.49009433 152.42641288  
Axis -0.92398609 0.32367018 -0.20368435  
Axis point 0.00000000 143.46420820 -3.29010900  
Rotation angle (degrees) 123.68248730  
Shift along axis -158.67733240  
  
Average map value = 0.4839 for 10778 atoms, 7874 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.1  
steps = 44, shift = 0.0513, angle = 0.261 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76980623 -0.29785606 0.56451762 190.60797453  
-0.63787415 -0.39045288 0.66382463 150.49314585  
0.02269339 -0.87110754 -0.49056769 152.43958809  
Axis -0.92305103 0.32583291 -0.20447421  
Axis point 0.00000000 143.66475323 -3.37466702  
Rotation angle (degrees) 123.75254581  
Shift along axis -158.07523244  
  
Average map value = 0.4842 for 10778 atoms, 7872 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.2  
steps = 48, shift = 0.0539, angle = 0.0361 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76988041 -0.29820070 0.56423445 190.54895202  
-0.63780635 -0.39010088 0.66409668 150.51826115  
0.02207432 -0.87114733 -0.49052527 152.41895338  
Axis -0.92306479 0.32597355 -0.20418775  
Axis point 0.00000000 143.70694765 -3.36903897  
Rotation angle (degrees) 123.73640159  
Shift along axis -157.94614081  
  
Average map value = 0.4842 for 10778 atoms, 7875 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1915, overlap = 131.1  
steps = 60, shift = 0.0938, angle = 0.332 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77345635 -0.29501380 0.56100993 190.87165630  
-0.63342471 -0.39215208 0.66707564 150.47276097  
0.02320475 -0.87131144 -0.49018149 152.42432235  
Axis -0.92426195 0.32311300 -0.20331706  
Axis point 0.00000000 143.39594818 -3.22252342  
Rotation angle (degrees) 123.67205698  
Shift along axis -158.78616901  
  
Average map value = 0.4839 for 10778 atoms, 7876 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1915, overlap = 131  
steps = 48, shift = 0.0896, angle = 0.196 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77546666 -0.29277552 0.55940502 191.10941090  
-0.63093815 -0.39278795 0.66905508 150.51372029  
0.02384466 -0.87177988 -0.48931714 152.39506891  
Axis -0.92490504 0.32147666 -0.20298626  
Axis point 0.00000000 143.27389103 -3.25320669  
Rotation angle (degrees) 123.59502519  
Shift along axis -159.30551379  
  
Average map value = 0.4835 for 10778 atoms, 7873 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1914, overlap = 131  
steps = 48, shift = 0.0343, angle = 0.264 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77261405 -0.29519300 0.56207530 190.88134944  
-0.63444259 -0.39170001 0.66637357 150.49529786  
0.02345614 -0.87145408 -0.48991589 152.40714114  
Axis -0.92397194 0.32361819 -0.20383110  
Axis point 0.00000000 143.45397195 -3.32957451  
Rotation angle (degrees) 123.67634730  
Shift along axis -158.73131115  
  
Average map value = 0.4838 for 10778 atoms, 7871 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.1  
steps = 48, shift = 0.0803, angle = 0.243 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77001168 -0.29766446 0.56433847 190.62452376  
-0.63762309 -0.39058810 0.66398627 150.49058518  
0.02277883 -0.87111241 -0.49055507 152.44186430  
Axis -0.92312044 0.32566296 -0.20443165  
Axis point 0.00000000 143.64549824 -3.36457809  
Rotation angle (degrees) 123.74969123  
Shift along axis -158.12412693  
  
Average map value = 0.4842 for 10778 atoms, 7871 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.2  
steps = 48, shift = 0.0568, angle = 0.0265 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76994692 -0.29780031 0.56435515 190.59089798  
-0.63769430 -0.39093661 0.66371272 150.43131255  
0.02297329 -0.87090962 -0.49090594 152.47217689  
Axis -0.92311756 0.32565608 -0.20445559  
Axis point 0.00000000 143.59797404 -3.29850111  
Rotation angle (degrees) 123.77602336  
Shift along axis -158.12272145  
  
Average map value = 0.4843 for 10778 atoms, 7877 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.1  
steps = 60, shift = 0.042, angle = 0.118 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77120990 -0.29670499 0.56320641 190.71419500  
-0.63616481 -0.39120601 0.66502046 150.46263057  
0.02301489 -0.87116246 -0.49045517 152.44563119  
Axis -0.92352014 0.32475153 -0.20407594  
Axis point 0.00000000 143.54321641 -3.30405440  
Rotation angle (degrees) 123.72625852  
Shift along axis -158.37591778  
  
Average map value = 0.4841 for 10778 atoms, 7872 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1913, overlap = 131.2  
steps = 28, shift = 0.0774, angle = 0.192 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.76918945 -0.29879027 0.56486458 190.48956597  
-0.63862925 -0.39037520 0.66314397 150.45650798  
0.02236820 -0.87082238 -0.49108863 152.45726981  
Axis -0.92286362 0.32637624 -0.20445366  
Axis point 0.00000000 143.68756638 -3.31591143  
Rotation angle (degrees) 123.78907786  
Shift along axis -157.86090711  
  
Average map value = 0.4844 for 10778 atoms, 7874 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1915, overlap = 131.1  
steps = 84, shift = 0.0951, angle = 0.413 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77366663 -0.29488243 0.56078901 190.88702623  
-0.63316593 -0.39232113 0.66722190 150.46740653  
0.02325741 -0.87127981 -0.49023521 152.42858096  
Axis -0.92433545 0.32295025 -0.20324152  
Axis point 0.00000000 143.37554689 -3.20250441  
Rotation angle (degrees) 123.67248698  
Shift along axis -158.82997575  
  
Average map value = 0.4839 for 10778 atoms, 7875 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1916, overlap = 131  
steps = 44, shift = 0.0496, angle = 0.212 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77594100 -0.29286073 0.55870222 191.08811336  
-0.63036507 -0.39308293 0.66942193 150.50081092  
0.02356896 -0.87161828 -0.48961828 152.39627515  
Axis -0.92507317 0.32123589 -0.20260095  
Axis point 0.00000000 143.24192442 -3.17551548  
Rotation angle (degrees) 123.59921316  
Shift along axis -159.29985357  
  
Average map value = 0.4836 for 10778 atoms, 7869 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1915, overlap = 131  
steps = 64, shift = 0.0475, angle = 0.123 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77466009 -0.29403405 0.55986225 190.96541435  
-0.63193897 -0.39292035 0.66803201 150.45147015  
0.02355717 -0.87129650 -0.49019123 152.43190911  
Axis -0.92467005 0.32215686 -0.20297848  
Axis point 0.00000000 143.28573388 -3.15158551  
Rotation angle (degrees) 123.65740350  
Shift along axis -159.05142123  
  
Average map value = 0.4838 for 10778 atoms, 7875 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1915, overlap = 131.1  
steps = 64, shift = 0.0216, angle = 0.087 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77372149 -0.29480247 0.56075536 190.89605961  
-0.63309823 -0.39231653 0.66728884 150.47139200  
0.02327524 -0.87130894 -0.49018259 152.42593799  
Axis -0.92435170 0.32290483 -0.20323977  
Axis point 0.00000000 143.37440707 -3.20854926  
Rotation angle (degrees) 123.66862872  
Shift along axis -158.84617084  
  
Average map value = 0.4839 for 10778 atoms, 7875 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4422, correlation about mean = 0.1915, overlap = 131  
steps = 44, shift = 0.0823, angle = 0.185 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.77563623 -0.29274986 0.55918332 191.11856556  
-0.63072997 -0.39295166 0.66915523 150.50343141  
0.02383696 -0.87171472 -0.48943359 152.40028495  
Axis -0.92496683 0.32136237 -0.20288565  
Axis point 0.00000000 143.25581139 -3.22545077  
Rotation angle (degrees) 123.59882844  
Shift along axis -159.33202472  
  
Average map value = 0.4835 for 10778 atoms, 7872 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.4314, correlation about mean = 0.2021, overlap = 128.9  
steps = 100, shift = 1.92, angle = 2.82 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.26906502 -0.14243095 0.95253213 185.39965960  
-0.19445799 -0.97667031 -0.09111112 182.76344710  
0.94328688 -0.16071267 -0.29048458 216.25440595  
Axis -0.79646575 0.10579538 -0.59535674  
Axis point 0.00000000 104.56236075 35.95325959  
Rotation angle (degrees) 177.49572074  
Shift along axis -257.07746905  
  
Average map value = 0.4835 for 10778 atoms, 7928 outside contour  

> fitmap #11 inMap #10 resolution 17 metric correlation

Fit map Kendall_Fran_SHAPE_MaP.pdb map 17 in map
cryosparc_P12_J2768_004_volume_map.mrc using 1964 points  
correlation = 0.445, correlation about mean = 0.2261, overlap = 127.3  
steps = 80, shift = 2.9, angle = 3.06 degrees  
  
Position of Kendall_Fran_SHAPE_MaP.pdb map 17 (#2) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.64243805 0.36368561 0.67454142 209.65980011  
0.02173606 0.87121262 -0.49042444 240.37169293  
-0.76602925 0.32972922 0.55179508 181.00976629  
Axis 0.48455842 0.85110961 -0.20202865  
Axis point 286.94625660 0.00000000 34.95867633  
Rotation angle (degrees) 57.81038611  
Shift along axis 269.60592082  
  
Average map value = 0.4782 for 10778 atoms, 7818 outside contour  

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2773_004_volume_map.mrc

Opened cryosparc_P12_J2773_004_volume_map.mrc as #12, grid size 128,128,128,
pixel 2.96, shown at level 0.117, step 1, values float32  

> select subtract #11

Nothing selected  

> tile

4 models tiled  

> hide #!10 models

> hide #11 models

> tile

2 models tiled  

> surface dust #12 size 29.6

> volume #12 level 0.2

> volume #12 level 0.5

> tile

2 models tiled  

> show #!10 models

> tile

3 models tiled  

> select add #10

2 models selected  

> view matrix models
> #10,0.29649,-0.95114,0.08615,941.77,-0.9454,-0.30508,-0.1146,558.04,0.13529,-0.047467,-0.98967,-53.69

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.36498,-0.52841,0.76653,853.23,0.89444,-0.42751,0.13118,182.29,0.25839,0.7335,0.62866,-544.83

> view matrix models
> #10,-0.34315,-0.76369,0.54684,936.88,0.89822,-0.096558,0.4288,60.319,-0.27467,0.63832,0.7191,-443.44

> select subtract #10

Nothing selected  

> tile

3 models tiled  

> ui mousemode right "translate selected models"

> select add #10

2 models selected  

> view matrix models
> #10,-0.34315,-0.76369,0.54684,930.93,0.89822,-0.096558,0.4288,58.684,-0.27467,0.63832,0.7191,-438.61

> volume #12 level 0.5

> volume #10 level 0.791

> volume #10 level 0.4142

> tile

3 models tiled  

> tile

3 models tiled  

> select subtract #10

Nothing selected  

> tile

3 models tiled  

> tile

3 models tiled  

> tile

3 models tiled  

> hide #!12 models

> tile

2 models tiled  

> show #!3 models

> tile

3 models tiled  

> transparency #3.1#10.1 0

> transparency #3.1#10.1 50

> scalebar off

> scalebar 50

> tile

3 models tiled  

> scalebar off

> scalebar 50

> select add #3

2 models selected  

> view matrix models
> #3,-0.25103,-0.42142,-0.87143,442.75,0.626,-0.75734,0.18592,82.073,-0.73832,-0.49884,0.45392,241.96

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.62326,-0.080194,0.77789,-109.75,-0.7775,-0.17025,0.6054,146.98,0.083885,-0.98213,-0.16846,304.87

> scalebar off

> scalebar 50

> select subtract #3

Nothing selected  

> save /Users/francescappadoo/Desktop/image20.png supersample 3

> select add #3

2 models selected  

> view matrix models
> #3,-0.0063732,-0.51704,-0.85594,412.77,0.90355,-0.36971,0.2166,-51.295,-0.42843,-0.772,0.46953,234.44

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.0063732,-0.51704,-0.85594,551.25,0.90355,-0.36971,0.2166,4.4364,-0.42843,-0.772,0.46953,171.8

> fitmap #3 inMap #10

Fit map cryosparc_P12_J2741_004_volume_map_sharp.mrc in map
cryosparc_P12_J2768_004_volume_map.mrc using 5172 points  
correlation = 0.7821, correlation about mean = 0.5863, overlap = 3664  
steps = 64, shift = 4.27, angle = 11.9 degrees  
  
Position of cryosparc_P12_J2741_004_volume_map_sharp.mrc (#3) relative to
cryosparc_P12_J2768_004_volume_map.mrc (#10) coordinates:  
Matrix rotation and translation  
0.99878244 0.02127691 0.04450727 -10.28520065  
-0.03060942 0.97481934 0.22088525 -30.37055245  
-0.03868679 -0.22197863 0.97428374 60.65782921  
Axis -0.97635765 0.18341337 -0.11439092  
Axis point 0.00000000 252.95623138 164.28289173  
Rotation angle (degrees) 13.10838751  
Shift along axis -2.46703603  
  

> scalebar off

> scalebar 50

> tile

3 models tiled  

> open
> /Users/francescappadoo/Downloads/rnacomposer-2024-07-03-103043/Kendall_Fran_SHAPE_MaP.pdb

Chain information for Kendall_Fran_SHAPE_MaP.pdb #13  
---  
Chain | Description  
A | No description available  
  

> hide #13 models

> show #13 models

> tile

4 models tiled  

> hide #!3 models

> tile

3 models tiled  


[deleted to fit within ticket limits]

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2810_class_03_00102_volume.mrc

Opened cryosparc_P12_J2810_class_03_00102_volume.mrc as #2, grid size
128,128,128, pixel 2.96, shown at level 0.082, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2810_class_04_00102_volume.mrc

Opened cryosparc_P12_J2810_class_04_00102_volume.mrc as #3, grid size
128,128,128, pixel 2.96, shown at level 0.0488, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2810_class_05_00102_volume.mrc

Opened cryosparc_P12_J2810_class_05_00102_volume.mrc as #4, grid size
128,128,128, pixel 2.96, shown at level 0.0483, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2810_class_06_00102_volume.mrc

Opened cryosparc_P12_J2810_class_06_00102_volume.mrc as #5, grid size
128,128,128, pixel 2.96, shown at level 0.0568, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2810_class_07_00102_volume.mrc

Opened cryosparc_P12_J2810_class_07_00102_volume.mrc as #6, grid size
128,128,128, pixel 2.96, shown at level 0.0591, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2810_class_08_00102_volume.mrc

Opened cryosparc_P12_J2810_class_08_00102_volume.mrc as #7, grid size
128,128,128, pixel 2.96, shown at level 0.061, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2810_class_09_00102_volume.mrc

Opened cryosparc_P12_J2810_class_09_00102_volume.mrc as #8, grid size
128,128,128, pixel 2.96, shown at level 0.0622, step 1, values float32  

> tile

8 models tiled  

> surface dust #1 size 29.6

> surface dust #2 size 29.6

> surface dust #3 size 29.6

> surface dust #4 size 29.6

> surface dust #5 size 29.6

> surface dust #6 size 29.6

> surface dust #7 size 29.6

> surface dust #8 size 29.6

> volume #1 level 0.2

> volume #2 level 0.2

> volume #3 level 0.2

> volume #4 level 0.2

> volume #5 level 0.2

> volume #6 level 0.2

> volume #7 level 0.2

> volume #8 level 0.2

> tile

8 models tiled  

> volume #7 level 0.3301

> volume #8 level 0.233

> tile

8 models tiled  

> volume #6 level 0.4064

> volume #5 level 0.4297

> volume #6 level 0.4499

> volume #4 level 0.2

> volume #3 level 0.2328

> volume #2 level 0.3833

> close #1-2

> volume #4 level 0.233

> hide #!3 models

> hide #!4 models

> tile

4 models tiled  

> tile

4 models tiled  

> volume #5 level 0.45

> hide #!5 models

> hide #!6 models

> tile

2 models tiled  

> close #4

> tile

2 models tiled  

> close

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2812_005_volume_map.mrc

Opened cryosparc_P12_J2812_005_volume_map.mrc as #1, grid size 128,128,128,
pixel 2.96, shown at level 0.0331, step 1, values float32  

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2813_005_volume_map.mrc

Opened cryosparc_P12_J2813_005_volume_map.mrc as #2, grid size 128,128,128,
pixel 2.96, shown at level 0.0431, step 1, values float32  

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2814_005_volume_map.mrc

Opened cryosparc_P12_J2814_005_volume_map.mrc as #3, grid size 128,128,128,
pixel 2.96, shown at level 0.0502, step 1, values float32  

> tile

3 models tiled  

> surface dust #1 size 29.6

> surface dust #2 size 29.6

> surface dust #3 size 29.6

> volume #1 level 0.3611

> volume #2 level 0.2577

> volume #1 level 0.258

> volume #3 level 0.258

> tile

3 models tiled  

> volume #2 level 0.4353

> tile

3 models tiled  

> volume #3 level 0.2938

> tile

3 models tiled  

> tile

3 models tiled  

> volume #2 level 0.3687

> volume #2 level 0.3872

> close #1

> tile

2 models tiled  

> tile

2 models tiled  

> tile

2 models tiled  

> tile

2 models tiled  

> fitmap #2 inMap #3

Fit map cryosparc_P12_J2813_005_volume_map.mrc in map
cryosparc_P12_J2814_005_volume_map.mrc using 2444 points  
correlation = 0.9524, correlation about mean = 0.8198, overlap = 1695  
steps = 576, shift = 107, angle = 0.513 degrees  
  
Position of cryosparc_P12_J2813_005_volume_map.mrc (#2) relative to
cryosparc_P12_J2814_005_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99996369 0.00762587 0.00380386 -2.09520822  
-0.00763629 0.99996710 0.00273431 0.64836021  
-0.00378289 -0.00276326 0.99998903 0.94048014  
Axis -0.30698020 0.42363881 -0.85222844  
Axis point 77.28516154 270.43439045 0.00000000  
Rotation angle (degrees) 0.51304843  
Shift along axis 0.11635405  
  

> transparency 50

> fitmap #2 inMap #3

Fit map cryosparc_P12_J2813_005_volume_map.mrc in map
cryosparc_P12_J2814_005_volume_map.mrc using 2444 points  
correlation = 0.9525, correlation about mean = 0.8199, overlap = 1694  
steps = 76, shift = 20.1, angle = 0.0941 degrees  
  
Position of cryosparc_P12_J2813_005_volume_map.mrc (#2) relative to
cryosparc_P12_J2814_005_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99995317 0.00803449 0.00539475 -2.39805690  
-0.00804933 0.99996386 0.00273517 0.71122236  
-0.00537258 -0.00277847 0.99998171 1.25325851  
Axis -0.27396650 0.53501665 -0.79918680  
Axis point 84.63403521 297.73889718 0.00000000  
Rotation angle (degrees) 0.57655535  
Shift along axis 0.03591540  
  

> fitmap #2 inMap #3

Fit map cryosparc_P12_J2813_005_volume_map.mrc in map
cryosparc_P12_J2814_005_volume_map.mrc using 2444 points  
correlation = 0.9524, correlation about mean = 0.8198, overlap = 1695  
steps = 88, shift = 19.3, angle = 0.0684 degrees  
  
Position of cryosparc_P12_J2813_005_volume_map.mrc (#2) relative to
cryosparc_P12_J2814_005_volume_map.mrc (#3) coordinates:  
Matrix rotation and translation  
0.99996034 0.00784337 0.00421798 -2.18723497  
-0.00785465 0.99996561 0.00266284 0.69795564  
-0.00419695 -0.00269586 0.99998756 1.00826760  
Axis -0.28810422 0.45241899 -0.84398638  
Axis point 82.18196504 275.79164297 0.00000000  
Rotation angle (degrees) 0.53285412  
Shift along axis 0.09495590  
  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 2 maps.  

> surface dust #2 size 29.6

> surface dust #3 size 29.6

> vop subtract #2 #3 minrms True

Opened volume difference as #1, grid size 128,128,128, pixel 2.96, shown at
step 1, values float32  
Minimum RMS scale factor for "cryosparc_P12_J2814_005_volume_map.mrc #3" above
level 0.29384 is 0.7766  
  

> hide #!1 models

> show #!2 models

> show #!3 models

> select ~sel

6 models selected  

> select up

6 models selected  

> close

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2817_class_00_00102_volume.mrc

Opened cryosparc_P12_J2817_class_00_00102_volume.mrc as #1, grid size
128,128,128, pixel 2.96, shown at level 0.0544, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2817_class_01_00102_volume.mrc

Opened cryosparc_P12_J2817_class_01_00102_volume.mrc as #2, grid size
128,128,128, pixel 2.96, shown at level 0.0537, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2817_class_02_00102_volume.mrc

Opened cryosparc_P12_J2817_class_02_00102_volume.mrc as #3, grid size
128,128,128, pixel 2.96, shown at level 0.0579, step 1, values float32  

> open
> /Users/francescappadoo/Downloads/cryosparc_P12_J2817_class_03_00102_volume.mrc

Opened cryosparc_P12_J2817_class_03_00102_volume.mrc as #4, grid size
128,128,128, pixel 2.96, shown at level 0.0598, step 1, values float32  

> tile

4 models tiled  

> surface dust #1 size 29.6

> surface dust #2 size 29.6

> surface dust #3 size 29.6

> surface dust #4 size 29.6

> volume #1 level 0.3

> volume #2 level 0.3

> volume #3 level 0.3

> volume #4 level 0.3

> tile

4 models tiled  

> tile

4 models tiled  

> volume #3 level 0.2547

> volume #1 level 0.255

> volume #2 level 0.255

> volume #4 level 0.255

> volume #4 level 0.2495

> tile

4 models tiled  

> tile

4 models tiled  

> tile

4 models tiled  

> scalebar 50

> tile

5 models tiled  

> scalebar off

> scalebar 50

> tile

5 models tiled  

> tile

5 models tiled  

> scalebar off

> tile

4 models tiled  

> volume #4 level 0.244

> volume #1 level 0.3702

> volume #2 level 0.3871

> tile

4 models tiled  

> volume #3 level 0.232

> tile

4 models tiled  

> tile

4 models tiled  

> tile

4 models tiled  

> tile

4 models tiled  

> tile

4 models tiled  

> close

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2818_007_volume_map.mrc

Opened cryosparc_P12_J2818_007_volume_map.mrc as #1, grid size 128,128,128,
pixel 2.96, shown at level 0.0455, step 1, values float32  

> tile

1 model tiled  

> surface dust #1 size 29.6

> volume #1 level 0.4017

> tile

1 model tiled  

> tile

1 model tiled  

> tile

1 model tiled  

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2819_007_volume_map.mrc

Opened cryosparc_P12_J2819_007_volume_map.mrc as #2, grid size 128,128,128,
pixel 2.96, shown at level 0.0532, step 1, values float32  

> tile

2 models tiled  

> surface dust #1 size 29.6

> surface dust #2 size 29.6

> volume #2 level 0.4074

> tile

2 models tiled  

> select add #2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.88558,0.46448,0,18.047,-0.46448,0.88558,0,120.62,0,0,1,-16.91

> view matrix models
> #2,-0.17366,0.17138,0.96978,88.013,0.11139,-0.975,0.19225,321.41,0.97849,0.14142,0.15023,-66.249

> select subtract #2

Nothing selected  

> tile

2 models tiled  

> volume #2 level 0.2693

> tile

2 models tiled  

> tile

2 models tiled  

> scalebar 50

> scalebar off

> scalebar 50

> tile

3 models tiled  

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.33304,0.010429,0.94285,125.34,-0.18526,-0.98117,-0.054586,431.2,0.92453,-0.19286,0.3287,-30.857

> transparency sel 50

> fitmap #1 inMap #2

Fit map cryosparc_P12_J2818_007_volume_map.mrc in map
cryosparc_P12_J2819_007_volume_map.mrc using 2290 points  
correlation = 0.9421, correlation about mean = 0.7819, overlap = 1664  
steps = 144, shift = 58.8, angle = 19.1 degrees  
  
Position of cryosparc_P12_J2818_007_volume_map.mrc (#1) relative to
cryosparc_P12_J2819_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99996913 0.00415055 0.00667112 -1.99638937  
-0.00415099 0.99999138 0.00005165 0.46837791  
-0.00667085 -0.00007934 0.99997774 1.12894591  
Axis -0.00833547 0.84903075 -0.52827767  
Axis point 153.81424804 0.00000000 300.19753960  
Rotation angle (degrees) 0.45018788  
Shift along axis -0.18208882  
  

> transparency sel 0

> transparency sel 50

> select subtract #1

Nothing selected  

> transparency 0

> transparency 50

> fitmap #1 inMap #2

Fit map cryosparc_P12_J2818_007_volume_map.mrc in map
cryosparc_P12_J2819_007_volume_map.mrc using 2290 points  
correlation = 0.9422, correlation about mean = 0.782, overlap = 1663  
steps = 72, shift = 21.7, angle = 0.0751 degrees  
  
Position of cryosparc_P12_J2818_007_volume_map.mrc (#1) relative to
cryosparc_P12_J2819_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99995835 0.00454896 0.00791196 -2.25248334  
-0.00454833 0.99998965 -0.00009773 0.55963971  
-0.00791232 0.00006174 0.99996869 1.34299381  
Axis 0.00873662 0.86691277 -0.49838330  
Axis point 155.76589802 0.00000000 285.28842643  
Rotation angle (degrees) 0.52293426  
Shift along axis -0.20384597  
  

> vop subtract #1 #2 minrms True

Opened volume difference as #5, grid size 128,128,128, pixel 2.96, shown at
step 1, values float32  
Minimum RMS scale factor for "cryosparc_P12_J2819_007_volume_map.mrc #2" above
level 0.26934 is 0.75554  
  

> close #5

> show #!1 models

> show #!2 models

> tile

3 models tiled  

> fitmap #1 inMap #2

Fit map cryosparc_P12_J2818_007_volume_map.mrc in map
cryosparc_P12_J2819_007_volume_map.mrc using 2290 points  
correlation = 0.9421, correlation about mean = 0.782, overlap = 1664  
steps = 564, shift = 124, angle = 0.05 degrees  
  
Position of cryosparc_P12_J2818_007_volume_map.mrc (#1) relative to
cryosparc_P12_J2819_007_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99996570 0.00414084 0.00717203 -2.05720799  
-0.00414182 0.99999141 0.00012291 0.44516601  
-0.00717146 -0.00015261 0.99997427 1.24408914  
Axis -0.01663273 0.86586809 -0.49999579  
Axis point 158.33521295 0.00000000 288.06380832  
Rotation angle (degrees) 0.47457076  
Shift along axis -0.20236731  
  

> vop subtract #1 #2 minrms True

Opened volume difference as #3, grid size 128,128,128, pixel 2.96, shown at
step 1, values float32  
Minimum RMS scale factor for "cryosparc_P12_J2819_007_volume_map.mrc #2" above
level 0.26934 is 0.67804  
  

> show #!2 models

> show #!1 models

> tile

4 models tiled  

> tile

4 models tiled  

> close #3

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2821_007_volume_map.mrc

Opened cryosparc_P12_J2821_007_volume_map.mrc as #3, grid size 128,128,128,
pixel 2.96, shown at level 0.00753, step 1, values float32  

> close #1-2

> tile

2 models tiled  

> tile

2 models tiled  

> surface dust #3 size 29.6

> volume #3 level 0.3

> volume #3 level 0.4

> tile

2 models tiled  

> volume #3 level 0.3938

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2822_007_volume_map.mrc

Opened cryosparc_P12_J2822_007_volume_map.mrc as #1, grid size 128,128,128,
pixel 2.96, shown at level 0.0127, step 1, values float32  

> volume #1 level 0.573

> tile

3 models tiled  

> surface dust #3 size 29.6

> surface dust #1 size 29.6

> select add #1

2 models selected  

> view matrix models
> #1,0.97223,-0.21106,-0.10114,380.42,0.22848,0.94958,0.21468,-275.43,0.050733,-0.23183,0.97143,18.353

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.051286,0.012031,0.99861,321.51,-0.08411,-0.99643,0.0076852,185.93,0.99514,-0.083599,0.052114,-11.552

> volume #1 level 0.286

> surface dust #1 size 29.6

[Repeated 5 time(s)]

> volume #1 level 0.4

> select subtract #1

Nothing selected  

> tile

3 models tiled  

> close #1

> close

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2821_005_volume_map.mrc

Opened cryosparc_P12_J2821_005_volume_map.mrc as #1, grid size 128,128,128,
pixel 2.96, shown at level 0.0073, step 1, values float32  

> tile

1 model tiled  

> surface dust #1 size 29.6

> volume #1 level 0.3975

> tile

1 model tiled  

> volume #1 level 0.4

> volume #1 level 0.3825

> tile

1 model tiled  

> open /Users/francescappadoo/Downloads/cryosparc_P12_J2822_005_volume_map.mrc

Opened cryosparc_P12_J2822_005_volume_map.mrc as #2, grid size 128,128,128,
pixel 2.96, shown at level 0.0126, step 1, values float32  

> tile

2 models tiled  

> surface dust #1 size 29.6

> surface dust #2 size 29.6

> volume #2 level 0.4943

> tile

2 models tiled  

> select add #2

2 models selected  

> view matrix models
> #2,0.99447,-0.10498,0,136.19,0.10498,0.99447,0,-35.791,0,0,1,0.7

> view matrix models
> #2,0.92683,-0.37547,0,199.54,0.37547,0.92683,0,-74.55,0,0,1,0.7

> view matrix models
> #2,-0.13744,0.20727,0.96858,106.61,-0.077827,-0.9771,0.19804,328.92,0.98745,-0.048162,0.15043,-14.472

> tile

2 models tiled  

> volume #2 level 0.325

> tile

2 models tiled  

> select subtract #2

Nothing selected  

> volume #2 level 0.3576

> volume #2 level 0.383

> fitmap #1 inMap #2

Fit map cryosparc_P12_J2821_005_volume_map.mrc in map
cryosparc_P12_J2822_005_volume_map.mrc using 2499 points  
correlation = 0.9329, correlation about mean = 0.7838, overlap = 1733  
steps = 252, shift = 115, angle = 13.1 degrees  
  
Position of cryosparc_P12_J2821_005_volume_map.mrc (#1) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99986367 0.01408905 0.00861070 -4.21776779  
-0.01406473 0.99989695 -0.00287889 3.05898223  
-0.00865037 0.00275739 0.99995879 1.01377657  
Axis 0.16823976 0.51523339 -0.84037488  
Axis point 214.75038890 301.61653129 0.00000000  
Rotation angle (degrees) 0.95979097  
Shift along axis 0.01454116  
  

> vop subtract #1 #2 minrms True

Opened volume difference as #3, grid size 128,128,128, pixel 2.96, shown at
step 1, values float32  
Minimum RMS scale factor for "cryosparc_P12_J2822_005_volume_map.mrc #2" above
level 0.383 is 0.74831  
  

> close #3

> show #!2 models

> show #!1 models

> fitmap #1 inMap #2

Fit map cryosparc_P12_J2821_005_volume_map.mrc in map
cryosparc_P12_J2822_005_volume_map.mrc using 2499 points  
correlation = 0.933, correlation about mean = 0.7838, overlap = 1732  
steps = 56, shift = 5.02, angle = 0.03 degrees  
  
Position of cryosparc_P12_J2821_005_volume_map.mrc (#1) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99985758 0.01420410 0.00911423 -4.31684383  
-0.01417765 0.99989511 -0.00296025 3.09314746  
-0.00915532 0.00283061 0.99995409 1.09790908  
Axis 0.16909240 0.53346925 -0.82874503  
Axis point 215.51896605 306.19844274 0.00000000  
Rotation angle (degrees) 0.98114281  
Shift along axis 0.01026686  
  

> fitmap #1 inMap #2

Fit map cryosparc_P12_J2821_005_volume_map.mrc in map
cryosparc_P12_J2822_005_volume_map.mrc using 2499 points  
correlation = 0.9329, correlation about mean = 0.7839, overlap = 1733  
steps = 40, shift = 0.0492, angle = 0.0398 degrees  
  
Position of cryosparc_P12_J2821_005_volume_map.mrc (#1) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99986166 0.01433770 0.00843224 -4.25885057  
-0.01431303 0.99989313 -0.00297978 3.13705429  
-0.00847406 0.00285868 0.99996001 0.95662847  
Axis 0.17286149 0.50055124 -0.84827317  
Axis point 216.14940696 299.39645368 0.00000000  
Rotation angle (degrees) 0.96763870  
Shift along axis 0.02258289  
  

> fitmap #1 inMap #2

Fit map cryosparc_P12_J2821_005_volume_map.mrc in map
cryosparc_P12_J2822_005_volume_map.mrc using 2499 points  
correlation = 0.9329, correlation about mean = 0.7838, overlap = 1733  
steps = 40, shift = 0.00179, angle = 0.0176 degrees  
  
Position of cryosparc_P12_J2821_005_volume_map.mrc (#1) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99986626 0.01416021 0.00818251 -4.17933891  
-0.01413629 0.99989566 -0.00297394 3.10101918  
-0.00822377 0.00285787 0.99996211 0.90849306  
Axis 0.17552757 0.49380027 -0.85167562  
Axis point 216.33321702 297.48675606 0.00000000  
Rotation angle (degrees) 0.95185593  
Shift along axis 0.02395348  
  

> fitmap #1 inMap #2

Fit map cryosparc_P12_J2821_005_volume_map.mrc in map
cryosparc_P12_J2822_005_volume_map.mrc using 2499 points  
correlation = 0.9329, correlation about mean = 0.7838, overlap = 1732  
steps = 40, shift = 0.0323, angle = 0.0446 degrees  
  
Position of cryosparc_P12_J2821_005_volume_map.mrc (#1) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99985575 0.01446824 0.00889707 -4.34250930  
-0.01444198 0.99989118 -0.00300914 3.15911421  
-0.00893963 0.00288021 0.99995590 1.04540061  
Axis 0.17082184 0.51735734 -0.83854713  
Axis point 215.89373206 302.48199933 0.00000000  
Rotation angle (degrees) 0.98772950  
Shift along axis 0.01597784  
  

> vop subtract #1 #2 minrms True

Opened volume difference as #3, grid size 128,128,128, pixel 2.96, shown at
step 1, values float32  
Minimum RMS scale factor for "cryosparc_P12_J2822_005_volume_map.mrc #2" above
level 0.383 is 0.74849  
  

> close #3

> show #!2 models

> show #!1 models

> tile

2 models tiled  

> tile

2 models tiled  

> volume #2 level 0.3309

> fitmap #1 inMap #2

Fit map cryosparc_P12_J2821_005_volume_map.mrc in map
cryosparc_P12_J2822_005_volume_map.mrc using 2499 points  
correlation = 0.9329, correlation about mean = 0.7838, overlap = 1733  
steps = 920, shift = 127, angle = 0.0599 degrees  
  
Position of cryosparc_P12_J2821_005_volume_map.mrc (#1) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99987023 0.01400269 0.00796610 -4.11419036  
-0.01397990 0.99989805 -0.00290899 3.05817413  
-0.00800602 0.00279724 0.99996404 0.87753868  
Axis 0.17438787 0.48812340 -0.85517508  
Axis point 215.72763897 296.12310142 0.00000000  
Rotation angle (degrees) 0.93744325  
Shift along axis 0.02485227  
  

> vop subtract #1 #2 minrms True

Opened volume difference as #3, grid size 128,128,128, pixel 2.96, shown at
step 1, values float32  
Minimum RMS scale factor for "cryosparc_P12_J2822_005_volume_map.mrc #2" above
level 0.33092 is 0.74609  
  

> close #3

> show #!2 models

> show #!1 models

> tile

2 models tiled  

> hide #!2 models

> open
> /Users/francescappadoo/Downloads/rnacomposer-2024-07-05-171619/RNAFramework.pdb
> format pdb

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

> transparency #1.1 50

> tile

2 models tiled  

> select add #3

10778 atoms, 11624 bonds, 336 residues, 1 model selected  

> view matrix models
> #3,-0.33015,0.011227,-0.94386,570.9,-0.56855,0.79583,0.20833,192.84,0.7535,0.60541,-0.25636,181.83

> view matrix models
> #3,-0.33078,-0.079337,-0.94037,570.24,-0.71759,0.66831,0.19603,192.41,0.61291,0.73964,-0.27799,182.76

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.0001867, steps = 272  
shifted from previous position = 49.9  
rotated from previous position = 52.2 degrees  
atoms outside contour = 10778, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.14917059 0.54482354 -0.82517601 144.60378530  
0.66711748 -0.67142498 -0.32271155 219.06293694  
-0.72986464 -0.50235027 -0.46361817 371.17593286  
Axis -0.75701879 -0.40165338 0.51536115  
Axis point 0.00000000 85.89031387 226.29287795  
Rotation angle (degrees) 173.18587352  
Shift along axis -6.16549766  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.0001863, steps = 44  
shifted from previous position = 0.0751  
rotated from previous position = 0.0679 degrees  
atoms outside contour = 10778, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.14851792 0.54414586 -0.82574070 144.62991725  
0.66741450 -0.67130945 -0.32233756 219.03537411  
-0.72972618 -0.50323841 -0.46287232 371.11667397  
Axis -0.75678768 -0.40167087 0.51568684  
Axis point 0.00000000 85.96492578 226.25210055  
Rotation angle (degrees) 173.13566257  
Shift along axis -6.05428471  
  

> view matrix models
> #3,-0.66102,-0.65126,-0.37271,614.17,-0.74996,0.58971,0.29967,175.68,0.024628,0.4776,-0.87823,162.08

> tile

2 models tiled  

> view matrix models
> #3,-0.1464,0.32546,-0.93415,644.1,-0.78463,0.53689,0.31002,191.61,0.60244,0.77835,0.17677,187.02

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.1464,0.32546,-0.93415,440.69,-0.78463,0.53689,0.31002,170.68,0.60244,0.77835,0.17677,187.02

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 168  
shifted from previous position = 18.6  
rotated from previous position = 32.3 degrees  
atoms outside contour = 7895, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42116682 0.90348570 -0.07957448 190.04332499  
0.65163889 -0.36245340 -0.66632896 194.46179074  
-0.63086073 0.22878183 -0.74139976 184.33555862  
Axis 0.82803758 0.50997679 -0.23297521  
Axis point 0.00000000 -2.78479300 134.06413330  
Rotation angle (degrees) 147.28222808  
Shift along axis 213.58839894  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 132  
shifted from previous position = 36.1  
rotated from previous position = 0.0125 degrees  
atoms outside contour = 7898, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42127992 0.90343835 -0.07951332 190.01131411  
0.65151012 -0.36245960 -0.66645150 194.47843198  
-0.63091821 0.22895890 -0.74129618 184.34728502  
Axis 0.82806382 0.50993202 -0.23297993  
Axis point 0.00000000 -2.77446531 134.07710592  
Rotation angle (degrees) 147.27107396  
Shift along axis 213.56305591  
  

> select up

10778 atoms, 11624 bonds, 336 residues, 5 models selected  

> select up

10778 atoms, 11624 bonds, 336 residues, 5 models selected  

> select down

10778 atoms, 11624 bonds, 336 residues, 1 model selected  

> select up

10778 atoms, 11624 bonds, 336 residues, 5 models selected  

> select down

10778 atoms, 11624 bonds, 336 residues, 1 model selected  

> fitmap #3 inMap #1 search 200 resolution 15

Opened RNAFramework.pdb map 15 as #4, grid size 43,37,50, pixel 5, shown at
level 0.0376, step 1, values float32  
Found 52 unique fits from 200 random placements having fraction of points
inside contour >= 0.100 (200 of 200).  
  
Correlations and times found:  
0.5725 (33), 0.5616 (20), 0.549 (8), 0.534 (19), 0.5285 (1), 0.5262 (1),
0.5178 (4), 0.5177 (8), 0.5174 (4), 0.5155 (4), 0.5044 (4), 0.5042 (6), 0.5032
(2), 0.5028 (1), 0.5019 (3), 0.5013 (1), 0.5001 (7), 0.4977 (1), 0.4977 (1),
0.497 (2), 0.4953 (10), 0.4946 (4), 0.494 (5), 0.4923 (2), 0.4917 (2), 0.4888
(1), 0.4852 (1), 0.485 (1), 0.4844 (1), 0.4844 (1), 0.4824 (2), 0.4809 (1),
0.4721 (2), 0.465 (4), 0.4623 (5), 0.4585 (2), 0.4554 (1), 0.4553 (2), 0.4415
(1), 0.4368 (5), 0.4332 (1), 0.4331 (4), 0.4322 (1), 0.4216 (1), 0.418 (1),
0.3986 (2), 0.3846 (1), 0.3835 (1), 0.3817 (1), 0.3815 (1), 0.3756 (1), 0.3599
(2)  
  
Best fit found:  
Fit map RNAFramework.pdb map 15 in map cryosparc_P12_J2821_005_volume_map.mrc
using 2353 points  
correlation = 0.5725, correlation about mean = 0.3095, overlap = 107  
steps = 452, shift = 20.2, angle = 105 degrees  
Position of RNAFramework.pdb map 15 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.48220738 0.87323413 -0.07027229 190.18022175  
0.67216748 -0.42023230 -0.60958647 196.19389648  
-0.56184242 0.24671235 -0.78959866 183.62545689  
Axis 0.84981539 0.48784822 -0.19954429  
Axis point 0.00000000 7.30102482 128.22094810  
Rotation angle (degrees) 149.74730431  
Shift along axis 220.68951131  
  
Found 52 fits.  

> ui tool show "Fit in Map"

Opened RNAFramework.pdb map 20 as #4, grid size 37,32,42, pixel 6.67, shown at
level 0.0286, step 1, values float32  
Opened RNAFramework.pdb map 20 as #5, grid size 37,32,42, pixel 6.67, shown at
level 0.0286, step 1, values float32  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5946, correlation about mean = 0.4182, overlap = 42.97  
steps = 72, shift = 1.98, angle = 3.86 degrees  
  
Position of RNAFramework.pdb map 20 (#5) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.52300102 0.84899342 -0.07536652 190.82843055  
0.67703002 -0.46752308 -0.56837707 198.36850067  
-0.51778400 0.24623639 -0.81930903 183.47405654  
Axis 0.86402279 0.46925174 -0.18239362  
Axis point 0.00000000 14.83307688 125.36294115  
Rotation angle (degrees) 151.87430724  
Shift along axis 224.50037909  
  
Average map value = 0.2611 for 10778 atoms, 7908 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5946, correlation about mean = 0.4183, overlap = 42.97  
steps = 100, shift = 32.9, angle = 0.0253 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.52323619 0.84887949 -0.07501667 190.77806226  
0.67698675 -0.46751743 -0.56843324 198.40322954  
-0.51760294 0.24663956 -0.81930217 183.47938799  
Axis 0.86408545 0.46920025 -0.18222914  
Axis point 0.00000000 14.86227869 125.35366714  
Rotation angle (degrees) 151.85925879  
Shift along axis 224.50410194  
  
Average map value = 0.261 for 10778 atoms, 7911 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5947, correlation about mean = 0.4183, overlap = 42.97  
steps = 68, shift = 13.2, angle = 0.0264 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.52303137 0.84897085 -0.07541008 190.79180727  
0.67692096 -0.46753253 -0.56849919 198.39682827  
-0.51789592 0.24629625 -0.81922029 183.47902367  
Axis 0.86402785 0.46922218 -0.18244568  
Axis point 0.00000000 14.85139546 125.37779860  
Rotation angle (degrees) 151.86764486  
Shift along axis 224.46667252  
  
Average map value = 0.261 for 10778 atoms, 7907 outside contour  

> select subtract #3

Nothing selected  

> select down

Nothing selected  

> select #3:63-68

189 atoms, 203 bonds, 6 residues, 1 model selected  

> color sel orange

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5947, correlation about mean = 0.4184, overlap = 42.97  
steps = 52, shift = 3.8, angle = 0.037 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.52277747 0.84907534 -0.07599199 190.79646872  
0.67684058 -0.46761518 -0.56852690 198.39895416  
-0.51825720 0.24577859 -0.81914729 183.47964272  
Axis 0.86396004 0.46923356 -0.18273726  
Axis point 0.00000000 14.85460458 125.40940339  
Rotation angle (degrees) 151.88366182  
Shift along axis 224.40740714  
  
Average map value = 0.261 for 10778 atoms, 7908 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5947, correlation about mean = 0.4183, overlap = 42.97  
steps = 44, shift = 0.01, angle = 0.0426 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.52306744 0.84895654 -0.07532097 190.79063410  
0.67693720 -0.46751879 -0.56849114 198.39678351  
-0.51783826 0.24637164 -0.81923407 183.47904317  
Axis 0.86403754 0.46922200 -0.18240024  
Axis point 0.00000000 14.85125551 125.37276377  
Rotation angle (degrees) 151.86545631  
Shift along axis 224.47578377  
  
Average map value = 0.261 for 10778 atoms, 7907 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5772, correlation about mean = 0.4185, overlap = 40.7  
steps = 44, shift = 0.735, angle = 1.03 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.46549444 -0.86965418 0.16436700 187.88701322  
-0.77314804 0.48995422 0.40272437 168.18463505  
-0.43076320 0.06038592 -0.90044239 192.95859825  
Axis -0.49376873 0.85838060 0.13919475  
Axis point 161.28338062 0.00000000 59.23013495  
Rotation angle (degrees) 159.71691777  
Shift along axis 78.45252100  
  
Average map value = 0.2525 for 10778 atoms, 7947 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5652, correlation about mean = 0.3603, overlap = 40.47  
steps = 60, shift = 1.37, angle = 1.93 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.52676158 -0.84634551 -0.07887641 192.42309184  
-0.84260823 0.53214147 -0.08268476 178.84285558  
0.11195333 0.02290675 -0.99344936 188.58374838  
Axis 0.48408202 -0.87485487 0.01713349  
Axis point 139.76375642 0.00000000 102.96734513  
Rotation angle (degrees) 173.73865756  
Shift along axis -60.08188424  
  
Average map value = 0.2493 for 10778 atoms, 8093 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5652, correlation about mean = 0.3603, overlap = 40.47  
steps = 28, shift = 0.0511, angle = 0.0248 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.52688305 -0.84624920 -0.07909822 192.46507861  
-0.84247972 0.53229475 -0.08300697 178.81576367  
0.11234819 0.02290367 -0.99340485 188.58844444  
Axis 0.48400397 -0.87489623 0.01722624  
Axis point 139.74793201 -0.00000000 103.00124996  
Rotation angle (degrees) 173.71864061  
Shift along axis -60.04270678  
  
Average map value = 0.2495 for 10778 atoms, 8088 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5457, correlation about mean = 0.3501, overlap = 36.67  
steps = 68, shift = 1.25, angle = 4.44 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.57869561 0.74887648 -0.32294799 193.28898432  
-0.64385703 0.66257154 0.38268397 188.62991332  
0.50055919 -0.01352524 0.86559659 200.38866384  
Axis -0.23785080 -0.49436469 -0.83608047  
Axis point 109.38237612 -99.13642631 0.00000000  
Rotation angle (degrees) 56.39722504  
Shift along axis -306.76695640  
  
Average map value = 0.2203 for 10778 atoms, 8305 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5196, correlation about mean = 0.2823, overlap = 36.78  
steps = 68, shift = 2.2, angle = 2.76 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.27622428 -0.96109318 0.00029408 196.13098039  
0.95673476 -0.27494249 0.09521146 209.49368048  
-0.09142626 0.02658109 0.99545699 196.99965941  
Axis -0.03572180 0.04774003 0.99822084  
Axis point 26.29576756 176.57324184 0.00000000  
Rotation angle (degrees) 106.13221934  
Shift along axis 199.64424837  
  
Average map value = 0.2252 for 10778 atoms, 8351 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5196, correlation about mean = 0.2824, overlap = 36.77  
steps = 28, shift = 0.0537, angle = 0.017 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.27618214 -0.96110534 0.00002104 196.08278610  
0.95672980 -0.27492269 0.09531837 209.46975477  
-0.09160524 0.02634538 0.99544680 197.00430204  
Axis -0.03589985 0.04769070 0.99821681  
Axis point 26.29149011 176.56315761 0.00000000  
Rotation angle (degrees) 106.13067596  
Shift along axis 199.60342224  
  
Average map value = 0.2251 for 10778 atoms, 8353 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5196, correlation about mean = 0.2823, overlap = 36.79  
steps = 52, shift = 4.13, angle = 0.019 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.27610543 -0.96112732 0.00031410 196.13700509  
0.95677155 -0.27482302 0.09518665 209.49227138  
-0.09140021 0.02658209 0.99545936 197.00061896  
Axis -0.03570707 0.04773516 0.99822160  
Axis point 26.28779192 176.58411995 0.00000000  
Rotation angle (degrees) 106.12504160  
Shift along axis 199.64694119  
  
Average map value = 0.2252 for 10778 atoms, 8352 outside contour  

> select down

189 atoms, 203 bonds, 6 residues, 1 model selected  

> select down

189 atoms, 203 bonds, 6 residues, 1 model selected  

> select down

189 atoms, 203 bonds, 6 residues, 1 model selected  

> select down

189 atoms, 203 bonds, 6 residues, 1 model selected  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5946, correlation about mean = 0.4182, overlap = 42.97  
steps = 72, shift = 1.98, angle = 3.86 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.52300054 0.84899370 -0.07536681 190.82847917  
0.67703012 -0.46752279 -0.56837724 198.36853323  
-0.51778436 0.24623600 -0.81930891 183.47401480  
Axis 0.86402266 0.46925188 -0.18239383  
Axis point 0.00000000 14.83305542 125.36295022  
Rotation angle (degrees) 151.87431120  
Shift along axis 224.50040889  
  
Average map value = 0.2611 for 10778 atoms, 7908 outside contour  

> fitmap #3 inMap #1 resolution 20 metric correlation

Fit map RNAFramework.pdb map 20 in map cryosparc_P12_J2821_005_volume_map.mrc
using 1268 points  
correlation = 0.5947, correlation about mean = 0.4183, overlap = 42.97  
steps = 40, shift = 0.0321, angle = 0.0157 degrees  
  
Position of RNAFramework.pdb map 20 (#4) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.52294154 0.84901450 -0.07554159 190.80379769  
0.67689974 -0.46751535 -0.56853861 198.38855178  
-0.51801435 0.24617837 -0.81918084 183.47664664  
Axis 0.86400154 0.46923920 -0.18252647  
Axis point 0.00000000 14.83995181 125.38571089  
Rotation angle (degrees) 151.86966188  
Shift along axis 224.45711452  
  
Average map value = 0.2611 for 10778 atoms, 7908 outside contour  

> select add #3

10778 atoms, 11624 bonds, 336 residues, 1 model selected  

> view matrix models
> #3,-0.35283,0.18449,-0.91732,412.63,-0.74405,0.53913,0.39462,169.67,0.56736,0.82177,-0.052956,184.95

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 92  
shifted from previous position = 9.72  
rotated from previous position = 9.37 degrees  
atoms outside contour = 7899, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42166250 0.90326335 -0.07947364 189.99625655  
0.65158664 -0.36278984 -0.66619697 194.48668114  
-0.63058351 0.22912632 -0.74152915 184.34566206  
Axis 0.82819858 0.50979173 -0.23280786  
Axis point -0.00000000 -2.71462857 134.04770180  
Rotation angle (degrees) 147.28064696  
Shift along axis 213.58521399  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 148  
shifted from previous position = 21.8  
rotated from previous position = 0.00836 degrees  
atoms outside contour = 7900, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42153738 0.90331747 -0.07952230 190.00096666  
0.65160433 -0.36272364 -0.66621571 194.48868578  
-0.63064888 0.22901775 -0.74150709 184.33191072  
Axis 0.82815945 0.50983426 -0.23285391  
Axis point 0.00000000 -2.72138513 134.04649584  
Rotation angle (degrees) 147.28260084  
Shift along axis 213.58568499  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 48  
shifted from previous position = 0.0223  
rotated from previous position = 0.0136 degrees  
atoms outside contour = 7899, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42174548 0.90322580 -0.07946020 189.98682693  
0.65156498 -0.36284402 -0.66618865 194.49239763  
-0.63055040 0.22918857 -0.74153806 184.34754129  
Axis 0.82822476 0.50975895 -0.23278650  
Axis point 0.00000000 -2.70276906 134.04656501  
Rotation angle (degrees) 147.27959330  
Shift along axis 213.58241756  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 28  
shifted from previous position = 0.0756  
rotated from previous position = 0.0154 degrees  
atoms outside contour = 7893, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42182874 0.90319590 -0.07935806 190.04924002  
0.65171306 -0.36289476 -0.66601614 194.45927482  
-0.63034164 0.22922607 -0.74170394 184.32146553  
Axis 0.82825892 0.50975821 -0.23266654  
Axis point 0.00000000 -2.71856138 134.01124249  
Rotation angle (degrees) 147.28666186  
Shift along axis 213.65175469  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 28  
shifted from previous position = 0.0842  
rotated from previous position = 0.0112 degrees  
atoms outside contour = 7900, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42176877 0.90321301 -0.07948193 189.97720373  
0.65160978 -0.36289653 -0.66611622 194.49872714  
-0.63048853 0.22915582 -0.74160079 184.33976167  
Axis 0.82823713 0.50974911 -0.23276404  
Axis point 0.00000000 -2.68533320 134.03708081  
Rotation angle (degrees) 147.28446682  
Shift along axis 213.58405880  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 164  
shifted from previous position = 26.1  
rotated from previous position = 0.0155 degrees  
atoms outside contour = 7899, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42157607 0.90330209 -0.07949196 189.99730653  
0.65156861 -0.36272184 -0.66625162 194.48561735  
-0.63065992 0.22908127 -0.74147808 184.34857683  
Axis 0.82816856 0.50982152 -0.23284942  
Axis point 0.00000000 -2.72660324 134.05584018  
Rotation angle (degrees) 147.27891732  
Shift along axis 213.57728868  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 44  
shifted from previous position = 0.0568  
rotated from previous position = 0.0186 degrees  
atoms outside contour = 7896, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42128661 0.90343175 -0.07955298 190.04418777  
0.65166509 -0.36255089 -0.66625031 194.46163653  
-0.63075366 0.22884044 -0.74147271 184.33285694  
Axis 0.82807948 0.50993485 -0.23291806  
Axis point 0.00000000 -2.76950162 134.05342293  
Rotation angle (degrees) 147.28491405  
Shift along axis 213.60000569  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 28  
shifted from previous position = 0.0678  
rotated from previous position = 0.012 degrees  
atoms outside contour = 7898, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42131912 0.90341562 -0.07956402 189.98779273  
0.65152069 -0.36253482 -0.66640026 194.49059834  
-0.63088110 0.22892957 -0.74133676 184.35407693  
Axis 0.82808063 0.50990706 -0.23297482  
Axis point 0.00000000 -2.75117292 134.07827763  
Rotation angle (degrees) 147.27513419  
Shift along axis 213.54748052  
  

> fitmap #3 inMap #1

Fit molecule RNAFramework.pdb (#3) to map
cryosparc_P12_J2821_005_volume_map.mrc (#1) using 10778 atoms  
average map value = 0.2663, steps = 24  
shifted from previous position = 0.0264  
rotated from previous position = 0.0814 degrees  
atoms outside contour = 7900, contour level = 0.38253  
  
Position of RNAFramework.pdb (#3) relative to
cryosparc_P12_J2821_005_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.42237169 0.90294122 -0.07936825 189.98674416  
0.65172014 -0.36337614 -0.66574669 194.49531789  
-0.62997064 0.22946666 -0.74194471 184.33245716  
Axis 0.82844612 0.50953708 -0.23248439  
Axis point 0.00000000 -2.61530487 133.98860569  
Rotation angle (degrees) 147.29616256  
Shift along axis 213.64193805  
  

> hide #!1 models

> show #!2 models

> transparency #2.1 50

> fitmap #3 inMap #2 search 200 resolution 15

Opened RNAFramework.pdb map 15 as #4, grid size 43,37,50, pixel 5, shown at
level 0.0376, step 1, values float32  
Found 42 unique fits from 200 random placements having fraction of points
inside contour >= 0.100 (199 of 200).  
  
Correlations and times found:  
0.6021 (28), 0.5683 (22), 0.5634 (17), 0.5542 (10), 0.5489 (17), 0.539 (6),
0.5382 (4), 0.5367 (6), 0.5351 (6), 0.5283 (8), 0.5278 (5), 0.5265 (5), 0.5251
(6), 0.5246 (4), 0.5183 (8), 0.5142 (4), 0.5113 (4), 0.5089 (3), 0.5068 (1),
0.5044 (2), 0.5019 (3), 0.4996 (2), 0.4989 (3), 0.4968 (1), 0.496 (2), 0.4916
(1), 0.4912 (1), 0.4878 (2), 0.473 (2), 0.4596 (1), 0.4567 (1), 0.4553 (2),
0.4535 (1), 0.4519 (1), 0.437 (1), 0.4361 (1), 0.4311 (2), 0.4296 (1), 0.4187
(2), 0.4127 (1), 0.4057 (1), 0.3679 (1)  
  
Best fit found:  
Fit map RNAFramework.pdb map 15 in map cryosparc_P12_J2822_005_volume_map.mrc
using 2353 points  
correlation = 0.6021, correlation about mean = 0.338, overlap = 135.4  
steps = 256, shift = 11.2, angle = 79.2 degrees  
Position of RNAFramework.pdb map 15 (#4) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.55599115 0.82149720 -0.12655501 192.43366753  
0.61278467 -0.50798978 -0.60534401 199.62120735  
-0.56157702 0.25901494 -0.78583865 181.56038097  
Axis 0.87316938 0.43945620 -0.21083994  
Axis point 0.00000000 16.89837566 129.79282410  
Rotation angle (degrees) 150.33322218  
Shift along axis 217.47178444  
  
Found 42 fits.  
Opened RNAFramework.pdb map 20 as #4, grid size 37,32,42, pixel 6.67, shown at
level 0.0286, step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 147, in fitmap  
show_fit_list(fits, show_first, session)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 273, in show_fit_list  
flist[0].place_models(session)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 179, in place_models  
m.position = tf  
^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 252, in _model_set_position  
if pos != self.position:  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing "RNAFramework.pdb
map 15"  
  
RuntimeError: Tried to get the position of deleted drawing "RNAFramework.pdb
map 15"  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
  
See log for complete Python traceback.  
  

> fitmap #3 inMap #2 search 200 resolution 15

Opened RNAFramework.pdb map 15 as #4, grid size 43,37,50, pixel 5, shown at
level 0.0376, step 1, values float32  
Found 42 unique fits from 200 random placements having fraction of points
inside contour >= 0.100 (199 of 200).  
  
Correlations and times found:  
0.6021 (26), 0.5683 (22), 0.5633 (16), 0.5543 (10), 0.5489 (18), 0.5391 (4),
0.5383 (4), 0.5367 (9), 0.5351 (5), 0.5283 (6), 0.5278 (6), 0.5265 (4), 0.5252
(8), 0.5246 (4), 0.5183 (8), 0.5141 (4), 0.5111 (5), 0.5093 (1), 0.5089 (5),
0.5068 (1), 0.5026 (1), 0.502 (4), 0.4996 (1), 0.4989 (2), 0.4968 (2), 0.4966
(1), 0.496 (3), 0.4909 (1), 0.4878 (1), 0.473 (2), 0.4568 (1), 0.4553 (2),
0.4535 (1), 0.4519 (1), 0.4369 (1), 0.431 (1), 0.4296 (1), 0.4187 (3), 0.4058
(1), 0.4037 (1), 0.3679 (1), 0.3601 (1)  
  
Best fit found:  
Fit map RNAFramework.pdb map 15 in map cryosparc_P12_J2822_005_volume_map.mrc
using 2353 points  
correlation = 0.6021, correlation about mean = 0.338, overlap = 135.4  
steps = 248, shift = 31.5, angle = 63.6 degrees  
Position of RNAFramework.pdb map 15 (#4) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.55598003 0.82149415 -0.12662401 192.43601485  
0.61277507 -0.50802468 -0.60532447 199.61928023  
-0.56159854 0.25895620 -0.78584266 181.56451051  
Axis 0.87316778 0.43944723 -0.21086527  
Axis point 0.00000000 16.89992108 129.79685150  
Rotation angle (degrees) 150.33611802  
Shift along axis 217.46541876  
  
Found 42 fits.  
Opened RNAFramework.pdb map 20 as #4, grid size 37,32,42, pixel 6.67, shown at
level 0.0286, step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 147, in fitmap  
show_fit_list(fits, show_first, session)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 273, in show_fit_list  
flist[0].place_models(session)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 179, in place_models  
m.position = tf  
^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 252, in _model_set_position  
if pos != self.position:  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing "RNAFramework.pdb
map 15"  
  
RuntimeError: Tried to get the position of deleted drawing "RNAFramework.pdb
map 15"  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
  
See log for complete Python traceback.  
  

> select subtract #3

Nothing selected  

> fitmap #3 inMap #2 search 200 resolution 15

Opened RNAFramework.pdb map 15 as #4, grid size 43,37,50, pixel 5, shown at
level 0.0376, step 1, values float32  
Found 39 unique fits from 200 random placements having fraction of points
inside contour >= 0.100 (200 of 200).  
  
Correlations and times found:  
0.602 (28), 0.5684 (20), 0.5633 (16), 0.5542 (8), 0.5489 (17), 0.5391 (5),
0.5382 (8), 0.5367 (8), 0.5351 (6), 0.5283 (9), 0.5277 (7), 0.5266 (5), 0.525
(7), 0.5247 (1), 0.5184 (5), 0.5142 (4), 0.5108 (5), 0.5093 (1), 0.5089 (2),
0.5042 (1), 0.502 (6), 0.502 (1), 0.4997 (2), 0.4989 (3), 0.4968 (3), 0.496
(1), 0.4917 (2), 0.4877 (2), 0.473 (4), 0.4717 (1), 0.4571 (1), 0.4553 (1),
0.4535 (1), 0.437 (1), 0.4221 (1), 0.4187 (3), 0.4127 (1), 0.39 (1), 0.3679
(2)  
  
Best fit found:  
Fit map RNAFramework.pdb map 15 in map cryosparc_P12_J2822_005_volume_map.mrc
using 2353 points  
correlation = 0.602, correlation about mean = 0.3378, overlap = 135.4  
steps = 644, shift = 31.6, angle = 78.9 degrees  
Position of RNAFramework.pdb map 15 (#4) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.55642122 0.82107850 -0.12738012 192.49700580  
0.61225611 -0.50879760 -0.60520043 199.61619735  
-0.56172761 0.25875699 -0.78581605 181.57285517  
Axis 0.87331403 0.43905146 -0.21108392  
Axis point 0.00000000 16.95484171 129.83138545  
Rotation angle (degrees) 150.35378473  
Shift along axis 217.42500710  
  
Found 39 fits.  
Opened RNAFramework.pdb map 20 as #4, grid size 37,32,42, pixel 6.67, shown at
level 0.0286, step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 147, in fitmap  
show_fit_list(fits, show_first, session)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 273, in show_fit_list  
flist[0].place_models(session)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 179, in place_models  
m.position = tf  
^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 252, in _model_set_position  
if pos != self.position:  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing "RNAFramework.pdb
map 15"  
  
RuntimeError: Tried to get the position of deleted drawing "RNAFramework.pdb
map 15"  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGNA3B/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3 (22E252)
      Kernel Version: Darwin 22.4.0
      Time since boot: 9 days, 1 hour, 26 minutes

Graphics/Displays:

    Apple M1:

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      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
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          Resolution: 2560 x 1600 Retina
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    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
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Change History (4)

comment:1 by Eric Pettersen, 17 months ago

Component: Unassigned → Volume Data
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Fitmap: Tried to get the position of deleted drawing

Reported by Fran

comment:2 by Tom Goddard, 17 months ago

From the log it appears that a fit search was run with resolution 15

fitmap #3 inMap #2 search 200 resolution 15

It created a simulated map of resolution 15A

Opened RNAFramework.pdb map 15 as #4, grid size 43,37,50, pixel 5, shown at
level 0.0376, step 1, values float32

But then before the command showed the table of fits I see in the log that the simulated map was replaced by one simulated at 20A resolution:

Opened RNAFramework.pdb map 20 as #4, grid size 37,32,42, pixel 6.67, shown at
level 0.0286, step 1, values float32

And then the table of fits is shown and generates an error because the original 15A resolution simulated map was replaced.

I have not figured out how this 20A simulated map is being created before the search results table is shown. I see in the log about a dozen commands earlier a fit command with resolution 20 that would create replace the 15A map.

fitmap #3 inMap #1 resolution 20 metric correlation

But when I try to execute that command with the Fit in Map dialog before the search finishes by clicking the Fit button it doesn't get executed until after the table is created and there is no error.

So I don't have an idea how the 20A resolution fit preempted the 15A resolution fit search.

> fitmap #3 inMap #2 search 200 resolution 15

Opened RNAFramework.pdb map 15 as #4, grid size 43,37,50, pixel 5, shown at
level 0.0376, step 1, values float32  
Found 42 unique fits from 200 random placements having fraction of points
inside contour >= 0.100 (199 of 200).  
  
Correlations and times found:  
0.6021 (28), 0.5683 (22), 0.5634 (17), 0.5542 (10), 0.5489 (17), 0.539 (6),
0.5382 (4), 0.5367 (6), 0.5351 (6), 0.5283 (8), 0.5278 (5), 0.5265 (5), 0.5251
(6), 0.5246 (4), 0.5183 (8), 0.5142 (4), 0.5113 (4), 0.5089 (3), 0.5068 (1),
0.5044 (2), 0.5019 (3), 0.4996 (2), 0.4989 (3), 0.4968 (1), 0.496 (2), 0.4916
(1), 0.4912 (1), 0.4878 (2), 0.473 (2), 0.4596 (1), 0.4567 (1), 0.4553 (2),
0.4535 (1), 0.4519 (1), 0.437 (1), 0.4361 (1), 0.4311 (2), 0.4296 (1), 0.4187
(2), 0.4127 (1), 0.4057 (1), 0.3679 (1)  
  
Best fit found:  
Fit map RNAFramework.pdb map 15 in map cryosparc_P12_J2822_005_volume_map.mrc
using 2353 points  
correlation = 0.6021, correlation about mean = 0.338, overlap = 135.4  
steps = 256, shift = 11.2, angle = 79.2 degrees  
Position of RNAFramework.pdb map 15 (#4) relative to
cryosparc_P12_J2822_005_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.55599115 0.82149720 -0.12655501 192.43366753  
0.61278467 -0.50798978 -0.60534401 199.62120735  
-0.56157702 0.25901494 -0.78583865 181.56038097  
Axis 0.87316938 0.43945620 -0.21083994  
Axis point 0.00000000 16.89837566 129.79282410  
Rotation angle (degrees) 150.33322218  
Shift along axis 217.47178444  
  
Found 42 fits.  
Opened RNAFramework.pdb map 20 as #4, grid size 37,32,42, pixel 6.67, shown at
level 0.0286, step 1, values float32  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 147, in fitmap  
show_fit_list(fits, show_first, session)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 273, in show_fit_list  
flist[0].place_models(session)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/search.py", line 179, in place_models  
m.position = tf  
^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 266, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 252, in _model_set_position  
if pos != self.position:  
^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)  
RuntimeError: Tried to get the position of deleted drawing "RNAFramework.pdb
map 15"  
  
RuntimeError: Tried to get the position of deleted drawing "RNAFramework.pdb
map 15"  
  
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 503, in _drawing_get_position  
raise RuntimeError('Tried to get the position of deleted drawing "%s"' %
self.name)

comment:3 by Tom Goddard, 17 months ago

Aha! I got it the Fit in Map panel "Real-time correlation update" option was enabled and it apparently recomputes the map at the 20A resolution shown in the panel causing the search table which used the 15A resolution to throw an error.

comment:4 by Tom Goddard, 17 months ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Fit search code that prevented trying to position a deleted model did not work because the model got deleted in the loop that was setting model positions. Put test for deleted model into the loop to avoid this error.

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