Save mmCIF: 'Residue' object has no attribute 'display'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.10.198-gentoo-x86_64-Intel-R-_Xeon-R-_Silver_4110_CPU_@_2.10GHz-with-glibc2.37
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /home/pauline/Desktop/map316_modelbuilding/sheets.cxs

Opened cryosparc_P31_J316_010_volume_map.mrc as #1, grid size 900,900,900,
pixel 0.485, shown at level 0.0179, step 4, values float32  
Log from Fri Nov 17 14:43:17 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/pauline/Desktop/flipvol_maps/cryosparc_P31_J316_010_volume_map.mrc
> format mrc

Opened cryosparc_P31_J316_010_volume_map.mrc as #1, grid size 900,900,900,
pixel 0.485, shown at step 1, values float32  

> volume #1 region 0,0,0,899,899,899 step 4

[Repeated 1 time(s)]

> ui tool show "Segment Map"

Segmenting cryosparc_P31_J316_010_volume_map.mrc, density threshold 0.017861  
Only showing 60 of 1973 regions.  
Showing 60 of 1973 region surfaces  
5646 watershed regions, grouped to 1973 regions  
Showing cryosparc_P31_J316_010_volume_map.seg - 1973 regions, 60 surfaces  

> set bgColor white

Segmenting cryosparc_P31_J316_010_volume_map.mrc, density threshold 0.017861  
Only showing 60 of 2764 regions.  
Showing 60 of 2764 region surfaces  
5646 watershed regions, grouped to 2764 regions  
Showing cryosparc_P31_J316_010_volume_map.seg - 2764 regions, 60 surfaces  
Segmenting cryosparc_P31_J316_010_volume_map.mrc, density threshold 0.017861  
Only showing 60 of 448 regions.  
Showing 60 of 448 region surfaces  
5646 watershed regions, grouped to 448 regions  
Showing cryosparc_P31_J316_010_volume_map.seg - 448 regions, 60 surfaces  
Segmenting cryosparc_P31_J316_010_volume_map.mrc, density threshold 0.017861  
Only showing 60 of 503 regions.  
Showing 60 of 503 region surfaces  
5646 watershed regions, grouped to 503 regions  
Showing cryosparc_P31_J316_010_volume_map.seg - 503 regions, 60 surfaces  

> surface dust #1 size 4.85

> ui mousemode right select

> select #2.39

1 model selected  

> select #2.4

1 model selected  
Ungrouped to 2 regions  

> select #2.62

1 model selected  
Ungrouped to 2 regions, but did not show all surfaces, see Options  

> select #2.61

1 model selected  
Ungrouped to 2 regions, but did not show all surfaces, see Options  

> select #2.62

1 model selected  
Ungrouped to 2 regions, but did not show all surfaces, see Options  

> select #1

3 models selected  
Ungrouped to 396 regions, but did not show all surfaces, see Options  

> select clear

[Repeated 1 time(s)]

> select #2.114

1 model selected  
Ungrouped to 2 regions, but did not show their surfaces, see Options  

> select #2.130

1 model selected  
Ungrouped to 2 regions, but did not show their surfaces, see Options  

> select #1

3 models selected  

> select clear

> undo

[Repeated 1 time(s)]

> select clear

> select #2.158

1 model selected  
Ungrouped to 2 regions, but did not show their surfaces, see Options  
Segmenting cryosparc_P31_J316_010_volume_map.mrc, density threshold 0.017861  
Only showing 60 of 473 regions.  
Showing 60 of 473 region surfaces  
5646 watershed regions, grouped to 473 regions  
Showing cryosparc_P31_J316_010_volume_map.seg - 473 regions, 60 surfaces  

> select #2.18

1 model selected  

> select add #2.35

2 models selected  
Grouped 2 regions  

> select #2.4

1 model selected  
Ungrouped to 2 regions  

> select #2.61

1 model selected  

> select #2.35

1 model selected  
Ungrouped to 2 regions  

> select #2.62

1 model selected  
Ungrouped to 2 regions, but did not show all surfaces, see Options  

> select add #2.18

2 models selected  
Grouped 2 regions  

> select #2.18

1 model selected  

> select add #2.4

2 models selected  
Grouped 2 regions  
Drag select of 10795, 5557 of 942616 triangles, 10810, 171868 of 607224
triangles, 10793, 586 of 580844 triangles, 10802, 176008 of 426036 triangles,
10804, 104359 of 425624 triangles, 10792, 21974 of 358660 triangles, 10817,
12809 of 114180 triangles, 10789, 105631 of 107668 triangles, 9234, 9425 of
17812 triangles, 10720, 7282 of 112248 triangles, 10822, 203391 of 886016
triangles, 1 cryosparc_P31_J316_010_volume_map.mrc  

> select clear

> select #2.4

1 model selected  
Ungrouped to 2 regions  

> select clear

> select #1

3 models selected  

> select clear

> select #2.61

1 model selected  

> select add #2.35

2 models selected  
Grouped 2 regions  

> select clear

> select #2.43

1 model selected  

> select add #2.20

2 models selected  
Grouped 2 regions  

> select #2.42

1 model selected  

> select add #2.13

2 models selected  
Grouped 2 regions  

> select #2.39

1 model selected  

> select add #2.12

2 models selected  
Grouped 2 regions  

> select #2.33

1 model selected  

> select add #2.15

2 models selected  
Grouped 2 regions  

> select #1

3 models selected  

> surface dust #1 size 4.85

> select clear

> select #2.38

1 model selected  

> select add #2.11

2 models selected  
Grouped 2 regions  

> select #2.36

1 model selected  

> select add #2.17

2 models selected  
Grouped 2 regions  

> select #2.57

1 model selected  

> select add #2.7

2 models selected  
Grouped 2 regions  

> select #2.52

1 model selected  

> select add #2.3

2 models selected  
Grouped 2 regions  

> select #2.48

1 model selected  

> select add #2.2

2 models selected  
Grouped 2 regions  

> select #2.31

1 model selected  

> select add #2.15

2 models selected  
Grouped 2 regions  

> select #2.50

1 model selected  

> select add #2.5

2 models selected  
Grouped 2 regions  

> select #2.54

1 model selected  

> select add #2.15

2 models selected  
Grouped 2 regions  

> select #2.45

1 model selected  

> select add #2.20

2 models selected  
Grouped 2 regions  

> select #2.34

1 model selected  

> select add #2.10

2 models selected  
Grouped 2 regions  

> select #2.44

1 model selected  

> select add #2.14

2 models selected  
Grouped 2 regions  

> select #2.46

1 model selected  

> select add #2.19

2 models selected  
Grouped 2 regions  

> select #2.37

1 model selected  

> select clear

> select #2.37

1 model selected  

> select add #2.17

2 models selected  
Grouped 2 regions  

> select #2.29

1 model selected  

> select add #2.1

2 models selected  
Grouped 2 regions  

> select #2.32

1 model selected  

> select add #2.9

2 models selected  
Grouped 2 regions  

> select #1

3 models selected  

> select #1

3 models selected  

> select clear

> select #1

3 models selected  

> select #2.59

1 model selected  

> select add #2.4

2 models selected  
Grouped 2 regions  

> select #1

3 models selected  
Ungrouped to 316 regions, but did not show all surfaces, see Options  

> select #1

3 models selected  
Got 458 regions after grouping by connections  

> select clear

[Repeated 1 time(s)]Segmenting cryosparc_P31_J316_010_volume_map.mrc, density
threshold 0.017861  
Only showing 60 of 503 regions.  
Showing 60 of 503 region surfaces  
5646 watershed regions, grouped to 503 regions  

> select clear

Showing cryosparc_P31_J316_010_volume_map.seg - 503 regions, 60 surfaces  

> select #2.38

1 model selected  

> select clear

> surface dust #1 size 4.85

> select #2.5

1 model selected  

> select add #2.32

2 models selected  
Grouped 2 regions  

> select #2.30

1 model selected  

> select clear

> select #2.30

1 model selected  

> select add #2.1

2 models selected  
Grouped 2 regions  

> select #2.34

1 model selected  

> select add #2.1

2 models selected  
Grouped 2 regions  

> select #2.27

1 model selected  

> select add #2.6

2 models selected  

> select #2.27

1 model selected  
Ungrouped to 2 regions  

> select #2.32

1 model selected  

> select add #2.2

2 models selected  
Ungrouped to 4 regions  

> select #2.61

1 model selected  

> select #2.61

1 model selected  

> select #2.61

1 model selected  

> select clear

> select #2.61

1 model selected  

> select add #2.27

2 models selected  
Grouped 2 regions  

> select #2.33

1 model selected  

> select add #2.2

2 models selected  
Grouped 2 regions  

> select #2.2

1 model selected  

> select add #2.31

2 models selected  
Grouped 2 regions  

> select #2.40

1 model selected  

> select add #2.11

2 models selected  
Grouped 2 regions  

> select #2.42

1 model selected  

> select add #2.15

2 models selected  
Grouped 2 regions  

> select #2.54

1 model selected  

> select add #2.9

2 models selected  
Grouped 2 regions  

> select #2.43

1 model selected  

> select add #2.13

2 models selected  
Grouped 2 regions  

> select #2.38

1 model selected  

> select add #2.15

2 models selected  
Grouped 2 regions  

> select #1

3 models selected  

> select clear

> select #2.6

1 model selected  

> select add #2.30

2 models selected  
Grouped 2 regions  

> select #2.4

1 model selected  

> select add #2.39

2 models selected  
Grouped 2 regions  

> select #2.55

1 model selected  

> select add #2.20

2 models selected  
Grouped 2 regions  

> select #2.51

1 model selected  

> select add #2.18

2 models selected  
Grouped 2 regions  

> select #2.53

1 model selected  

> select add #2.20

2 models selected  
Grouped 2 regions  

> select #2.26

1 model selected  
Ungrouped to 2 regions  

> select #2.27

1 model selected  

> select add #2.12

2 models selected  
Grouped 2 regions  

> select #2.30

1 model selected  

> select add #2.2

2 models selected  
Grouped 2 regions  

> select clear

> select #2.37

1 model selected  

> select add #2.10

2 models selected  
Grouped 2 regions  

> select #2.47

1 model selected  

> select add #2.19

2 models selected  
Grouped 2 regions  

> select #2.52

1 model selected  

> select add #2.18

2 models selected  
Grouped 2 regions  

> select #2.4

1 model selected  
Ungrouped to 2 regions  

> select #2.27

1 model selected  
Ungrouped to 2 regions  

> select #2.30

1 model selected  
Ungrouped to 2 regions  

> select #2.27

1 model selected  

> select add #2.16

2 models selected  
Grouped 2 regions  

> select #2.41

1 model selected  

> select #2.46

1 model selected  

> select add #2.19

2 models selected  
Grouped 2 regions  

> select #2.41

1 model selected  

> select add #2.16

2 models selected  
Grouped 2 regions  

> select #2.31

1 model selected  

> select add #2.10

2 models selected  

> select #2.31

1 model selected  

> select #2.4

1 model selected  

> select add #2.31

2 models selected  
Grouped 2 regions  

> select #2.25

1 model selected  
Ungrouped to 2 regions  
[Repeated 1 time(s)]

> select #2.6

1 model selected  

> select #2.25

1 model selected  
Ungrouped to 2 regions  

> select #2.30

1 model selected  

> select add #2.32

2 models selected  
Grouped 2 regions  

> select #1

3 models selected  

> select #2.25

1 model selected  

> select add #2.12

2 models selected  
Grouped 2 regions  

> select #2.27

1 model selected  

> select add #2.1

2 models selected  
Grouped 2 regions  

> select clear

> select #2.57

1 model selected  

> select add #2.22

2 models selected  
Grouped 2 regions  

> select clear

> select #2.56

1 model selected  

> select add #2.17

2 models selected  
Grouped 2 regions  

> select #2.35

1 model selected  

> select add #2.10

2 models selected  
Grouped 2 regions  

> select clear

> select #2.26

1 model selected  

> select add #2.4

2 models selected  
Grouped 2 regions  

> select clear

> select #2.45

1 model selected  

> select add #2.7

2 models selected  
Grouped 2 regions  

> select #1

3 models selected  

> select clear

> select #1

3 models selected  

> select clear

> select #2.36

1 model selected  

> select add #2.11

2 models selected  
Grouped 2 regions  

> select clear

> select #2.34

1 model selected  

> select add #2.2

2 models selected  
Grouped 2 regions  

> select clear

> transparency 50

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

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

> ui tool show "Fit to Segments"

[Repeated 1 time(s)]

> select #2.1

1 model selected  
Simulating map res 4.000, grid 2.000  

> molmap #3 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened dimer_one.pdb map 4 as #4, grid size 37,47,121, pixel 2, shown at level
0.106, step 1, values float32  
Opened cryosparc_P31_J316_010_volume_map_masked as #5, grid size 900,900,900,
pixel 0.485, shown at step 1, values float32  
Top score: 0.64938, z-score: 2.03638 (avg: 0.6426, stdev: 0.0033)  

> select add #3

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #2.1,1,0,0,-2.7063,0,1,0,6.8376,0,0,1,-16.601,#3,0.30192,0.18705,0.9348,243.74,0.95195,-0.11198,-0.28506,268.92,0.051357,0.97595,-0.21187,189.29

> undo

> select subtract #3

1 model selected  

> select clear

> select /A

3210 atoms, 3304 bonds, 6 pseudobonds, 420 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.029869,0.64427,0.76422,245.85,0.3353,0.72671,-0.59955,260.98,-0.94164,0.23833,-0.23773,206.39

> view matrix models
> #3,-0.18661,0.66685,0.72145,245.92,-0.020399,0.73156,-0.68147,260.88,-0.98222,-0.14188,-0.12291,206.82

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.18661,0.66685,0.72145,237.48,-0.020399,0.73156,-0.68147,268.63,-0.98222,-0.14188,-0.12291,208.57

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.10228,0.59981,0.79358,237.59,0.05366,0.79992,-0.5977,268.65,-0.99331,-0.018547,-0.114,208.49

> view matrix models
> #3,-0.26389,0.49178,0.82977,237.74,0.057298,0.86674,-0.49546,268.73,-0.96285,-0.083203,-0.2569,208.35

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.26389,0.49178,0.82977,235.6,0.057298,0.86674,-0.49546,278.5,-0.96285,-0.083203,-0.2569,211.93

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.21447,0.40507,0.88878,235.75,-0.030671,0.90671,-0.42064,278.57,-0.97625,-0.11747,-0.18203,212.06

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.21447,0.40507,0.88878,235.21,-0.030671,0.90671,-0.42064,278.01,-0.97625,-0.11747,-0.18203,211.44

> view matrix models
> #3,-0.21447,0.40507,0.88878,238.45,-0.030671,0.90671,-0.42064,276.42,-0.97625,-0.11747,-0.18203,207.02

> ui mousemode right select

> select #2.1

1 model selected  
Opened cryosparc_P31_J316_010_volume_map_masked as #5, grid size 900,900,900,
pixel 0.485, shown at step 1, values float32  
Cross-correlation of fit: 0.649376  
Top score: 0.64938, z-score: 2.03638 (avg: 0.6426, stdev: 0.0033)  

> close session

> open
> /home/pauline/Desktop/flipvol_maps/cryosparc_P31_J316_010_volume_map.mrc
> format mrc

Opened cryosparc_P31_J316_010_volume_map.mrc as #1, grid size 900,900,900,
pixel 0.485, shown at step 1, values float32  

> volume #1 region 0,0,0,899,899,899 step 4

[Repeated 1 time(s)]

> surface dust #1 size 4.85

> vop gaussian #1 sdev 1.46

Opened cryosparc_P31_J316_010_volume_map.mrc gaussian as #2, grid size
900,900,900, pixel 0.485, shown at step 1, values float32  

> set bgColor white

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

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

> select /A

3210 atoms, 3304 bonds, 6 pseudobonds, 420 residues, 2 models selected  

> ui tool show "Fit in Map"

> fitmap #3 inMap #2 moveWholeMolecules false

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
gaussian (#2) using 6539 atoms  
average map value = 0.01496, steps = 44  
shifted from previous position = 0.042  
rotated from previous position = 0.208 degrees  
atoms outside contour = 4118, contour level = 0.016836  
  

> fitmap #3 inMap #1 moveWholeMolecules false

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.016, steps = 48  
shifted from previous position = 0.171  
rotated from previous position = 0.228 degrees  
atoms outside contour = 4215, contour level = 0.017861  
  

> select /B

3094 atoms, 3186 bonds, 7 pseudobonds, 413 residues, 3 models selected  

> fitmap #3 inMap #1 moveWholeMolecules false

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.016, steps = 40  
shifted from previous position = 0.00691  
rotated from previous position = 0.0303 degrees  
atoms outside contour = 4214, contour level = 0.017861  
  

> combine #3

> select clear

> select add #4

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  
Drag select of 2 cryosparc_P31_J316_010_volume_map.mrc gaussian , 14 residues  

> ui mousemode right "translate selected models"

> view matrix models
> #2,1,0,0,2.893,0,1,0,-1.0405,0,0,1,9.1978,#3,1,0,0,2.893,0,1,0,-1.0405,0,0,1,9.1978,#4,1,0,0,2.893,0,1,0,-1.0405,0,0,1,9.1978

> select clear

> select add #4

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #4,1,0,0,-30.423,0,1,0,-3.4816,0,0,1,63.667

> view matrix models #4,1,0,0,-35.864,0,1,0,-5.9171,0,0,1,65.805

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.85198,-0.52275,0.029467,142.32,0.51339,0.82301,-0.24306,-25.899,0.10281,0.22221,0.96956,-15.624

> view matrix models
> #4,0.9094,-0.41234,0.054421,91.764,0.41385,0.88407,-0.21712,-25.159,0.041415,0.21997,0.97463,-1.4329

> view matrix models
> #4,0.884,-0.46742,0.0079892,123.46,0.46527,0.87801,-0.11231,-58.023,0.045484,0.103,0.99364,26.946

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.884,-0.46742,0.0079892,127.21,0.46527,0.87801,-0.11231,-56.289,0.045484,0.103,0.99364,26.039

> select #3/B

3094 atoms, 3186 bonds, 7 pseudobonds, 413 residues, 3 models selected  

> select #4/A

3210 atoms, 3304 bonds, 6 pseudobonds, 420 residues, 2 models selected  

> fitmap sel inMap #1 moveWholeMolecules false

Fit molecule copy of dimer_one.pdb (#4) to map
cryosparc_P31_J316_010_volume_map.mrc (#1) using 3210 atoms  
average map value = 0.01601, steps = 220  
shifted from previous position = 15.1  
rotated from previous position = 6.11 degrees  
atoms outside contour = 2109, contour level = 0.017861  
  

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.884,-0.46742,0.0079892,129.94,0.46527,0.87801,-0.11231,-57.608,0.045484,0.103,0.99364,38.228

> view matrix models
> #4,0.884,-0.46742,0.0079892,129.75,0.46527,0.87801,-0.11231,-56.627,0.045484,0.103,0.99364,35.715

> fitmap sel inMap #1 moveWholeMolecules false

Fit molecule copy of dimer_one.pdb (#4) to map
cryosparc_P31_J316_010_volume_map.mrc (#1) using 3210 atoms  
average map value = 0.01601, steps = 144  
shifted from previous position = 10  
rotated from previous position = 0.0236 degrees  
atoms outside contour = 2110, contour level = 0.017861  
  

> ui mousemode right "move picked models"

> view matrix models
> #4,0.884,-0.46742,0.0079892,133.71,0.46527,0.87801,-0.11231,-56.02,0.045484,0.103,0.99364,45.909

> close #4

> combine #3

> select add #4

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui mousemode right "translate selected models"

> hide #!2 models

> show #!1 models

> transparency #1.2 50

> view matrix models #4,1,0,0,2.9593,0,1,0,-11.821,0,0,1,41.288

> view matrix models #4,1,0,0,-15.777,0,1,0,-19.259,0,0,1,45.233

> view matrix models #4,1,0,0,-20.79,0,1,0,-21.469,0,0,1,48.038

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.96179,-0.27375,-0.0052703,67.619,0.26253,0.9275,-0.26614,-6.5837,0.077743,0.25459,0.96392,-35.493

> view matrix models
> #4,0.96311,-0.26826,-0.021417,69.177,0.2669,0.96233,-0.051786,-63.274,0.034502,0.044159,0.99843,27.525

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.96311,-0.26826,-0.021417,67.637,0.2669,0.96233,-0.051786,-59.811,0.034502,0.044159,0.99843,19.057

> view matrix models
> #4,0.96311,-0.26826,-0.021417,72.016,0.2669,0.96233,-0.051786,-43.151,0.034502,0.044159,0.99843,15.859

> view matrix models
> #4,0.96311,-0.26826,-0.021417,67.396,0.2669,0.96233,-0.051786,-47.957,0.034502,0.044159,0.99843,14.662

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.9395,-0.33578,-0.067741,102.14,0.3254,0.93663,-0.12974,-37.97,0.10701,0.099849,0.98923,-16.54

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.9395,-0.33578,-0.067741,104.51,0.3254,0.93663,-0.12974,-36.578,0.10701,0.099849,0.98923,-15.542

> view matrix models
> #4,0.9395,-0.33578,-0.067741,108.68,0.3254,0.93663,-0.12974,-31.462,0.10701,0.099849,0.98923,2.5531

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.96013,-0.26217,-0.097052,88.93,0.22696,0.93369,-0.27697,24.239,0.16323,0.2439,0.95597,-44.885

> view matrix models
> #4,0.98496,-0.16296,0.057516,21.985,0.15995,0.98567,0.053504,-45.019,-0.065411,-0.0435,0.99691,82.867

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.98496,-0.16296,0.057516,17.206,0.15995,0.98567,0.053504,-41.336,-0.065411,-0.0435,0.99691,76.869

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.96917,-0.24211,0.045656,46.057,0.24498,0.96667,-0.074318,-28.971,-0.026142,0.083212,0.99619,31.551

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.96917,-0.24211,0.045656,35.909,0.24498,0.96667,-0.074318,-33.038,-0.026142,0.083212,0.99619,34.637

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.97691,-0.20857,0.046354,24.356,0.20827,0.97801,0.011399,-45.772,-0.047712,-0.0014822,0.99886,63.355

> view matrix models
> #4,0.86062,-0.46809,0.20058,93.214,0.48664,0.87198,-0.053098,-67.991,-0.15005,0.14331,0.97824,50.797

> view matrix models
> #4,0.95141,-0.043466,-0.30486,58.092,0.067546,0.99534,0.068885,-28.917,0.30044,-0.086129,0.9499,14.931

> view matrix models
> #4,0.84481,-0.52811,-0.08598,176.34,0.47042,0.80965,-0.35095,17.776,0.25496,0.25604,0.93244,-68.667

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.84481,-0.52811,-0.08598,173.59,0.47042,0.80965,-0.35095,12.466,0.25496,0.25604,0.93244,-58.828

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.87125,-0.48197,-0.092868,155.56,0.4173,0.82696,-0.37682,25.708,0.25841,0.28955,0.92162,-66.925

> view matrix models
> #4,0.64867,-0.75711,-0.077622,284.01,0.73731,0.65042,-0.18255,-41.644,0.1887,0.061182,0.98013,2.4587

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.64867,-0.75711,-0.077622,280.04,0.73731,0.65042,-0.18255,-40.715,0.1887,0.061182,0.98013,-8.509

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.72836,-0.68437,0.033809,216.51,0.63838,0.65983,-0.39634,25.755,0.24894,0.31026,0.91748,-80.66

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.72836,-0.68437,0.033809,216.65,0.63838,0.65983,-0.39634,24.938,0.24894,0.31026,0.91748,-70.58

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.72836,-0.68437,0.033809,216.07,0.63838,0.65983,-0.39634,24.998,0.24894,0.31026,0.91748,-72.525

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.79984,-0.59952,0.028958,175.85,0.58999,0.77644,-0.22148,-34.079,0.1103,0.19424,0.97473,-18.492

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.79984,-0.59952,0.028958,178.08,0.58999,0.77644,-0.22148,-42.204,0.1103,0.19424,0.97473,-24.769

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.90433,-0.41255,0.10952,82.518,0.42344,0.83479,-0.3519,8.6805,0.053752,0.3646,0.92961,-50.365

> view matrix models
> #4,0.96593,-0.22397,0.12966,9.4437,0.25757,0.88082,-0.39727,44.685,-0.02523,0.41713,0.9085,-42.079

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.96593,-0.22397,0.12966,14.31,0.25757,0.88082,-0.39727,43.812,-0.02523,0.41713,0.9085,-33.831

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.96602,-0.25804,-0.014632,54.935,0.22824,0.87829,-0.42014,56.414,0.12126,0.40252,0.90734,-64.284

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.96602,-0.25804,-0.014632,57.738,0.22824,0.87829,-0.42014,58.632,0.12126,0.40252,0.90734,-66.393

> select #4/A

3210 atoms, 3304 bonds, 6 pseudobonds, 420 residues, 2 models selected  

> fitmap sel inMap #1 moveWholeMolecules false

Fit molecule copy of dimer_one.pdb (#4) to map
cryosparc_P31_J316_010_volume_map.mrc (#1) using 3210 atoms  
average map value = 0.01601, steps = 276  
shifted from previous position = 7.55  
rotated from previous position = 28 degrees  
atoms outside contour = 2109, contour level = 0.017861  
  

> undo

[Repeated 10 time(s)]No undo action is available  

> close #4

> fitmap #3 inMap #1 moveWholeMolecules false

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.016, steps = 168  
shifted from previous position = 9.69  
rotated from previous position = 0.0133 degrees  
atoms outside contour = 4214, contour level = 0.017861  
  

> ui tool show "Segment Map"

Select a density map in the Segment map field  
Segmenting cryosparc_P31_J316_010_volume_map.mrc, density threshold 0.017861  
Only showing 60 of 428 regions.  
Showing 60 of 428 region surfaces  
5646 watershed regions, grouped to 428 regions  
Showing cryosparc_P31_J316_010_volume_map.seg - 428 regions, 60 surfaces  

> ui mousemode right select

> select #4.1

1 model selected  
Ungrouped to 2 regions  

> select #4.61

1 model selected  

> select clear

> select #4.61

1 model selected  
Ungrouped to 2 regions, but did not show all surfaces, see Options  

> select clear

> select #4.1

1 model selected  
Ungrouped to 2 regions, but did not show all surfaces, see Options  

> select clear

> select #1

3 models selected  
Ungrouped to 290 regions, but did not show all surfaces, see Options  

> select #1

3 models selected  

> select #4.170

1 model selected  

> select #4.176

1 model selected  

> select #4.176

1 model selected  

> select #4.176

1 model selected  

> select #4.176

1 model selected  

> select clear

> select #4.120

1 model selected  
Ungrouped to 2 regions, but did not show their surfaces, see Options  

> select #1

3 models selected  
Ungrouped to 264 regions, but did not show all surfaces, see Options  

> select #4.214

1 model selected  

> select add #4.213

2 models selected  
Grouped 2 regions  

> select clear

> select #4.223

1 model selected  

> select #4.200

1 model selected  

> select #4.200

1 model selected  

> select add #4.199

2 models selected  
Grouped 2 regions  

> select #4.223

1 model selected  

> select add #4.1

2 models selected  
Grouped 2 regions  

> select clear

> select #4.225

1 model selected  

> select add #4.1

2 models selected  
Grouped 2 regions  

> select #4.210

1 model selected  

> select add #4.209

2 models selected  
Grouped 2 regions  

> select #4.188

1 model selected  

> select add #4.187

2 models selected  
Grouped 2 regions  

> ui mousemode right "translate selected models"

> select add #3

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 4 models selected  

> select clear

> select add #3

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #3,1,0,0,-73.237,0,1,0,-68.812,0,0,1,16.575

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.051304,-0.96884,0.2423,403.08,0.81331,-0.18133,-0.55285,190.38,0.57957,0.1687,0.79727,-127.18

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.051304,-0.96884,0.2423,413.75,0.81331,-0.18133,-0.55285,193.1,0.57957,0.1687,0.79727,-65.255

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.5684,-0.80716,-0.15941,569.98,0.82272,-0.55934,-0.10138,207.84,-0.0073291,-0.18877,0.98199,139

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.5684,-0.80716,-0.15941,564.64,0.82272,-0.55934,-0.10138,200.39,-0.0073291,-0.18877,0.98199,99.903

> view matrix models
> #3,-0.5684,-0.80716,-0.15941,553.15,0.82272,-0.55934,-0.10138,196.98,-0.0073291,-0.18877,0.98199,97.864

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.4558,-0.88229,-0.1175,539.66,0.89002,-0.45338,-0.04812,140.08,-0.010816,-0.12651,0.99191,78.876

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.4558,-0.88229,-0.1175,530.72,0.89002,-0.45338,-0.04812,138.94,-0.010816,-0.12651,0.99191,83.339

> fitmap #3 inMap #1 moveWholeMolecules false

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01595, steps = 160  
shifted from previous position = 3.43  
rotated from previous position = 9.2 degrees  
atoms outside contour = 4243, contour level = 0.017861  
  

> ui tool show "Fit to Segments"

Simulating map res 4.000, grid 2.000  

> molmap #3 4.000000 sigmaFactor 0.187 gridSpacing 2.000000 replace false

Opened dimer_one.pdb map 4 as #5, grid size 37,47,121, pixel 2, shown at level
0.106, step 1, values float32  
Please select a region to fit to  

> ui mousemode right select

> select #4.208

1 model selected  

> select add #4.66

2 models selected  
Opened cryosparc_P31_J316_010_volume_map_masked as #6, grid size 900,900,900,
pixel 0.485, shown at step 1, values float32  
Top score: 0.64925, z-score: 1.67364 (avg: 0.6433, stdev: 0.0036)  

> close session

> open
> /home/pauline/Desktop/flipvol_maps/cryosparc_P31_J316_010_volume_map.mrc
> format mrc

Opened cryosparc_P31_J316_010_volume_map.mrc as #1, grid size 900,900,900,
pixel 0.485, shown at step 1, values float32  

> volume #1 region 0,0,0,899,899,899 step 4

[Repeated 1 time(s)]

> volume #1 style mesh

> color #1 #ffbe6fff models

> color #1 #ffa348ff models

> color #1 #ffbe6fff models

> color #1 #99c1f1ff models

> volume style mesh

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #2  
---  
Chain | Description  
A B | No description available  
  

> set bgColor white

> select add #2

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui tool show "Fit in Map"

> fitmap sel inMap #1 moveWholeMolecules false

Fit molecule dimer_one.pdb (#2) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.016, steps = 64  
shifted from previous position = 0.212  
rotated from previous position = 0.43 degrees  
atoms outside contour = 4215, contour level = 0.017861  
  

> select /A

3210 atoms, 3304 bonds, 6 pseudobonds, 420 residues, 2 models selected  

> fitmap sel inMap #1 moveWholeMolecules false

Fit molecule dimer_one.pdb (#2) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 3210 atoms  
average map value = 0.01618, steps = 52  
shifted from previous position = 0.152  
rotated from previous position = 0.588 degrees  
atoms outside contour = 2059, contour level = 0.017861  
  

> select /B

3094 atoms, 3186 bonds, 7 pseudobonds, 413 residues, 3 models selected  

> fitmap sel inMap #1 moveWholeMolecules false

Fit molecule dimer_one.pdb (#2) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 3094 atoms  
average map value = 0.01635, steps = 40  
shifted from previous position = 0.196  
rotated from previous position = 0.329 degrees  
atoms outside contour = 1925, contour level = 0.017861  
  

> color #1 #8ff0a4ff models

> color #1 #ffbe6fff models

> select clear

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

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

> select add #3

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  
Drag select of 1 cryosparc_P31_J316_010_volume_map.mrc , 65 residues  

> select clear

> ui mousemode right "translate selected models"

> select add #3

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #3,1,0,0,-32.497,0,1,0,-0.58726,0,0,1,48.42

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.8607,-0.4459,-0.24571,180.29,0.39643,0.88979,-0.22608,-15.557,0.31944,0.097181,0.94261,-43.285

> view matrix models
> #3,0.87651,-0.43818,-0.19932,164.58,0.43117,0.89875,-0.079699,-57.501,0.21406,-0.016082,0.97669,6.9447

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.87651,-0.43818,-0.19932,165.08,0.43117,0.89875,-0.079699,-57.47,0.21406,-0.016082,0.97669,12.289

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.81983,-0.56681,0.081295,156.13,0.57248,0.80834,-0.13729,-52.756,0.012101,0.15909,0.98719,8.0111

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.81983,-0.56681,0.081295,148.37,0.57248,0.80834,-0.13729,-53.806,0.012101,0.15909,0.98719,4.5271

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.91246,-0.40336,0.068669,82.197,0.40901,0.89471,-0.17944,-30.588,0.010942,0.19182,0.98137,-3.2827

> view matrix models
> #3,0.90645,-0.4195,0.048543,92.538,0.42171,0.90526,-0.051569,-63.909,-0.022311,0.067216,0.99749,36.783

> view matrix models
> #3,0.91682,-0.39518,0.057272,81.21,0.39883,0.89922,-0.17982,-29.389,0.01956,0.1877,0.98203,-4.2893

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.91682,-0.39518,0.057272,83.092,0.39883,0.89922,-0.17982,-27.363,0.01956,0.1877,0.98203,1.6719

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.89153,-0.44062,0.10502,91.907,0.45279,0.87333,-0.17964,-32.87,-0.012564,0.20771,0.97811,4.4493

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.89153,-0.44062,0.10502,100.31,0.45279,0.87333,-0.17964,-36.331,-0.012564,0.20771,0.97811,1.8682

> view matrix models
> #3,0.89153,-0.44062,0.10502,99.948,0.45279,0.87333,-0.17964,-37.299,-0.012564,0.20771,0.97811,4.5683

> select #3/A

3210 atoms, 3304 bonds, 6 pseudobonds, 420 residues, 2 models selected  

> fitmap sel inMap #1 moveWholeMolecules false

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 3210 atoms  
average map value = 0.01601, steps = 212  
shifted from previous position = 12.3  
rotated from previous position = 12 degrees  
atoms outside contour = 2109, contour level = 0.017861  
  

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 3210 atoms  
average map value = 0.01601, steps = 40  
shifted from previous position = 0.00644  
rotated from previous position = 0.0479 degrees  
atoms outside contour = 2110, contour level = 0.017861  
  
Position of dimer_one.pdb (#3) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.89146241 -0.44075176 0.10503643 99.99519990  
0.45291023 0.87343847 -0.17882271 -37.53277137  
-0.01292643 0.20698580 0.97825855 4.81006819  
Axis 0.39347834 0.12030794 0.91142789  
Axis point 137.44392446 158.01937463 0.00000000  
Rotation angle (degrees) 29.35726505  
Shift along axis 39.21448495  
  

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 3210 atoms  
average map value = 0.01601, steps = 36  
shifted from previous position = 0.000544  
rotated from previous position = 0.00229 degrees  
atoms outside contour = 2110, contour level = 0.017861  
  
Position of dimer_one.pdb (#3) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.89145537 -0.44076453 0.10504266 99.99938268  
0.45292353 0.87343925 -0.17878521 -37.54384882  
-0.01294620 0.20695533 0.97826473 4.82158172  
Axis 0.39340896 0.12033444 0.91145434  
Axis point 137.46729203 158.01982905 0.00000000  
Rotation angle (degrees) 29.35726996  
Shift along axis 39.21748645  
  

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 3210 atoms  
average map value = 0.01601, steps = 28  
shifted from previous position = 0.0105  
rotated from previous position = 0.00764 degrees  
atoms outside contour = 2110, contour level = 0.017861  
  
Position of dimer_one.pdb (#3) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.89143956 -0.44078067 0.10510904 99.99265155  
0.45295453 0.87340116 -0.17889274 -37.52152350  
-0.01294989 0.20708168 0.97823795 4.79871799  
Axis 0.39358991 0.12038830 0.91136910  
Axis point 137.41808846 157.99444828 0.00000000  
Rotation angle (degrees) 29.36198449  
Shift along axis 39.21234920  
  

> ui mousemode right select

Drag select of 1 cryosparc_P31_J316_010_volume_map.mrc , 59 atoms, 63 bonds  

> select clear

> close #3

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

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

> select add #3

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-27.748,0,1,0,-0.093746,0,0,1,47.661

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.95052,-0.30114,0.076374,53.686,0.29778,0.9532,0.052341,-68.788,-0.088561,-0.027008,0.9957,77.367

> view matrix models
> #3,0.7195,-0.69412,0.022799,232.15,0.69178,0.7192,0.064723,-98.479,-0.061323,-0.030796,0.99764,71.552

> view matrix models
> #3,0.873,-0.48016,-0.085565,157.62,0.48749,0.86451,0.1224,-103.49,0.015202,-0.14856,0.98879,88.788

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.873,-0.48016,-0.085565,150.69,0.48749,0.86451,0.1224,-103.36,0.015202,-0.14856,0.98879,88.242

> select subtract #3

Nothing selected  

> color #3 #99c1f1ff

> color #3 #62a0eaff

> color #2 #62a0eaff

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #4  
---  
Chain | Description  
A B | No description available  
  

> select add #4

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #4,1,0,0,8.3868,0,1,0,11.766,0,0,1,70.383

> view matrix models #4,1,0,0,-48.699,0,1,0,-27.672,0,0,1,99.322

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.67308,-0.7351,0.081237,221.68,0.66588,0.55455,-0.49908,46.94,0.32182,0.39001,0.86274,-59.636

> view matrix models
> #4,0.67454,-0.71398,0.18767,192.64,0.70997,0.55774,-0.42997,20.799,0.20232,0.42328,0.88312,-44.954

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.67454,-0.71398,0.18767,186.92,0.70997,0.55774,-0.42997,19.331,0.20232,0.42328,0.88312,-41.278

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.67454,-0.71398,0.18767,181.57,0.70997,0.55774,-0.42997,18.801,0.20232,0.42328,0.88312,-31.105

> view matrix models
> #4,0.67454,-0.71398,0.18767,171.18,0.70997,0.55774,-0.42997,30.313,0.20232,0.42328,0.88312,-27.244

> view matrix models
> #4,0.67454,-0.71398,0.18767,179.97,0.70997,0.55774,-0.42997,36.855,0.20232,0.42328,0.88312,-37.938

> view matrix models
> #4,0.67454,-0.71398,0.18767,181.52,0.70997,0.55774,-0.42997,37.876,0.20232,0.42328,0.88312,-35.358

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.69995,-0.69943,0.14446,180.52,0.69413,0.61861,-0.36811,11.025,0.16811,0.35793,0.91849,-16.026

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.69995,-0.69943,0.14446,178.67,0.69413,0.61861,-0.36811,10.291,0.16811,0.35793,0.91849,-17.883

> view matrix models
> #4,0.69995,-0.69943,0.14446,178.36,0.69413,0.61861,-0.36811,9.5096,0.16811,0.35793,0.91849,-19.235

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.69024,-0.7112,0.13331,186.43,0.70189,0.6133,-0.36225,7.9265,0.17587,0.34361,0.9225,-17.842

> view matrix models
> #4,0.63799,-0.74082,0.21014,190.97,0.75708,0.55356,-0.34699,8.5936,0.14073,0.38047,0.91402,-18.198

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.63799,-0.74082,0.21014,190.18,0.75708,0.55356,-0.34699,6.3325,0.14073,0.38047,0.91402,-16.004

> select subtract #4

Nothing selected  

> color #4 #62a0eaff

> color #4 #99c1f1ff

> color #4 #62a0eaff

> color #4 #99c1f1ff

> color #4 #62a0eaff

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #5  
---  
Chain | Description  
A B | No description available  
  

> select add #5

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #5,1,0,0,20.614,0,1,0,-26.017,0,0,1,-54.516

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.87014,0.4512,0.1982,-119.12,-0.49087,0.82915,0.26751,82.849,-0.043633,-0.33006,0.94295,62.059

> view matrix models
> #5,0.92622,0.31253,0.21078,-95.61,-0.34147,0.93247,0.11791,49.467,-0.1597,-0.18119,0.9704,41.458

> view matrix models
> #5,0.94171,0.31123,0.12771,-81.33,-0.33245,0.91904,0.21174,31.27,-0.051471,-0.24186,0.96895,33.291

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.94171,0.31123,0.12771,-82.389,-0.33245,0.91904,0.21174,33.085,-0.051471,-0.24186,0.96895,32.603

> view matrix models
> #5,0.94171,0.31123,0.12771,-83.735,-0.33245,0.91904,0.21174,34.357,-0.051471,-0.24186,0.96895,33.623

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.88129,0.45129,0.14023,-111.91,-0.47194,0.85583,0.21171,85.602,-0.024467,-0.25275,0.96722,30.662

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.88129,0.45129,0.14023,-108.71,-0.47194,0.85583,0.21171,84.758,-0.024467,-0.25275,0.96722,30.365

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.86976,0.48843,0.070363,-101.76,-0.49334,0.85733,0.14698,103.14,0.011463,-0.16255,0.98663,-8.0145

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.86976,0.48843,0.070363,-103.97,-0.49334,0.85733,0.14698,103.54,0.011463,-0.16255,0.98663,-6.1685

> view matrix models
> #5,0.86976,0.48843,0.070363,-103.23,-0.49334,0.85733,0.14698,101.97,0.011463,-0.16255,0.98663,-6.5554

> color #5 #62a0eaff

> select subtract #5

Nothing selected  

> select add #5

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#5) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01579, steps = 224  
shifted from previous position = 12.1  
rotated from previous position = 8.92 degrees  
atoms outside contour = 4332, contour level = 0.017861  
  
Position of dimer_one.pdb (#5) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.87916079 0.47650234 0.00467224 -78.64187968  
-0.47652520 0.87912269 0.00818768 128.43846300  
-0.00020602 -0.00942473 0.99995556 -46.90784265  
Axis -0.01847709 0.00511776 -0.99981619  
Axis point 213.86480188 217.37475443 0.00000000  
Rotation angle (degrees) 28.46366658  
Shift along axis 49.00961139  
  

> select add #4

13078 atoms, 13476 bonds, 34 pseudobonds, 1700 residues, 6 models selected  

> select subtract #5

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#4) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01544, steps = 268  
shifted from previous position = 4.71  
rotated from previous position = 25 degrees  
atoms outside contour = 4530, contour level = 0.017861  
  
Position of dimer_one.pdb (#4) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.53927414 -0.84210858 -0.00604509 285.87549419  
0.84212990 0.53926680 0.00292428 -83.89005000  
0.00079736 -0.00666774 0.99997745 100.34860078  
Axis -0.00569503 -0.00406254 0.99997553  
Axis point 219.52450185 220.04172217 0.00000000  
Rotation angle (degrees) 57.36677671  
Shift along axis 99.05888253  
  

> select subtract #4

Nothing selected  

> select add #3

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#3) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01588, steps = 164  
shifted from previous position = 1.31  
rotated from previous position = 8.14 degrees  
atoms outside contour = 4296, contour level = 0.017861  
  
Position of dimer_one.pdb (#3) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.87662503 -0.48115743 -0.00400980 132.95516457  
0.48117409 0.87659836 0.00684147 -79.66199773  
0.00022316 -0.00792681 0.99996856 51.40693524  
Axis -0.01534440 -0.00439810 0.99987259  
Axis point 221.79068769 221.03893428 0.00000000  
Rotation angle (degrees) 28.76557453  
Shift along axis 49.71062984  
  

> select subtract #3

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #6  
---  
Chain | Description  
A B | No description available  
  

> select add #6

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #6,1,0,0,33.63,0,1,0,-42.764,0,0,1,-102.55

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.67174,0.68988,0.26989,-142.09,-0.73969,0.60478,0.29512,183.49,0.040373,-0.39787,0.91655,18.958

> view matrix models
> #6,0.48778,0.72265,0.48973,-153.9,-0.87291,0.39734,0.28311,276.96,0.010002,-0.56559,0.82462,93.409

> view matrix models
> #6,0.72169,0.49335,0.48557,-143.32,-0.66422,0.69103,0.28511,142.99,-0.19488,-0.52828,0.8264,131.19

> view matrix models
> #6,0.38534,0.79989,0.46009,-145.5,-0.9175,0.38537,0.098438,330.13,-0.098568,-0.46007,0.8824,76.578

> view matrix models
> #6,0.45918,0.71759,0.52366,-152.98,-0.87092,0.47983,0.10614,290.45,-0.1751,-0.5048,0.84529,115.39

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.45918,0.71759,0.52366,-150.47,-0.87092,0.47983,0.10614,287.4,-0.1751,-0.5048,0.84529,114.98

> view matrix models
> #6,0.45918,0.71759,0.52366,-149.67,-0.87092,0.47983,0.10614,285.7,-0.1751,-0.5048,0.84529,114.43

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.42866,0.90162,-0.057774,-71.796,-0.89656,0.4324,0.095936,307.6,0.11148,0.010675,0.99371,-132.14

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.42866,0.90162,-0.057774,-73.406,-0.89656,0.4324,0.095936,300.76,0.11148,0.010675,0.99371,-127.92

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.35957,0.9153,0.18148,-111.63,-0.93084,0.33827,0.13825,326.77,0.065148,-0.21864,0.97363,-47.235

> view matrix models
> #6,0.42999,0.84913,0.30673,-136.01,-0.89906,0.37168,0.23139,289.99,0.082475,-0.37526,0.92324,3.9333

> view matrix models
> #6,0.46448,0.8853,0.022321,-94.201,-0.885,0.46494,-0.024613,314.11,-0.032168,-0.0083217,0.99945,-89.493

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.46448,0.8853,0.022321,-83.166,-0.885,0.46494,-0.024613,315.87,-0.032168,-0.0083217,0.99945,-86.909

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#6) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01533, steps = 148  
shifted from previous position = 4.76  
rotated from previous position = 5.49 degrees  
atoms outside contour = 4591, contour level = 0.017861  
  
Position of dimer_one.pdb (#6) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.54238266 0.84011418 0.00540490 -84.80645938  
-0.84013117 0.54236489 0.00446554 282.17861548  
0.00082013 -0.00696285 0.99997542 -97.20617448  
Axis -0.00680144 0.00272855 -0.99997315  
Axis point 216.70306290 218.18850248 0.00000000  
Rotation angle (degrees) 57.15545929  
Shift along axis 98.55030963  
  

> color #6 #99c1f1ff

> color #6 #62a0eaff

> select subtract #6

Nothing selected  

> hide #!1 models

> show #!1 models

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #7  
---  
Chain | Description  
A B | No description available  
  

> select add #7

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #7,1,0,0,-27.559,0,1,0,-55.56,0,0,1,144.37

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.61049,-0.7899,0.057869,278.55,0.76844,0.57304,-0.28484,-55.994,0.19184,0.21836,0.95683,45.491

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.61049,-0.7899,0.057869,231.46,0.76844,0.57304,-0.28484,-54.56,0.19184,0.21836,0.95683,55.453

> ui mousemode right "rotate selected models"

> view matrix models
> #7,-0.27892,-0.94425,0.17493,462.52,0.9554,-0.25445,0.14988,44.541,-0.097012,0.20893,0.97311,123.51

> view matrix models
> #7,0.42939,-0.80262,0.41403,201.91,0.903,0.37404,-0.21139,-46.273,0.014804,0.46464,0.88538,42.353

> view matrix models
> #7,0.23065,-0.96395,0.1327,355.55,0.97304,0.22838,-0.032278,-59.713,0.00080844,0.13657,0.99063,117.08

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.23065,-0.96395,0.1327,361.48,0.97304,0.22838,-0.032278,-48.459,0.00080844,0.13657,0.99063,113.71

> view matrix models
> #7,0.23065,-0.96395,0.1327,355.78,0.97304,0.22838,-0.032278,-47.168,0.00080844,0.13657,0.99063,121.14

> view matrix models
> #7,0.23065,-0.96395,0.1327,355.3,0.97304,0.22838,-0.032278,-48.713,0.00080844,0.13657,0.99063,118.37

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#7) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01338, steps = 260  
shifted from previous position = 11.4  
rotated from previous position = 13.9 degrees  
atoms outside contour = 5134, contour level = 0.017861  
  
Position of dimer_one.pdb (#7) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.05502663 -0.99808273 -0.02833604 430.77581097  
0.99848466 0.05498548 0.00222968 -11.26389261  
-0.00066733 -0.02841579 0.99959597 155.80762590  
Axis -0.01534580 -0.01385518 0.99978625  
Axis point 221.44147761 224.24087172 0.00000000  
Rotation angle (degrees) 86.85838586  
Shift along axis 149.31978749  
  

> color #7 #62a0eaff

> hide #!1 models

> select subtract #7

Nothing selected  

> show #!1 models

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #8  
---  
Chain | Description  
A B | No description available  
  

> select add #8

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #8,1,0,0,-38.348,0,1,0,-34.824,0,0,1,-147.13

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.60474,0.68386,0.4082,-225.67,-0.78503,0.59823,0.16079,232.51,-0.13424,-0.41768,0.89862,25.371

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.60474,0.68386,0.4082,-187.2,-0.78503,0.59823,0.16079,228.32,-0.13424,-0.41768,0.89862,70.563

> view matrix models
> #8,0.60474,0.68386,0.4082,-196.3,-0.78503,0.59823,0.16079,219.48,-0.13424,-0.41768,0.89862,35.975

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.41609,0.64837,0.63756,-189.48,-0.87691,0.47163,0.092669,291.84,-0.24061,-0.59764,0.76481,140.85

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.41609,0.64837,0.63756,-139.2,-0.87691,0.47163,0.092669,289.66,-0.24061,-0.59764,0.76481,146.47

> view matrix models
> #8,0.41609,0.64837,0.63756,-136.39,-0.87691,0.47163,0.092669,282.73,-0.24061,-0.59764,0.76481,118.55

> view matrix models
> #8,0.41609,0.64837,0.63756,-134.18,-0.87691,0.47163,0.092669,269.32,-0.24061,-0.59764,0.76481,115.12

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#8) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01163, steps = 528  
shifted from previous position = 9.85  
rotated from previous position = 48.4 degrees  
atoms outside contour = 5545, contour level = 0.017861  
  
Position of dimer_one.pdb (#8) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.06007601 0.99815776 -0.00848314 -11.21875708  
-0.99812288 0.06017088 0.01141010 421.42300926  
0.01189952 0.00778175 0.99989892 -152.74382537  
Axis -0.00181746 -0.01020977 -0.99994623  
Axis point 219.12001793 217.30544092 0.00000000  
Rotation angle (degrees) 86.55600277  
Shift along axis 148.45336931  
  

> color #8 #62a0eaff

> select subtract #8

Nothing selected  

> select add #1

3 models selected  

> select add #1

3 models selected  

> select clear

> hide #!1 models

> show #!1 models

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #9  
---  
Chain | Description  
A B | No description available  
  

> select add #9

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #9,1,0,0,8.1725,0,1,0,-101.26,0,0,1,-26.481

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.48522,0.74379,0.4597,52.455,-0.86596,-0.48161,-0.1348,556.35,0.12114,-0.46349,0.87778,102.81

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.48522,0.74379,0.4597,44.268,-0.86596,-0.48161,-0.1348,540.93,0.12114,-0.46349,0.87778,83.963

> view matrix models
> #9,-0.48522,0.74379,0.4597,57.425,-0.86596,-0.48161,-0.1348,542.12,0.12114,-0.46349,0.87778,98.955

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.81276,0.55786,0.16796,250.16,-0.52684,-0.82685,0.1969,489.43,0.24872,0.071543,0.96593,-102.62

> view matrix models
> #9,-0.81638,0.57655,0.033334,274.32,-0.50208,-0.7371,0.45233,403.44,0.28536,0.35254,0.89123,-175.75

> view matrix models
> #9,-0.82242,0.56543,0.062571,272.5,-0.54935,-0.81793,0.17088,497.83,0.1478,0.10616,0.9833,-92.105

> view matrix models
> #9,-0.44395,0.79082,-0.42132,220.79,-0.83772,-0.19945,0.50837,317.64,0.318,0.57864,0.75103,-218.43

> view matrix models
> #9,-0.46355,0.8792,-0.11011,133.93,-0.86969,-0.42766,0.24649,446.35,0.16962,0.21002,0.96287,-122.59

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.46355,0.8792,-0.11011,145.46,-0.86969,-0.42766,0.24649,434.84,0.16962,0.21002,0.96287,-125.83

> view matrix models
> #9,-0.46355,0.8792,-0.11011,155.95,-0.86969,-0.42766,0.24649,445.92,0.16962,0.21002,0.96287,-125.21

> view matrix models
> #9,-0.46355,0.8792,-0.11011,154.05,-0.86969,-0.42766,0.24649,449.97,0.16962,0.21002,0.96287,-128.86

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.4561,0.84837,-0.2688,194.98,-0.87318,-0.36829,0.31924,418.22,0.17183,0.38031,0.90876,-166.55

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.4561,0.84837,-0.2688,191.78,-0.87318,-0.36829,0.31924,418.68,0.17183,0.38031,0.90876,-159.99

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.47367,0.86323,-0.17455,171.58,-0.86808,-0.42418,0.25787,446.57,0.14856,0.27367,0.95028,-132.78

> view matrix models
> #9,-0.51343,0.85391,-0.085009,164.61,-0.84215,-0.48236,0.24104,460.62,0.16482,0.19535,0.96678,-117.79

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.51343,0.85391,-0.085009,164.79,-0.84215,-0.48236,0.24104,461.39,0.16482,0.19535,0.96678,-120.81

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.53934,0.8165,-0.20602,207.53,-0.82426,-0.46181,0.3276,432.75,0.17234,0.3465,0.92208,-156.29

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.53934,0.8165,-0.20602,206.69,-0.82426,-0.46181,0.3276,433.4,0.17234,0.3465,0.92208,-152.3

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.51266,0.80608,-0.29568,222.48,-0.84795,-0.42127,0.32173,428.68,0.13478,0.41566,0.89948,-158.31

> view matrix models
> #9,-0.50138,0.82505,-0.26059,206.85,-0.8485,-0.40993,0.33467,422.8,0.1693,0.38891,0.90559,-160.19

> view matrix models
> #9,-0.42735,0.86,-0.27887,183.15,-0.88864,-0.34279,0.30466,419.33,0.16641,0.37801,0.91072,-157.46

> view matrix models
> #9,-0.41106,0.88845,-0.20419,155.15,-0.89778,-0.35567,0.25979,434.79,0.15818,0.2901,0.94383,-137.4

> ui mousemode right "translate selected models"

> view matrix models
> #9,-0.41106,0.88845,-0.20419,156.32,-0.89778,-0.35567,0.25979,436.44,0.15818,0.2901,0.94383,-135.37

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#9) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01592, steps = 260  
shifted from previous position = 7.74  
rotated from previous position = 19.8 degrees  
atoms outside contour = 4288, contour level = 0.017861  
  
Position of dimer_one.pdb (#9) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.36372393 0.93147353 0.00787185 92.47376055  
-0.93150676 -0.36371318 -0.00280728 501.53532162  
0.00024819 -0.00835375 0.99996508 -34.94683843  
Axis -0.00297717 0.00409213 -0.99998720  
Axis point 217.52702433 219.07623662 0.00000000  
Rotation angle (degrees) 111.32981561  
Shift along axis 36.72342902  
  

> color #9 #f66151ff

> select subtract #9

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #10  
---  
Chain | Description  
A B | No description available  
  

> select add #10

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.21865,0.86652,-0.4487,138.77,-0.97464,-0.17149,0.14376,537.69,0.047621,0.46876,0.88204,-120.19

> view matrix models
> #10,-0.25435,0.80783,-0.53172,181.85,-0.94798,-0.099431,0.3024,476.78,0.19142,0.58097,0.79109,-167.26

> view matrix models
> #10,-0.54596,0.76589,-0.33961,222.6,-0.80954,-0.37785,0.4493,492.27,0.21579,0.52023,0.82632,-163.16

> ui mousemode right "translate selected models"

> view matrix models
> #10,-0.54596,0.76589,-0.33961,269.09,-0.80954,-0.37785,0.4493,412.3,0.21579,0.52023,0.82632,-151.24

> view matrix models
> #10,-0.54596,0.76589,-0.33961,262.14,-0.80954,-0.37785,0.4493,405.43,0.21579,0.52023,0.82632,-130.37

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.14312,0.64575,-0.75001,219.18,-0.92037,0.3655,0.13906,284.36,0.36393,0.67038,0.64664,-170.63

> view matrix models
> #10,0.03157,0.83431,-0.5504,149.6,-0.97347,0.15053,0.17235,351.62,0.22664,0.53035,0.81692,-133.73

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.03157,0.83431,-0.5504,152.92,-0.97347,0.15053,0.17235,354.39,0.22664,0.53035,0.81692,-144.1

> ui mousemode right "rotate selected models"

> view matrix models
> #10,-0.015065,0.96651,-0.25617,63.411,-0.98844,0.024258,0.14965,399.05,0.15086,0.25546,0.95498,-76.38

> view matrix models
> #10,-0.059711,0.9982,-0.0049743,11.425,-0.99288,-0.058876,0.10358,433.72,0.10311,0.011124,0.99461,-3.5284

> view matrix models
> #10,0.23186,0.91185,-0.33879,37.75,-0.94766,0.29033,0.13287,316.78,0.21952,0.29025,0.93143,-97.601

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.23186,0.91185,-0.33879,45.666,-0.94766,0.29033,0.13287,315.26,0.21952,0.29025,0.93143,-103.25

> ui mousemode right "rotate selected models"

> view matrix models
> #10,0.25618,0.95763,-0.13161,-17.44,-0.95841,0.26935,0.094287,332.06,0.12574,0.10198,0.98681,-38.882

> ui mousemode right "translate selected models"

> view matrix models
> #10,0.25618,0.95763,-0.13161,-18.269,-0.95841,0.26935,0.094287,333.49,0.12574,0.10198,0.98681,-46.088

> view matrix models
> #10,0.25618,0.95763,-0.13161,-20.724,-0.95841,0.26935,0.094287,339.42,0.12574,0.10198,0.98681,-43.496

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#10) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01598, steps = 264  
shifted from previous position = 2.08  
rotated from previous position = 12.5 degrees  
atoms outside contour = 4235, contour level = 0.017861  
  
Position of dimer_one.pdb (#10) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.12644147 0.99194928 0.00701252 -27.49657003  
-0.99197398 0.12643535 0.00131110 406.79734314  
0.00041391 -0.00712201 0.99997455 14.08832724  
Axis -0.00425066 0.00332599 -0.99998543  
Axis point 217.21571172 219.06446963 0.00000000  
Rotation angle (degrees) 82.73690512  
Shift along axis -12.61823945  
  

> color #10 #f66151ff

> select subtract #10

Nothing selected  

> hide #!1 models

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

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

> show #!1 models

> select add #11

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #11,1,0,0,-6.3504,0,1,0,-51.207,0,0,1,-1.9981

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.16078,0.84261,0.51396,-78.839,-0.97526,-0.21568,0.048515,517.83,0.15173,-0.49345,0.85644,133.06

> view matrix models
> #11,-0.30524,0.75501,0.58033,-33.302,-0.94308,-0.32417,-0.074289,567.32,0.13204,-0.56997,0.81098,169.52

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.30524,0.75501,0.58033,-70.176,-0.94308,-0.32417,-0.074289,561.48,0.13204,-0.56997,0.81098,93.033

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.4747,0.84536,0.245,14.964,-0.86122,-0.38873,-0.32739,613.7,-0.18152,-0.36641,0.91257,88.18

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.4747,0.84536,0.245,13.999,-0.86122,-0.38873,-0.32739,557.27,-0.18152,-0.36641,0.91257,88.785

> view matrix models
> #11,-0.4747,0.84536,0.245,65.198,-0.86122,-0.38873,-0.32739,541.37,-0.18152,-0.36641,0.91257,79.377

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.85807,0.45345,0.24106,269.2,-0.51046,-0.70178,-0.49693,582.84,-0.056159,-0.54944,0.83364,118.36

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.85807,0.45345,0.24106,263.12,-0.51046,-0.70178,-0.49693,583.99,-0.056159,-0.54944,0.83364,112.32

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.76396,0.61115,0.20702,202.81,-0.62038,-0.60745,-0.49612,583.07,-0.17744,-0.50745,0.84321,127.21

> ui mousemode right "translate selected models"

> view matrix models
> #11,-0.76396,0.61115,0.20702,215.5,-0.62038,-0.60745,-0.49612,591.86,-0.17744,-0.50745,0.84321,129.99

> view matrix models
> #11,-0.76396,0.61115,0.20702,216.57,-0.62038,-0.60745,-0.49612,582.63,-0.17744,-0.50745,0.84321,124.03

> ui mousemode right "rotate selected models"

> view matrix models
> #11,-0.70293,0.6973,0.14021,191.49,-0.67786,-0.59708,-0.42896,579.24,-0.2154,-0.39657,0.89238,91.075

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#11) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.0155, steps = 316  
shifted from previous position = 7.41  
rotated from previous position = 27.1 degrees  
atoms outside contour = 4510, contour level = 0.017861  
  
Position of dimer_one.pdb (#11) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.76547946 0.64343540 0.00566400 243.51381671  
-0.64346031 -0.76544751 -0.00699600 527.35536971  
-0.00016598 -0.00899986 0.99995949 -84.08523921  
Axis -0.00155710 0.00453022 -0.99998853  
Axis point 217.85342032 219.08627356 0.00000000  
Rotation angle (degrees) 139.95004685  
Shift along axis 86.09413186  
  

> color #11 #f66151ff

> select subtract #11

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #12  
---  
Chain | Description  
A B | No description available  
  

> select add #12

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models #12,1,0,0,-118.73,0,1,0,-106.42,0,0,1,-78.846

> ui mousemode right "rotate selected models"

> view matrix models
> #12,0.97206,0.10465,-0.21011,-97.227,-0.10841,0.99409,-0.006448,-77.533,0.2082,0.029047,0.97766,-131.99

> view matrix models
> #12,-0.8937,0.27406,0.35525,178.68,-0.44241,-0.67009,-0.59603,601.67,0.074704,-0.68983,0.7201,159.38

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.8937,0.27406,0.35525,262.57,-0.44241,-0.67009,-0.59603,649.47,0.074704,-0.68983,0.7201,135.69

> view matrix models
> #12,-0.8937,0.27406,0.35525,262.31,-0.44241,-0.67009,-0.59603,562.8,0.074704,-0.68983,0.7201,83.606

> ui mousemode right "rotate selected models"

> view matrix models
> #12,-0.95504,0.25128,0.15734,325.28,-0.26057,-0.96458,-0.041188,486.62,0.14141,-0.080334,0.98669,-162.54

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.95504,0.25128,0.15734,339.95,-0.26057,-0.96458,-0.041188,482.24,0.14141,-0.080334,0.98669,-138.2

> view matrix models
> #12,-0.95504,0.25128,0.15734,346.24,-0.26057,-0.96458,-0.041188,489.32,0.14141,-0.080334,0.98669,-138.14

> view matrix models
> #12,-0.95504,0.25128,0.15734,346.66,-0.26057,-0.96458,-0.041188,494.26,0.14141,-0.080334,0.98669,-139.95

> ui mousemode right "rotate selected models"

> view matrix models
> #12,-0.96726,0.16133,0.19589,367.06,-0.10701,-0.95923,0.2616,391.64,0.23011,0.23208,0.94509,-241.4

> view matrix models
> #12,-0.97952,0.096833,0.17656,392.56,-0.05252,-0.96929,0.24023,386.06,0.1944,0.22604,0.95452,-233.15

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.97952,0.096833,0.17656,387.78,-0.05252,-0.96929,0.24023,385.85,0.1944,0.22604,0.95452,-229.6

> view matrix models
> #12,-0.97952,0.096833,0.17656,388.73,-0.05252,-0.96929,0.24023,385.98,0.1944,0.22604,0.95452,-225.79

> view matrix models
> #12,-0.97952,0.096833,0.17656,388.25,-0.05252,-0.96929,0.24023,385.89,0.1944,0.22604,0.95452,-225.84

> ui mousemode right "rotate selected models"

> view matrix models
> #12,-0.96407,0.19113,0.18451,355.91,-0.13439,-0.94999,0.28187,391.04,0.22916,0.24694,0.94154,-237.3

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.96407,0.19113,0.18451,346.11,-0.13439,-0.94999,0.28187,389.38,0.22916,0.24694,0.94154,-237.69

> view matrix models
> #12,-0.96407,0.19113,0.18451,345.82,-0.13439,-0.94999,0.28187,390.12,0.22916,0.24694,0.94154,-242.37

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#12) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01332, steps = 304  
shifted from previous position = 4.32  
rotated from previous position = 19.1 degrees  
atoms outside contour = 5130, contour level = 0.017861  
  
Position of dimer_one.pdb (#12) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98236050 0.18684504 0.00753491 390.90704896  
-0.18678217 -0.98236601 0.00833330 471.99271860  
0.00895908 0.00677891 0.99993689 -139.62209844  
Axis -0.00416018 -0.00381167 -0.99998408  
Axis point 218.00855492 217.81635370 0.00000000  
Rotation angle (degrees) 169.23293870  
Shift along axis 136.19455254  
  

> color #12 #f66151ff

> select subtract #12

Nothing selected  

> hide #!1 models

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

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

> show #!1 models

> select add #13

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #13,-0.32258,0.91321,-0.24898,108.16,-0.75816,-0.091792,0.64558,356.18,0.56669,0.39702,0.72197,-189.72

> ui mousemode right "translate selected models"

> view matrix models
> #13,-0.32258,0.91321,-0.24898,103.2,-0.75816,-0.091792,0.64558,314.45,0.56669,0.39702,0.72197,-121.33

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.74647,0.57893,-0.32807,-39.791,-0.63404,0.76843,-0.08664,192.74,0.20194,0.27268,0.94067,-45.305

> view matrix models
> #13,0.60801,0.73804,-0.29261,-59.847,-0.78506,0.61384,-0.082991,272.24,0.11837,0.28018,0.95262,-30.054

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.60801,0.73804,-0.29261,-26.564,-0.78506,0.61384,-0.082991,268.58,0.11837,0.28018,0.95262,-24.579

> view matrix models
> #13,0.60801,0.73804,-0.29261,-24.89,-0.78506,0.61384,-0.082991,263.4,0.11837,0.28018,0.95262,-30.838

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.56073,0.76449,-0.31802,-15.748,-0.81938,0.56761,-0.080255,284.24,0.11915,0.30558,0.94468,-36.598

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.56073,0.76449,-0.31802,-1.7845,-0.81938,0.56761,-0.080255,287.14,0.11915,0.30558,0.94468,-32.377

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.50283,0.82224,-0.26661,-15.488,-0.85548,0.51754,-0.017324,296.62,0.12374,0.23679,0.96365,-17.843

> view matrix models
> #13,0.45887,0.87841,-0.13352,-49.461,-0.88395,0.46653,0.031366,307.59,0.089844,0.10363,0.99055,22.542

> ui mousemode right "translate selected models"

> view matrix models
> #13,0.45887,0.87841,-0.13352,-46.896,-0.88395,0.46653,0.031366,306.35,0.089844,0.10363,0.99055,15.529

> view matrix models
> #13,0.45887,0.87841,-0.13352,-48.659,-0.88395,0.46653,0.031366,310.27,0.089844,0.10363,0.99055,15.655

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#13) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01586, steps = 216  
shifted from previous position = 1.97  
rotated from previous position = 11.5 degrees  
atoms outside contour = 4305, contour level = 0.017861  
  
Position of dimer_one.pdb (#13) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.58630885 0.81007175 0.00506979 -87.70627402  
-0.81008730 0.58629160 0.00455423 265.96173318  
0.00071688 -0.00677716 0.99997678 63.33792614  
Axis -0.00699380 0.00268664 -0.99997193  
Axis point 216.49011915 219.36327861 0.00000000  
Rotation angle (degrees) 54.10592343  
Shift along axis -62.00820448  
  

> color #13 #f66151ff

> select subtract #13

Nothing selected  

> select add #13

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#13) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01586, steps = 28  
shifted from previous position = 0.00148  
rotated from previous position = 0.00289 degrees  
atoms outside contour = 4304, contour level = 0.017861  
  
Position of dimer_one.pdb (#13) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.58631352 0.81006867 0.00502032 -87.69531841  
-0.81008389 0.58629636 0.00454658 265.96071193  
0.00073965 -0.00673260 0.99997706 63.31912976  
Axis -0.00696161 0.00264207 -0.99997228  
Axis point 216.49480551 219.34923282 0.00000000  
Rotation angle (degrees) 54.10557970  
Shift along axis -62.00418702  
  

> select subtract #13

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

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

> select add #14

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #14,1,0,0,-7.4306,0,1,0,-49.441,0,0,1,102.72

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.7831,0.58809,-0.20227,-80.609,-0.62078,0.75869,-0.19755,209.63,0.037284,0.28026,0.9592,22.509

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.7831,0.58809,-0.20227,-61.842,-0.62078,0.75869,-0.19755,228.39,0.037284,0.28026,0.9592,8.7878

> view matrix models
> #14,0.7831,0.58809,-0.20227,-66.867,-0.62078,0.75869,-0.19755,220.35,0.037284,0.28026,0.9592,27.668

> view matrix models
> #14,0.7831,0.58809,-0.20227,-45.216,-0.62078,0.75869,-0.19755,238.76,0.037284,0.28026,0.9592,39.046

> view matrix models
> #14,0.7831,0.58809,-0.20227,-43.133,-0.62078,0.75869,-0.19755,237.78,0.037284,0.28026,0.9592,38.906

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#14) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.0152, steps = 276  
shifted from previous position = 6.24  
rotated from previous position = 21.1 degrees  
atoms outside contour = 4627, contour level = 0.017861  
  
Position of dimer_one.pdb (#14) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.90333130 0.42893364 0.00291389 -73.07064279  
-0.42894312 0.90330005 0.00753795 112.80512830  
0.00060116 -0.00805916 0.99996734 113.12247182  
Axis -0.01817799 0.00269542 -0.99983113  
Axis point 213.37423777 223.16638815 0.00000000  
Rotation angle (degrees) 25.40480112  
Shift along axis -111.47103442  
  

> color #14 #f66151ff

> select subtract #14

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #15  
---  
Chain | Description  
A B | No description available  
  

> select add #15

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #15,1,0,0,-19.839,0,1,0,-76.195,0,0,1,120.06

> view matrix models #15,1,0,0,-18.76,0,1,0,-49.532,0,0,1,156.52

> view matrix models #15,1,0,0,-8.8989,0,1,0,-16.34,0,0,1,145.33

> view matrix models #15,1,0,0,-10.217,0,1,0,-18.815,0,0,1,156.85

> view matrix models #15,1,0,0,-0.28824,0,1,0,-7.5937,0,0,1,151.75

> view matrix models #15,1,0,0,0.2349,0,1,0,-8.6056,0,0,1,156.49

> view matrix models #15,1,0,0,-0.84795,0,1,0,-3.8586,0,0,1,163.36

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#15) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01177, steps = 164  
shifted from previous position = 5.78  
rotated from previous position = 4.68 degrees  
atoms outside contour = 5501, contour level = 0.017861  
  
Position of dimer_one.pdb (#15) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99725319 -0.07399010 -0.00339615 18.66874585  
0.07406294 0.99667247 0.03403935 -23.37592847  
0.00086627 -0.03419738 0.99941472 169.22320796  
Axis -0.41843245 -0.02613744 0.90787175  
Axis point 311.96679582 1068.84403584 0.00000000  
Rotation angle (degrees) 4.67700542  
Shift along axis 146.43234829  
  

> color #15 #f66151ff

> select subtract #15

Nothing selected  

> hide #!1 models

> show #!1 models

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #16  
---  
Chain | Description  
A B | No description available  
  

> select add #16

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #16,1,0,0,-54.481,0,1,0,-68.489,0,0,1,-16.563

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.42337,-0.90595,-0.0047429,544.66,0.8307,-0.3861,-0.40108,214.12,0.36152,-0.17374,0.91603,-35.392

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.42337,-0.90595,-0.0047429,556.59,0.8307,-0.3861,-0.40108,205.04,0.36152,-0.17374,0.91603,142.56

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.7693,-0.033959,0.63798,254.58,0.16331,-0.97586,0.14498,417.13,0.61766,0.21572,0.75628,4.1308

> view matrix models
> #16,-0.8315,0.38753,0.39804,199.56,-0.25539,-0.90295,0.34562,453.73,0.49335,0.18573,0.84977,22.615

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.8315,0.38753,0.39804,205.78,-0.25539,-0.90295,0.34562,385.09,0.49335,0.18573,0.84977,14.093

> view matrix models
> #16,-0.8315,0.38753,0.39804,207.48,-0.25539,-0.90295,0.34562,392.99,0.49335,0.18573,0.84977,34.645

> view matrix models
> #16,-0.8315,0.38753,0.39804,199.13,-0.25539,-0.90295,0.34562,399.43,0.49335,0.18573,0.84977,39.932

> view matrix models
> #16,-0.8315,0.38753,0.39804,181.33,-0.25539,-0.90295,0.34562,418.24,0.49335,0.18573,0.84977,-5.9082

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.81767,0.38477,0.4282,172.45,-0.23702,-0.90286,0.3587,411.07,0.52463,0.19181,0.82944,-10.806

> view matrix models
> #16,-0.97179,0.18401,0.1475,326.12,-0.15994,-0.97387,0.1612,454.86,0.17331,0.13307,0.97584,58.777

> view matrix models
> #16,-0.97129,0.18438,0.15034,325.29,-0.16043,-0.97426,0.15835,455.7,0.17567,0.12969,0.97587,59.178

> view matrix models
> #16,-0.97639,0.17993,0.11953,334.34,-0.1555,-0.96953,0.18927,446.58,0.14994,0.16622,0.97462,55.153

> view matrix models
> #16,-0.9961,-0.081705,0.033365,432.23,0.084779,-0.9909,0.10451,413.49,0.024523,0.10693,0.99396,97.892

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.9961,-0.081705,0.033365,425.26,0.084779,-0.9909,0.10451,423.09,0.024523,0.10693,0.99396,101.32

> view matrix models
> #16,-0.9961,-0.081705,0.033365,438.95,0.084779,-0.9909,0.10451,402.42,0.024523,0.10693,0.99396,95.544

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.99374,0.051873,0.098969,386.27,-0.06164,-0.99324,-0.09832,481.15,0.0932,-0.10381,0.99022,140.16

> view matrix models
> #16,-0.98114,0.12739,0.14538,351.88,-0.15184,-0.97337,-0.17176,512.55,0.11963,-0.1906,0.97435,161.99

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.98114,0.12739,0.14538,369.75,-0.15184,-0.97337,-0.17176,514.52,0.11963,-0.1906,0.97435,158.79

> view matrix models
> #16,-0.98114,0.12739,0.14538,368.63,-0.15184,-0.97337,-0.17176,516.65,0.11963,-0.1906,0.97435,159.84

> view matrix models
> #16,-0.98114,0.12739,0.14538,366.89,-0.15184,-0.97337,-0.17176,506.75,0.11963,-0.1906,0.97435,156.61

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.83387,0.099559,0.54291,255.6,-0.35481,-0.85015,-0.38906,565.82,0.42282,-0.51705,0.74424,226.04

> view matrix models
> #16,-0.90683,0.11565,0.40531,297.39,-0.35917,-0.71524,-0.59952,572.72,0.22056,-0.68924,0.69015,334.74

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.90683,0.11565,0.40531,292.91,-0.35917,-0.71524,-0.59952,581.73,0.22056,-0.68924,0.69015,303.69

> view matrix models
> #16,-0.90683,0.11565,0.40531,293.06,-0.35917,-0.71524,-0.59952,587.43,0.22056,-0.68924,0.69015,301.56

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.96902,-0.070223,0.23679,396.82,-0.1402,-0.63289,-0.76145,545.84,0.20333,-0.77105,0.60343,347.47

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.96902,-0.070223,0.23679,397.41,-0.1402,-0.63289,-0.76145,537.73,0.20333,-0.77105,0.60343,348.87

> view matrix models
> #16,-0.96902,-0.070223,0.23679,401.12,-0.1402,-0.63289,-0.76145,535.11,0.20333,-0.77105,0.60343,345.46

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.98254,0.10988,0.15011,370.9,-0.18197,-0.73542,-0.65272,551.54,0.038673,-0.66864,0.74258,325.8

> view matrix models
> #16,-0.89274,-0.35002,0.28373,453.11,0.28201,-0.92518,-0.25401,411.28,0.3514,-0.14675,0.92465,63.175

> view matrix models
> #16,-0.92945,-0.35614,0.096365,503.22,0.27652,-0.84534,-0.4571,432.75,0.24425,-0.39821,0.88418,169.01

> view matrix models
> #16,-0.97331,-0.156,-0.16835,512.43,0.19345,-0.9523,-0.236,436.37,-0.1235,-0.26226,0.95706,202.38

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.97331,-0.156,-0.16835,509.39,0.19345,-0.9523,-0.236,442.44,-0.1235,-0.26226,0.95706,236.41

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.99751,0.010499,-0.069809,446.72,-0.0018841,-0.99249,-0.12235,476.32,-0.070569,-0.12191,0.99003,176.74

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.99751,0.010499,-0.069809,446.33,-0.0018841,-0.99249,-0.12235,477,-0.070569,-0.12191,0.99003,185.69

> ui mousemode right "rotate selected models"

> view matrix models
> #16,-0.99194,-0.079652,-0.09859,476.87,0.09233,-0.987,-0.13154,454.95,-0.086831,-0.13958,0.9864,195.38

> ui mousemode right "translate selected models"

> view matrix models
> #16,-0.99194,-0.079652,-0.09859,475.45,0.09233,-0.987,-0.13154,455.38,-0.086831,-0.13958,0.9864,195.38

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#16) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01433, steps = 256  
shifted from previous position = 14.8  
rotated from previous position = 10.1 degrees  
atoms outside contour = 4904, contour level = 0.017861  
  
Position of dimer_one.pdb (#16) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.98289407 -0.18411165 -0.00470702 473.40662101  
0.18416964 -0.98268554 -0.02026506 397.41439483  
-0.00089448 -0.02078530 0.99978357 141.53147466  
Axis -0.00141253 -0.01035167 0.99994542  
Axis point 218.28270295 221.43246183 0.00000000  
Rotation angle (degrees) 169.38838004  
Shift along axis 136.74114593  
  

> color #16 #63452cff

> select subtract #16

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #17  
---  
Chain | Description  
A B | No description available  
  

> select add #17

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #17,1,0,0,36.873,0,1,0,-97.839,0,0,1,84.018

> view matrix models #17,1,0,0,15.315,0,1,0,-46.704,0,0,1,57.628

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.5281,-0.13317,0.83867,-11.922,-0.59912,0.64149,0.47911,97.107,-0.6018,-0.75548,0.25899,572.71

> view matrix models
> #17,0.61785,-0.77761,0.11659,302.95,-0.75249,-0.54173,0.37455,493.77,-0.22809,-0.31915,-0.91985,607.45

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.61785,-0.77761,0.11659,300.38,-0.75249,-0.54173,0.37455,475.54,-0.22809,-0.31915,-0.91985,647.36

> view matrix models
> #17,0.61785,-0.77761,0.11659,232.41,-0.75249,-0.54173,0.37455,423.48,-0.22809,-0.31915,-0.91985,618.19

> view matrix models
> #17,0.61785,-0.77761,0.11659,222.15,-0.75249,-0.54173,0.37455,436.31,-0.22809,-0.31915,-0.91985,621.13

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.57084,-0.77724,0.26465,201.63,-0.81931,-0.51818,0.2454,473.12,-0.053599,-0.35691,-0.9326,593.02

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.57084,-0.77724,0.26465,198.38,-0.81931,-0.51818,0.2454,471.19,-0.053599,-0.35691,-0.9326,600.83

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.5848,-0.78001,0.22269,204.82,-0.81054,-0.55102,0.19851,488.54,-0.032132,-0.29658,-0.95447,583.12

> view matrix models
> #17,0.49381,-0.82867,0.26354,231.67,-0.86438,-0.50083,0.044851,519.86,0.094821,-0.24994,-0.96361,541.48

> view matrix models
> #17,0.37284,-0.83141,0.41201,229.46,-0.92109,-0.3853,0.056025,497.88,0.11217,-0.40039,-0.90945,568.84

> view matrix models
> #17,0.38873,-0.87147,0.29905,261.33,-0.91185,-0.41038,-0.010573,517.12,0.13194,-0.26858,-0.95418,535.96

> view matrix models
> #17,0.37458,-0.88882,0.26397,277.16,-0.92521,-0.37694,0.043672,499.13,0.060686,-0.26059,-0.96354,552.62

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.37458,-0.88882,0.26397,279.7,-0.92521,-0.37694,0.043672,497.06,0.060686,-0.26059,-0.96354,551.85

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.57584,-0.7795,0.24654,204.07,-0.80138,-0.47847,0.35896,428.67,-0.16185,-0.40428,-0.9002,632.67

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.57584,-0.7795,0.24654,206.63,-0.80138,-0.47847,0.35896,428.93,-0.16185,-0.40428,-0.9002,629.43

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.56164,-0.7389,0.37227,171.52,-0.81999,-0.43708,0.36956,419.23,-0.11035,-0.51282,-0.85137,637.83

> view matrix models
> #17,0.58544,-0.73568,0.34064,171.68,-0.80337,-0.47002,0.36561,425.56,-0.10886,-0.48771,-0.86619,633.43

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.58544,-0.73568,0.34064,169.47,-0.80337,-0.47002,0.36561,427.5,-0.10886,-0.48771,-0.86619,634.43

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#17) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01562, steps = 312  
shifted from previous position = 9.33  
rotated from previous position = 34.8 degrees  
atoms outside contour = 4448, contour level = 0.017861  
  
Position of dimer_one.pdb (#17) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.29577787 -0.95523264 -0.00678662 363.78411489  
-0.95525568 -0.29578068 -0.00060821 491.52250385  
-0.00142637 0.00666285 -0.99997678 507.50680258  
Axis 0.80491434 -0.59338554 -0.00255080  
Axis point 0.00000000 379.14073143 255.01923661  
Rotation angle (degrees) 179.74121314  
Shift along axis -0.14184776  
  

> color #17 #63452cff

> select subtract #17

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #18  
---  
Chain | Description  
A B | No description available  
  

> select add #18

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.40712,-0.91242,0.041723,586.7,0.90899,-0.40921,-0.079294,202.44,0.089423,0.0056441,0.99598,-22.059

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.40712,-0.91242,0.041723,598.45,0.90899,-0.40921,-0.079294,140.71,0.089423,0.0056441,0.99598,11.636

> view matrix models
> #18,-0.40712,-0.91242,0.041723,525.95,0.90899,-0.40921,-0.079294,128.89,0.089423,0.0056441,0.99598,-31.747

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.15089,-0.94886,-0.27731,542.97,0.98848,-0.14151,-0.053664,28.192,0.011677,-0.28221,0.95928,76.631

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.15089,-0.94886,-0.27731,546.41,0.98848,-0.14151,-0.053664,37.902,0.011677,-0.28221,0.95928,73.883

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.11175,-0.97686,-0.18237,524.97,0.9917,-0.097878,-0.083399,30.975,0.063619,-0.19018,0.97969,30.909

> view matrix models
> #18,0.25701,-0.84426,-0.47029,460.14,0.94174,0.32805,-0.074249,-80.791,0.21696,-0.42381,0.87938,82.385

> view matrix models
> #18,0.0056042,-0.98752,0.1574,427.82,0.99896,-0.0015796,-0.045477,-6.5857,0.045158,0.1575,0.98649,-65.167

> ui mousemode right "translate selected models"

> view matrix models
> #18,0.0056042,-0.98752,0.1574,422.88,0.99896,-0.0015796,-0.045477,1.4792,0.045158,0.1575,0.98649,-50.157

> view matrix models
> #18,0.0056042,-0.98752,0.1574,408.37,0.99896,-0.0015796,-0.045477,-8.7767,0.045158,0.1575,0.98649,-48.865

> ui mousemode right "rotate selected models"

> view matrix models
> #18,0.26074,-0.95624,-0.13274,400.44,0.95986,0.24206,0.1417,-108.83,-0.10336,-0.16436,0.98097,79.51

> view matrix models
> #18,0.179,-0.98385,0.0010775,399.35,0.98384,0.179,0.0048825,-67.495,-0.0049965,0.00018612,0.99999,5.1403

> ui mousemode right "translate selected models"

> view matrix models
> #18,0.179,-0.98385,0.0010775,405.53,0.98384,0.179,0.0048825,-38.056,-0.0049965,0.00018612,0.99999,-11.539

> ui mousemode right "rotate selected models"

> view matrix models
> #18,0.13846,-0.99032,-0.0094358,419.27,0.98958,0.13796,0.041113,-35.428,-0.039413,-0.01503,0.99911,1.1847

> view matrix models
> #18,-0.014309,-0.98567,0.16809,416.5,0.99813,-0.0040839,0.061019,-1.1358,-0.059458,0.16864,0.98388,-43.215

> view matrix models
> #18,0.27236,-0.91842,-0.28693,425.76,0.95898,0.23472,0.15896,-80.744,-0.078644,-0.31846,0.94467,108.6

> view matrix models
> #18,0.37127,-0.92222,-0.10803,365.41,0.92711,0.37462,-0.011811,-76.855,0.051361,-0.095768,0.99408,3.7038

> view matrix models
> #18,0.16673,-0.96719,-0.19167,444.72,0.98345,0.14914,0.10292,-50.273,-0.070957,-0.20566,0.97605,67.989

> ui mousemode right "translate selected models"

> view matrix models
> #18,0.16673,-0.96719,-0.19167,444.85,0.98345,0.14914,0.10292,-52.792,-0.070957,-0.20566,0.97605,66.274

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#18) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01598, steps = 232  
shifted from previous position = 13.3  
rotated from previous position = 12.3 degrees  
atoms outside contour = 4224, contour level = 0.017861  
  
Position of dimer_one.pdb (#18) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.12215462 -0.99247525 -0.00843295 410.18426228  
0.99251103 0.12215306 0.00070187 -25.12921426  
0.00033352 -0.00845553 0.99996419 -10.23761236  
Axis -0.00461324 -0.00441630 0.99997961  
Axis point 219.30436058 219.26339878 0.00000000  
Rotation angle (degrees) 82.98461022  
Shift along axis -12.01870320  
  

> color #18 #63452cff

> select subtract #18

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #19  
---  
Chain | Description  
A B | No description available  
  

> select add #19

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #19,-0.42733,-0.86676,-0.25715,641.57,0.89089,-0.45214,0.043527,192.7,-0.15399,-0.21049,0.96539,104.02

> ui mousemode right "translate selected models"

> view matrix models
> #19,-0.42733,-0.86676,-0.25715,645.93,0.89089,-0.45214,0.043527,119.87,-0.15399,-0.21049,0.96539,141.24

> view matrix models
> #19,-0.42733,-0.86676,-0.25715,567.88,0.89089,-0.45214,0.043527,76.62,-0.15399,-0.21049,0.96539,154.91

> view matrix models
> #19,-0.42733,-0.86676,-0.25715,552.55,0.89089,-0.45214,0.043527,121.72,-0.15399,-0.21049,0.96539,135.9

> view matrix models
> #19,-0.42733,-0.86676,-0.25715,554.18,0.89089,-0.45214,0.043527,123.77,-0.15399,-0.21049,0.96539,132.76

> view matrix models
> #19,-0.42733,-0.86676,-0.25715,552.73,0.89089,-0.45214,0.043527,120.34,-0.15399,-0.21049,0.96539,133.64

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#19) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01595, steps = 224  
shifted from previous position = 4.72  
rotated from previous position = 15.6 degrees  
atoms outside contour = 4243, contour level = 0.017861  
  
Position of dimer_one.pdb (#19) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.36797554 -0.92980652 -0.00733666 503.19827452  
0.92983546 -0.36796353 -0.00297441 96.38704037  
0.00006600 -0.00791640 0.99996866 39.08991922  
Axis -0.00265746 -0.00398065 0.99998855  
Axis point 218.84258637 219.32119076 0.00000000  
Rotation angle (degrees) 111.59141318  
Shift along axis 37.36855669  
  

> color #19 #63452cff

> select subtract #19

Nothing selected  

> hide #!1 models

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #20  
---  
Chain | Description  
A B | No description available  
  

> select add #20

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> show #!1 models

> ui mousemode right "translate selected models"

> view matrix models #20,1,0,0,6.032,0,1,0,-27.885,0,0,1,-59.567

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.46323,-0.84779,-0.25822,430.31,0.88215,0.41311,0.22616,-118.7,-0.085063,-0.33256,0.93924,68.375

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.46323,-0.84779,-0.25822,421.06,0.88215,0.41311,0.22616,-135.81,-0.085063,-0.33256,0.93924,69.68

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.36508,-0.90283,-0.22719,453.57,0.92551,0.32555,0.19354,-114.28,-0.10077,-0.28092,0.95443,55.492

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.36508,-0.90283,-0.22719,424.39,0.92551,0.32555,0.19354,-101.61,-0.10077,-0.28092,0.95443,65.161

> view matrix models
> #20,0.36508,-0.90283,-0.22719,423.93,0.92551,0.32555,0.19354,-107.75,-0.10077,-0.28092,0.95443,54.702

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.33127,-0.9207,-0.20631,432.66,0.93342,0.28785,0.21417,-103.25,-0.1378,-0.26352,0.95476,58.49

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.33127,-0.9207,-0.20631,418.02,0.93342,0.28785,0.21417,-97.462,-0.1378,-0.26352,0.95476,67.008

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.55018,-0.81253,-0.19263,332.17,0.83068,0.50899,0.2256,-138.45,-0.085257,-0.28413,0.95499,60.323

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.55018,-0.81253,-0.19263,330.75,0.83068,0.50899,0.2256,-141.6,-0.085257,-0.28413,0.95499,51.618

> view matrix models
> #20,0.55018,-0.81253,-0.19263,311.05,0.83068,0.50899,0.2256,-127.71,-0.085257,-0.28413,0.95499,50.665

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.46377,-0.85633,-0.22719,351.43,0.88396,0.43006,0.18347,-109,-0.05941,-0.28591,0.95641,44.718

> ui mousemode right "translate selected models"

> view matrix models
> #20,0.46377,-0.85633,-0.22719,355.44,0.88396,0.43006,0.18347,-101.58,-0.05941,-0.28591,0.95641,37.765

> ui mousemode right "rotate selected models"

> view matrix models
> #20,0.45353,-0.87842,-0.15066,347.98,0.89057,0.44012,0.11478,-91.487,-0.034518,-0.18623,0.9819,-1.9694

> view matrix models
> #20,0.45165,-0.88026,-0.14546,347.86,0.89117,0.43727,0.12089,-92.112,-0.042807,-0.18423,0.98195,-0.5742

> ui mousemode right "translate selected models"

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#20) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01577, steps = 200  
shifted from previous position = 3.71  
rotated from previous position = 13.7 degrees  
atoms outside contour = 4369, contour level = 0.017861  
  
Position of dimer_one.pdb (#20) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.58232597 -0.81291936 -0.00765419 270.40340865  
0.81295520 0.58229355 0.00616989 -87.62445959  
-0.00055863 -0.00981540 0.99995167 -59.07181166  
Axis -0.00983124 -0.00436389 0.99994215  
Axis point 220.44712388 218.62596323 0.00000000  
Rotation angle (degrees) 54.38853987  
Shift along axis -61.34441037  
  

> color #20 #63452cff

> select subtract #20

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #21  
---  
Chain | Description  
A B | No description available  
  

> select add #21

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #21,1,0,0,-28.445,0,1,0,-44.161,0,0,1,-114.86

> view matrix models #21,1,0,0,-20.799,0,1,0,-36.61,0,0,1,-102.42

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.74612,-0.66581,-0.00049756,229.61,0.65585,0.73483,0.17289,-153.96,-0.11475,-0.12933,0.98494,-34.994

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.74612,-0.66581,-0.00049756,206.03,0.65585,0.73483,0.17289,-135.84,-0.11475,-0.12933,0.98494,-36.185

> view matrix models
> #21,0.74612,-0.66581,-0.00049756,222.6,0.65585,0.73483,0.17289,-131.12,-0.11475,-0.12933,0.98494,-43.594

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.74575,-0.66565,-0.02769,228.42,0.66034,0.73301,0.16324,-129.63,-0.088364,-0.14002,0.9862,-47.091

> view matrix models
> #21,0.75965,-0.65011,-0.016942,218.4,0.64143,0.7447,0.18438,-132.94,-0.10725,-0.15093,0.98271,-38.744

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.75965,-0.65011,-0.016942,208.42,0.64143,0.7447,0.18438,-118.26,-0.10725,-0.15093,0.98271,-41.301

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.80669,-0.58628,-0.074336,191.19,0.58173,0.76561,0.27464,-129.13,-0.1041,-0.2648,0.95867,-4.5031

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.80669,-0.58628,-0.074336,194.23,0.58173,0.76561,0.27464,-130.06,-0.1041,-0.2648,0.95867,-4.6298

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#21) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01496, steps = 224  
shifted from previous position = 2.39  
rotated from previous position = 19.7 degrees  
atoms outside contour = 4760, contour level = 0.017861  
  
Position of dimer_one.pdb (#21) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.90209928 -0.43151049 -0.00394717 116.34382339  
0.43152138 0.90209928 0.00248728 -73.59400737  
0.00248745 -0.00394706 0.99998912 -110.71968090  
Axis -0.00745509 -0.00745542 0.99994442  
Axis point 221.78237290 217.38385473 0.00000000  
Rotation angle (degrees) 25.56532711  
Shift along axis -111.03220666  
  

> select subtract #21

Nothing selected  

> color #21 #63452cff

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #22  
---  
Chain | Description  
A B | No description available  
  

> hide #!1 models

> show #!1 models

> select add #22

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #22,0.71067,-0.70242,-0.039356,277.6,0.69558,0.69315,0.18897,-118.33,-0.10546,-0.16167,0.98119,75.233

> ui mousemode right "translate selected models"

> view matrix models
> #22,0.71067,-0.70242,-0.039356,225.93,0.69558,0.69315,0.18897,-185.65,-0.10546,-0.16167,0.98119,68.43

> view matrix models
> #22,0.71067,-0.70242,-0.039356,266.63,0.69558,0.69315,0.18897,-92,-0.10546,-0.16167,0.98119,-27.825

> view matrix models
> #22,0.71067,-0.70242,-0.039356,228.78,0.69558,0.69315,0.18897,-113.79,-0.10546,-0.16167,0.98119,-38.424

> ui mousemode right "rotate selected models"

> view matrix models
> #22,-0.53143,-0.77774,-0.33572,608.63,0.69467,-0.62692,0.35271,228.62,-0.48478,-0.045776,0.87344,41.491

> ui mousemode right "translate selected models"

> view matrix models
> #22,-0.53143,-0.77774,-0.33572,643.42,0.69467,-0.62692,0.35271,153.69,-0.48478,-0.045776,0.87344,57.245

> view matrix models
> #22,-0.53143,-0.77774,-0.33572,588.68,0.69467,-0.62692,0.35271,168.67,-0.48478,-0.045776,0.87344,47.727

> view matrix models
> #22,-0.53143,-0.77774,-0.33572,596.88,0.69467,-0.62692,0.35271,142.16,-0.48478,-0.045776,0.87344,28.06

> ui mousemode right "rotate selected models"

> view matrix models
> #22,-0.17001,-0.86188,0.47777,361.91,0.97949,-0.094568,0.17794,-40.498,-0.10818,0.49822,0.86027,-214.02

> view matrix models
> #22,-0.39851,-0.89967,-0.1783,567.24,0.90555,-0.41679,0.079109,90.026,-0.14549,-0.12994,0.98079,-51.128

> ui mousemode right "translate selected models"

> view matrix models
> #22,-0.39851,-0.89967,-0.1783,563.55,0.90555,-0.41679,0.079109,108.86,-0.14549,-0.12994,0.98079,-47.202

> view matrix models
> #22,-0.39851,-0.89967,-0.1783,563.83,0.90555,-0.41679,0.079109,100.3,-0.14549,-0.12994,0.98079,-44.493

> ui mousemode right "rotate selected models"

> view matrix models
> #22,-0.17209,-0.96671,-0.18935,531.4,0.98295,-0.18114,0.031468,24.924,-0.06472,-0.18071,0.98141,-49.318

> view matrix models
> #22,-0.51154,-0.84749,0.14175,507.82,0.85787,-0.5131,0.028142,150.15,0.04888,0.136,0.9895,-168.41

> view matrix models
> #22,-0.1913,-0.94198,0.27582,429.87,0.98099,-0.19286,0.021721,30.648,0.032732,0.27473,0.96097,-198.12

> view matrix models
> #22,-0.31128,-0.89125,0.32981,432.42,0.94031,-0.33909,-0.028825,93.005,0.13753,0.30115,0.94361,-226.92

> ui mousemode right "translate selected models"

> view matrix models
> #22,-0.31128,-0.89125,0.32981,420.74,0.94031,-0.33909,-0.028825,100.44,0.13753,0.30115,0.94361,-234.59

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> view matrix models
> #22,-0.31128,-0.89125,0.32981,421.8,0.94031,-0.33909,-0.028825,99.574,0.13753,0.30115,0.94361,-231.28

> ui mousemode right "rotate selected models"

> view matrix models
> #22,-0.32252,-0.89015,0.32188,425.86,0.93497,-0.35264,-0.03839,106.77,0.14768,0.28857,0.946,-230.61

> view matrix models
> #22,-0.40369,-0.88763,0.22167,465.91,0.88974,-0.43732,-0.13081,161.51,0.21306,0.14442,0.96631,-209.35

> ui mousemode right "translate selected models"

> view matrix models
> #22,-0.40369,-0.88763,0.22167,462,0.88974,-0.43732,-0.13081,164.87,0.21306,0.14442,0.96631,-211.82

> view matrix models
> #22,-0.40369,-0.88763,0.22167,462.54,0.88974,-0.43732,-0.13081,162.53,0.21306,0.14442,0.96631,-207.13

> view matrix models
> #22,-0.40369,-0.88763,0.22167,462.35,0.88974,-0.43732,-0.13081,158.45,0.21306,0.14442,0.96631,-209.26

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#22) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01437, steps = 356  
shifted from previous position = 12  
rotated from previous position = 16.3 degrees  
atoms outside contour = 4909, contour level = 0.017861  
  
Position of dimer_one.pdb (#22) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.31245717 -0.94992932 0.00219317 493.62523996  
0.94991845 -0.31246419 -0.00459005 79.81508777  
0.00504551 0.00064914 0.99998706 -124.84410726  
Axis 0.00275768 -0.00150134 0.99999507  
Axis point 218.16776221 218.57442126 0.00000000  
Rotation angle (degrees) 108.20797548  
Shift along axis -123.60206365  
  

> color #22 #c64600ff

> select subtract #22

Nothing selected  

> color #22 #e5a50aff

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #23  
---  
Chain | Description  
A B | No description available  
  

> select add #23

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #23,1,0,0,-12.234,0,1,0,-107.45,0,0,1,-12.914

> ui mousemode right "rotate selected models"

> view matrix models
> #23,-0.36197,-0.89019,-0.27666,624.83,0.92864,-0.37023,-0.023731,67.163,-0.081301,-0.2655,0.96068,90.548

> ui mousemode right "translate selected models"

> view matrix models
> #23,-0.36197,-0.89019,-0.27666,561.92,0.92864,-0.37023,-0.023731,93.032,-0.081301,-0.2655,0.96068,31.242

> view matrix models
> #23,-0.36197,-0.89019,-0.27666,569.18,0.92864,-0.37023,-0.023731,77.727,-0.081301,-0.2655,0.96068,30.522

> ui mousemode right "rotate selected models"

> view matrix models
> #23,-0.6248,-0.76271,-0.167,572.22,0.77995,-0.61959,-0.088266,197.87,-0.036151,-0.1854,0.982,-7.5737

> ui mousemode right "translate selected models"

> view matrix models
> #23,-0.6248,-0.76271,-0.167,550.75,0.77995,-0.61959,-0.088266,203.95,-0.036151,-0.1854,0.982,-7.2546

> view matrix models
> #23,-0.6248,-0.76271,-0.167,554.47,0.77995,-0.61959,-0.088266,198.48,-0.036151,-0.1854,0.982,-11.392

> view matrix models
> #23,-0.6248,-0.76271,-0.167,558.01,0.77995,-0.61959,-0.088266,194.35,-0.036151,-0.1854,0.982,-11.081

> ui mousemode right "rotate selected models"

> view matrix models
> #23,-0.63844,-0.76822,-0.047316,537.43,0.76915,-0.63907,-0.0023183,184.23,-0.028457,-0.037873,0.99888,-58.548

> ui mousemode right "translate selected models"

> view matrix models
> #23,-0.63844,-0.76822,-0.047316,543.78,0.76915,-0.63907,-0.0023183,182.64,-0.028457,-0.037873,0.99888,-55.997

> view matrix models
> #23,-0.63844,-0.76822,-0.047316,543.37,0.76915,-0.63907,-0.0023183,184.24,-0.028457,-0.037873,0.99888,-55.966

> view matrix models
> #23,-0.63844,-0.76822,-0.047316,540.74,0.76915,-0.63907,-0.0023183,187.36,-0.028457,-0.037873,0.99888,-57.181

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#23) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01562, steps = 188  
shifted from previous position = 4.01  
rotated from previous position = 7.85 degrees  
atoms outside contour = 4430, contour level = 0.017861  
  
Position of dimer_one.pdb (#23) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.73392832 -0.67919745 -0.00632866 528.10946828  
0.67922689 -0.73389951 -0.00650653 231.75067647  
-0.00022538 -0.00907393 0.99995881 -71.70420418  
Axis -0.00188996 -0.00449286 0.99998812  
Axis point 218.66041239 219.12422871 0.00000000  
Rotation angle (degrees) 137.21726040  
Shift along axis -73.74267967  
  

> color #23 #e5a50aff

> select subtract #23

Nothing selected  

> hide #!1 models

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #24  
---  
Chain | Description  
A B | No description available  
  

> select add #24

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> show #!1 models

> view matrix models #24,1,0,0,-108.38,0,1,0,-48.512,0,0,1,-4.8143

> view matrix models #24,1,0,0,-58.813,0,1,0,-113.73,0,0,1,9.3964

> ui mousemode right "rotate selected models"

> view matrix models
> #24,0.70768,-0.094509,-0.70018,186.24,-0.21724,0.9139,-0.34292,35.636,0.67231,0.39478,0.62622,-184.83

> view matrix models
> #24,0.3075,-0.59206,-0.74493,432.81,-0.85679,0.16829,-0.48743,432.38,0.41395,0.78813,-0.45552,-4.993

> view matrix models
> #24,0.5553,-0.77465,-0.30258,332.63,-0.7964,-0.39052,-0.46179,572.16,0.23956,0.49741,-0.83378,199.71

> ui mousemode right "translate selected models"

> view matrix models
> #24,0.5553,-0.77465,-0.30258,331.79,-0.7964,-0.39052,-0.46179,565.05,0.23956,0.49741,-0.83378,180.27

> view matrix models
> #24,0.5553,-0.77465,-0.30258,329.24,-0.7964,-0.39052,-0.46179,569.6,0.23956,0.49741,-0.83378,173.32

> view matrix models
> #24,0.5553,-0.77465,-0.30258,333.54,-0.7964,-0.39052,-0.46179,567.58,0.23956,0.49741,-0.83378,174.94

> ui mousemode right "rotate selected models"

> view matrix models
> #24,0.60884,-0.72422,-0.32377,310.84,-0.75387,-0.40112,-0.52037,572.79,0.24699,0.5609,-0.79018,145.87

> ui mousemode right "translate selected models"

> view matrix models
> #24,0.60884,-0.72422,-0.32377,315.22,-0.75387,-0.40112,-0.52037,571.62,0.24699,0.5609,-0.79018,145.95

> ui mousemode right "rotate selected models"

> view matrix models
> #24,0.73278,-0.58471,-0.34808,250.99,-0.67623,-0.56873,-0.46824,589.98,0.075821,0.5785,-0.81215,186.34

> ui mousemode right "translate selected models"

> view matrix models
> #24,0.73278,-0.58471,-0.34808,254.26,-0.67623,-0.56873,-0.46824,589.06,0.075821,0.5785,-0.81215,186.31

> view matrix models
> #24,0.73278,-0.58471,-0.34808,250.5,-0.67623,-0.56873,-0.46824,588.39,0.075821,0.5785,-0.81215,187.02

> ui mousemode right "rotate selected models"

> view matrix models
> #24,0.7049,-0.59986,-0.37853,267.87,-0.70808,-0.62648,-0.3258,582.55,-0.041709,0.49769,-0.86635,249.5

> view matrix models
> #24,0.73126,-0.55608,-0.39501,252.56,-0.66923,-0.69689,-0.25784,579.18,-0.1319,0.4529,-0.88175,286.99

> view matrix models
> #24,0.743,-0.55309,-0.37687,245.09,-0.66576,-0.66854,-0.3314,585.76,-0.068659,0.49714,-0.86495,255.77

> ui mousemode right "translate selected models"

> view matrix models
> #24,0.743,-0.55309,-0.37687,236.32,-0.66576,-0.66854,-0.3314,585.26,-0.068659,0.49714,-0.86495,258.51

> ui mousemode right "rotate selected models"

> view matrix models
> #24,0.79543,-0.49392,-0.35119,201.54,-0.60425,-0.69093,-0.39686,590.78,-0.04663,0.52788,-0.84804,240.93

> view matrix models
> #24,0.4836,-0.76816,-0.4196,368.51,-0.87482,-0.43989,-0.20295,542.75,-0.028683,0.46522,-0.88473,262.26

> ui mousemode right "translate selected models"

> view matrix models
> #24,0.4836,-0.76816,-0.4196,365.55,-0.87482,-0.43989,-0.20295,539.83,-0.028683,0.46522,-0.88473,262.27

> view matrix models
> #24,0.4836,-0.76816,-0.4196,368.27,-0.87482,-0.43989,-0.20295,544.05,-0.028683,0.46522,-0.88473,253.71

> view matrix models
> #24,0.4836,-0.76816,-0.4196,369.99,-0.87482,-0.43989,-0.20295,544.33,-0.028683,0.46522,-0.88473,250.63

> view matrix models
> #24,0.4836,-0.76816,-0.4196,372.92,-0.87482,-0.43989,-0.20295,543.49,-0.028683,0.46522,-0.88473,251.53

> ui mousemode right "rotate selected models"

> view matrix models
> #24,0.49055,-0.77627,-0.39594,368.6,-0.87131,-0.44402,-0.20897,545.1,-0.01359,0.4475,-0.89418,254.98

> view matrix models
> #24,0.50403,-0.79202,-0.34447,359.03,-0.86347,-0.45324,-0.22135,548.47,0.019188,0.40901,-0.91233,261.98

> view matrix models
> #24,0.46197,-0.85069,-0.25082,366.05,-0.85919,-0.35912,-0.36447,550.78,0.21997,0.38387,-0.8968,218.05

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#24) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01591, steps = 336  
shifted from previous position = 5.7  
rotated from previous position = 30.9 degrees  
atoms outside contour = 4285, contour level = 0.017861  
  
Position of dimer_one.pdb (#24) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.67893826 -0.73416637 -0.00652475 231.82117345  
-0.73419435 -0.67892533 -0.00436605 527.73055507  
-0.00122441 0.00775471 -0.99996918 396.00750912  
Axis 0.91622452 -0.40065964 -0.00211447  
Axis point 0.00000000 313.83756762 199.22381571  
Rotation angle (degrees) 179.62101357  
Shift along axis 0.12256302  
  

> color #24 #e5a50aff

> select subtract #24

Nothing selected  

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #25  
---  
Chain | Description  
A B | No description available  
  

> select add #25

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> ui mousemode right "translate selected models"

> view matrix models #25,1,0,0,-50.336,0,1,0,-51.792,0,0,1,-9.8815

> ui mousemode right "rotate selected models"

> view matrix models
> #25,-0.80301,0.20003,-0.5614,443.09,-0.57397,-0.51316,0.63814,383.48,-0.16044,0.83466,0.52688,-110.15

> view matrix models
> #25,-0.89483,0.30939,-0.32182,382.8,-0.42846,-0.39284,0.81369,277.11,0.12533,0.866,0.48408,-178.12

> view matrix models
> #25,-0.82987,0.54633,0.11334,206.92,-0.48939,-0.81027,0.32242,515.68,0.26799,0.2121,0.93979,-121.62

> ui mousemode right "translate selected models"

> view matrix models
> #25,-0.82987,0.54633,0.11334,187.77,-0.48939,-0.81027,0.32242,441.71,0.26799,0.2121,0.93979,-122.4

> view matrix models
> #25,-0.82987,0.54633,0.11334,226.95,-0.48939,-0.81027,0.32242,471.45,0.26799,0.2121,0.93979,-83.994

> view matrix models
> #25,-0.82987,0.54633,0.11334,212.92,-0.48939,-0.81027,0.32242,443.04,0.26799,0.2121,0.93979,-106.35

> ui mousemode right "rotate selected models"

> view matrix models
> #25,-0.83625,0.52028,0.17318,209.13,-0.4444,-0.82806,0.34181,433.24,0.32124,0.20888,0.92367,-114.71

> view matrix models
> #25,-0.95323,0.28111,0.11102,318.62,-0.26481,-0.95386,0.14152,468.98,0.14568,0.1055,0.98369,-56.057

> ui mousemode right "translate selected models"

> view matrix models
> #25,-0.95323,0.28111,0.11102,325.85,-0.26481,-0.95386,0.14152,478.63,0.14568,0.1055,0.98369,-49.996

> view matrix models
> #25,-0.95323,0.28111,0.11102,334.44,-0.26481,-0.95386,0.14152,475.88,0.14568,0.1055,0.98369,-37.388

> view matrix models
> #25,-0.95323,0.28111,0.11102,342.64,-0.26481,-0.95386,0.14152,470.96,0.14568,0.1055,0.98369,-32.283

> ui mousemode right "rotate selected models"

> view matrix models
> #25,-0.94453,0.31485,0.093479,334.67,-0.31651,-0.94858,-0.0031658,512.6,0.087675,-0.032577,0.99562,18.411

> ui mousemode right "translate selected models"

> view matrix models
> #25,-0.94453,0.31485,0.093479,335.17,-0.31651,-0.94858,-0.0031658,511.92,0.087675,-0.032577,0.99562,15.217

> ui mousemode right "rotate selected models"

> view matrix models
> #25,-0.94518,0.31062,0.10075,334.98,-0.31417,-0.94913,-0.021079,515.35,0.089075,-0.051575,0.99469,20.506

> ui mousemode right "translate selected models"

> view matrix models
> #25,-0.94518,0.31062,0.10075,326.91,-0.31417,-0.94913,-0.021079,510.1,0.089075,-0.051575,0.99469,19.953

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#25) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01599, steps = 208  
shifted from previous position = 12.5  
rotated from previous position = 6.87 degrees  
atoms outside contour = 4237, contour level = 0.017861  
  
Position of dimer_one.pdb (#25) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.96848980 0.24904449 0.00208356 374.72200910  
-0.24905311 -0.96846270 -0.00724866 485.67481424  
0.00021261 -0.00753917 0.99997156 26.60517188  
Axis -0.00058324 0.00375616 -0.99999278  
Axis point 218.08284960 219.18347883 0.00000000  
Rotation angle (degrees) 165.57866129  
Shift along axis -24.99925884  
  

> select subtract #25

Nothing selected  

> color #25 #e5a50aff

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #26  
---  
Chain | Description  
A B | No description available  
  

> select add #26

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #26,1,0,0,-47.936,0,1,0,-45.798,0,0,1,128.4

> ui mousemode right "rotate selected models"

> view matrix models
> #26,0.91606,-0.36,-0.17675,112.27,0.38252,0.91671,0.11541,-137.73,0.12048,-0.17334,0.97746,153.92

> view matrix models
> #26,0.30761,-0.46271,-0.83143,424.2,0.95061,0.18741,0.2474,-92.365,0.041345,-0.86647,0.49751,471.78

> view matrix models
> #26,0.64754,-0.086489,-0.75711,220.02,0.74928,-0.10876,0.65326,-45.524,-0.13885,-0.9903,-0.0056243,656.39

> view matrix models
> #26,0.74971,0.23075,-0.62023,76.206,0.63929,-0.49471,0.5887,104.52,-0.17099,-0.83786,-0.51841,728.66

> ui mousemode right "translate selected models"

> view matrix models
> #26,0.74971,0.23075,-0.62023,72.617,0.63929,-0.49471,0.5887,97.246,-0.17099,-0.83786,-0.51841,674.49

> view matrix models
> #26,0.74971,0.23075,-0.62023,133.13,0.63929,-0.49471,0.5887,3.9934,-0.17099,-0.83786,-0.51841,676.26

> view matrix models
> #26,0.74971,0.23075,-0.62023,146.95,0.63929,-0.49471,0.5887,12.795,-0.17099,-0.83786,-0.51841,664.49

> ui mousemode right "rotate selected models"

> view matrix models
> #26,0.95741,0.12807,-0.25876,49.862,0.19423,-0.94882,0.24903,321.19,-0.21362,-0.28868,-0.93329,605.43

> ui mousemode right "translate selected models"

> view matrix models
> #26,0.95741,0.12807,-0.25876,40.511,0.19423,-0.94882,0.24903,318.1,-0.21362,-0.28868,-0.93329,610.67

> view matrix models
> #26,0.95741,0.12807,-0.25876,43.488,0.19423,-0.94882,0.24903,332.9,-0.21362,-0.28868,-0.93329,615.45

> view matrix models
> #26,0.95741,0.12807,-0.25876,38.889,0.19423,-0.94882,0.24903,332.29,-0.21362,-0.28868,-0.93329,609.04

> ui mousemode right "rotate selected models"

> view matrix models
> #26,0.95906,0.061327,-0.27648,61.366,0.13409,-0.95823,0.2526,348.57,-0.24944,-0.27933,-0.92723,613.63

> view matrix models
> #26,0.95864,0.057065,-0.27886,63.194,0.07997,-0.99423,0.071459,410.39,-0.27317,-0.090803,-0.95767,571.88

> view matrix models
> #26,0.98114,0.10725,-0.1608,18.333,0.13036,-0.98141,0.14086,379.91,-0.14271,-0.15917,-0.97688,564.36

> view matrix models
> #26,0.98851,0.098077,-0.11501,9.4265,0.11119,-0.98726,0.11379,391.93,-0.10239,-0.12528,-0.98682,547.18

> ui mousemode right "translate selected models"

> view matrix models
> #26,0.98851,0.098077,-0.11501,7.8878,0.11119,-0.98726,0.11379,393.81,-0.10239,-0.12528,-0.98682,549.41

> ui mousemode right "rotate selected models"

> view matrix models
> #26,0.98105,0.19221,-0.024495,-36.483,0.19156,-0.98112,-0.026798,402.85,-0.029183,0.021598,-0.99934,492.72

> ui mousemode right "translate selected models"

> view matrix models
> #26,0.98105,0.19221,-0.024495,-38.642,0.19156,-0.98112,-0.026798,399.5,-0.029183,0.021598,-0.99934,493.36

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#26) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01574, steps = 124  
shifted from previous position = 7.33  
rotated from previous position = 2.08 degrees  
atoms outside contour = 4409, contour level = 0.017861  
  
Position of dimer_one.pdb (#26) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
0.98467460 0.17440133 -0.00031743 -34.73132728  
0.17439559 -0.98465407 -0.00652212 396.64557742  
-0.00145002 0.00636680 -0.99997868 495.23912207  
Axis 0.99616124 0.08753621 -0.00044355  
Axis point 0.00000000 199.04471427 248.25582560  
Rotation angle (degrees) 179.62933418  
Shift along axis -0.09681306  
  

> select subtract #26

Nothing selected  

> color #26 #e5a50aff

> open /home/pauline/Desktop/map316_modelbuilding/dimer_one.pdb format pdb

Chain information for dimer_one.pdb #27  
---  
Chain | Description  
A B | No description available  
  

> select add #27

6539 atoms, 6738 bonds, 17 pseudobonds, 850 residues, 3 models selected  

> view matrix models #27,1,0,0,-40.114,0,1,0,-67.136,0,0,1,144.56

> ui mousemode right "rotate selected models"

> view matrix models
> #27,-0.13283,0.94008,-0.314,28.39,-0.99114,-0.12559,0.043267,481.42,0.0012378,0.31697,0.94844,64.684

> ui mousemode right "translate selected models"

> view matrix models
> #27,-0.13283,0.94008,-0.314,74.625,-0.99114,-0.12559,0.043267,427.16,0.0012378,0.31697,0.94844,52.167

> view matrix models
> #27,-0.13283,0.94008,-0.314,97.712,-0.99114,-0.12559,0.043267,435.27,0.0012378,0.31697,0.94844,32.984

> view matrix models
> #27,-0.13283,0.94008,-0.314,93.6,-0.99114,-0.12559,0.043267,433.26,0.0012378,0.31697,0.94844,45.59

> ui mousemode right "rotate selected models"

> view matrix models
> #27,-0.42657,0.84946,-0.31057,188.75,-0.90247,-0.4225,0.083923,488.46,-0.059928,0.31608,0.94684,60.749

> ui mousemode right "translate selected models"

> view matrix models
> #27,-0.42657,0.84946,-0.31057,193.7,-0.90247,-0.4225,0.083923,490.43,-0.059928,0.31608,0.94684,65.582

> ui mousemode right "rotate selected models"

> view matrix models
> #27,-0.36759,0.91374,-0.17306,131.91,-0.92724,-0.3744,-0.0073008,502.11,-0.071465,0.15778,0.98488,105.46

> fitmap sel inMap #1

Fit molecule dimer_one.pdb (#27) to map cryosparc_P31_J316_010_volume_map.mrc
(#1) using 6539 atoms  
average map value = 0.01494, steps = 216  
shifted from previous position = 9.7  
rotated from previous position = 11.3 degrees  
atoms outside contour = 4711, contour level = 0.017861  
  
Position of dimer_one.pdb (#27) relative to
cryosparc_P31_J316_010_volume_map.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.31064274 0.95045611 0.01158708 75.72963964  
-0.95052673 -0.31062162 -0.00362593 494.04262728  
0.00015291 -0.01214020 0.99992629 126.65213101  
Axis -0.00447875 0.00601470 -0.99997188  
Axis point 217.00052022 220.14267856 0.00000000  
Rotation angle (degrees) 108.09955413  
Shift along axis -124.01622375  
  

> select subtract #27

Nothing selected  

> color #27 #e5a50aff

> hide #!1 models

> graphics silhouettes true

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes false

> lighting shadows true

> lighting shadows false

> lighting flat

> combine #2, #3, #4, #5, #6, #7, #8

Expected a keyword  

> combine #2 #3 #4 #5 #6 #7 #8

Remapping chain ID 'A' in dimer_one.pdb #3 to 'K'  
Remapping chain ID 'B' in dimer_one.pdb #3 to 'L'  
Remapping chain ID 'C' in dimer_one.pdb #3 to 'M'  
Remapping chain ID 'D' in dimer_one.pdb #3 to 'N'  
Remapping chain ID 'E' in dimer_one.pdb #3 to 'O'  
Remapping chain ID 'F' in dimer_one.pdb #3 to 'P'  
Remapping chain ID 'G' in dimer_one.pdb #3 to 'Q'  
Remapping chain ID 'H' in dimer_one.pdb #3 to 'R'  
Remapping chain ID 'I' in dimer_one.pdb #3 to 'S'  
Remapping chain ID 'J' in dimer_one.pdb #3 to 'T'  
Remapping chain ID 'A' in dimer_one.pdb #4 to 'U'  
Remapping chain ID 'B' in dimer_one.pdb #4 to 'V'  
Remapping chain ID 'C' in dimer_one.pdb #4 to 'W'  
Remapping chain ID 'D' in dimer_one.pdb #4 to 'X'  
Remapping chain ID 'E' in dimer_one.pdb #4 to 'Y'  
Remapping chain ID 'F' in dimer_one.pdb #4 to 'Z'  
Remapping chain ID 'G' in dimer_one.pdb #4 to 'a'  
Remapping chain ID 'H' in dimer_one.pdb #4 to 'b'  
Remapping chain ID 'I' in dimer_one.pdb #4 to 'c'  
Remapping chain ID 'J' in dimer_one.pdb #4 to 'd'  
Remapping chain ID 'A' in dimer_one.pdb #5 to 'e'  
Remapping chain ID 'B' in dimer_one.pdb #5 to 'f'  
Remapping chain ID 'C' in dimer_one.pdb #5 to 'g'  
Remapping chain ID 'D' in dimer_one.pdb #5 to 'h'  
Remapping chain ID 'E' in dimer_one.pdb #5 to 'i'  
Remapping chain ID 'F' in dimer_one.pdb #5 to 'j'  
Remapping chain ID 'G' in dimer_one.pdb #5 to 'k'  
Remapping chain ID 'H' in dimer_one.pdb #5 to 'l'  
Remapping chain ID 'I' in dimer_one.pdb #5 to 'm'  
Remapping chain ID 'J' in dimer_one.pdb #5 to 'n'  
Remapping chain ID 'A' in dimer_one.pdb #6 to 'o'  
Remapping chain ID 'B' in dimer_one.pdb #6 to 'p'  
Remapping chain ID 'C' in dimer_one.pdb #6 to 'q'  
Remapping chain ID 'D' in dimer_one.pdb #6 to 'r'  
Remapping chain ID 'E' in dimer_one.pdb #6 to 's'  
Remapping chain ID 'F' in dimer_one.pdb #6 to 't'  
Remapping chain ID 'G' in dimer_one.pdb #6 to 'u'  
Remapping chain ID 'H' in dimer_one.pdb #6 to 'v'  
Remapping chain ID 'I' in dimer_one.pdb #6 to 'w'  
Remapping chain ID 'J' in dimer_one.pdb #6 to 'x'  
Remapping chain ID 'A' in dimer_one.pdb #7 to 'y'  
Remapping chain ID 'B' in dimer_one.pdb #7 to 'z'  
Remapping chain ID 'C' in dimer_one.pdb #7 to '1'  
Remapping chain ID 'D' in dimer_one.pdb #7 to '2'  
Remapping chain ID 'E' in dimer_one.pdb #7 to '3'  
Remapping chain ID 'F' in dimer_one.pdb #7 to '4'  
Remapping chain ID 'G' in dimer_one.pdb #7 to '5'  
Remapping chain ID 'H' in dimer_one.pdb #7 to '6'  
Remapping chain ID 'I' in dimer_one.pdb #7 to '7'  
Remapping chain ID 'J' in dimer_one.pdb #7 to '8'  
Remapping chain ID 'A' in dimer_one.pdb #8 to '9'  
Remapping chain ID 'B' in dimer_one.pdb #8 to '0'  
Remapping chain ID 'C' in dimer_one.pdb #8 to 'AA'  
Remapping chain ID 'D' in dimer_one.pdb #8 to 'AB'  
Remapping chain ID 'E' in dimer_one.pdb #8 to 'AC'  
Remapping chain ID 'F' in dimer_one.pdb #8 to 'AD'  
Remapping chain ID 'G' in dimer_one.pdb #8 to 'AE'  
Remapping chain ID 'H' in dimer_one.pdb #8 to 'AF'  
Remapping chain ID 'I' in dimer_one.pdb #8 to 'AG'  
Remapping chain ID 'J' in dimer_one.pdb #8 to 'AH'  

> combine #9 #10 #11 #12 #13 #14 #15

Remapping chain ID 'A' in dimer_one.pdb #10 to 'K'  
Remapping chain ID 'B' in dimer_one.pdb #10 to 'L'  
Remapping chain ID 'C' in dimer_one.pdb #10 to 'M'  
Remapping chain ID 'D' in dimer_one.pdb #10 to 'N'  
Remapping chain ID 'E' in dimer_one.pdb #10 to 'O'  
Remapping chain ID 'F' in dimer_one.pdb #10 to 'P'  
Remapping chain ID 'G' in dimer_one.pdb #10 to 'Q'  
Remapping chain ID 'H' in dimer_one.pdb #10 to 'R'  
Remapping chain ID 'I' in dimer_one.pdb #10 to 'S'  
Remapping chain ID 'J' in dimer_one.pdb #10 to 'T'  
Remapping chain ID 'A' in dimer_one.pdb #11 to 'U'  
Remapping chain ID 'B' in dimer_one.pdb #11 to 'V'  
Remapping chain ID 'C' in dimer_one.pdb #11 to 'W'  
Remapping chain ID 'D' in dimer_one.pdb #11 to 'X'  
Remapping chain ID 'E' in dimer_one.pdb #11 to 'Y'  
Remapping chain ID 'F' in dimer_one.pdb #11 to 'Z'  
Remapping chain ID 'G' in dimer_one.pdb #11 to 'a'  
Remapping chain ID 'H' in dimer_one.pdb #11 to 'b'  
Remapping chain ID 'I' in dimer_one.pdb #11 to 'c'  
Remapping chain ID 'J' in dimer_one.pdb #11 to 'd'  
Remapping chain ID 'A' in dimer_one.pdb #12 to 'e'  
Remapping chain ID 'B' in dimer_one.pdb #12 to 'f'  
Remapping chain ID 'C' in dimer_one.pdb #12 to 'g'  
Remapping chain ID 'D' in dimer_one.pdb #12 to 'h'  
Remapping chain ID 'E' in dimer_one.pdb #12 to 'i'  
Remapping chain ID 'F' in dimer_one.pdb #12 to 'j'  
Remapping chain ID 'G' in dimer_one.pdb #12 to 'k'  
Remapping chain ID 'H' in dimer_one.pdb #12 to 'l'  
Remapping chain ID 'I' in dimer_one.pdb #12 to 'm'  
Remapping chain ID 'J' in dimer_one.pdb #12 to 'n'  
Remapping chain ID 'A' in dimer_one.pdb #13 to 'o'  
Remapping chain ID 'B' in dimer_one.pdb #13 to 'p'  
Remapping chain ID 'C' in dimer_one.pdb #13 to 'q'  
Remapping chain ID 'D' in dimer_one.pdb #13 to 'r'  
Remapping chain ID 'E' in dimer_one.pdb #13 to 's'  
Remapping chain ID 'F' in dimer_one.pdb #13 to 't'  
Remapping chain ID 'G' in dimer_one.pdb #13 to 'u'  
Remapping chain ID 'H' in dimer_one.pdb #13 to 'v'  
Remapping chain ID 'I' in dimer_one.pdb #13 to 'w'  
Remapping chain ID 'J' in dimer_one.pdb #13 to 'x'  
Remapping chain ID 'A' in dimer_one.pdb #14 to 'y'  
Remapping chain ID 'B' in dimer_one.pdb #14 to 'z'  
Remapping chain ID 'C' in dimer_one.pdb #14 to '1'  
Remapping chain ID 'D' in dimer_one.pdb #14 to '2'  
Remapping chain ID 'E' in dimer_one.pdb #14 to '3'  
Remapping chain ID 'F' in dimer_one.pdb #14 to '4'  
Remapping chain ID 'G' in dimer_one.pdb #14 to '5'  
Remapping chain ID 'H' in dimer_one.pdb #14 to '6'  
Remapping chain ID 'I' in dimer_one.pdb #14 to '7'  
Remapping chain ID 'J' in dimer_one.pdb #14 to '8'  
Remapping chain ID 'A' in dimer_one.pdb #15 to '9'  
Remapping chain ID 'B' in dimer_one.pdb #15 to '0'  
Remapping chain ID 'C' in dimer_one.pdb #15 to 'AA'  
Remapping chain ID 'D' in dimer_one.pdb #15 to 'AB'  
Remapping chain ID 'E' in dimer_one.pdb #15 to 'AC'  
Remapping chain ID 'F' in dimer_one.pdb #15 to 'AD'  
Remapping chain ID 'G' in dimer_one.pdb #15 to 'AE'  
Remapping chain ID 'H' in dimer_one.pdb #15 to 'AF'  
Remapping chain ID 'I' in dimer_one.pdb #15 to 'AG'  
Remapping chain ID 'J' in dimer_one.pdb #15 to 'AH'  

> combine #16 #17 #18 #19 #20 #21

Remapping chain ID 'A' in dimer_one.pdb #17 to 'K'  
Remapping chain ID 'B' in dimer_one.pdb #17 to 'L'  
Remapping chain ID 'C' in dimer_one.pdb #17 to 'M'  
Remapping chain ID 'D' in dimer_one.pdb #17 to 'N'  
Remapping chain ID 'E' in dimer_one.pdb #17 to 'O'  
Remapping chain ID 'F' in dimer_one.pdb #17 to 'P'  
Remapping chain ID 'G' in dimer_one.pdb #17 to 'Q'  
Remapping chain ID 'H' in dimer_one.pdb #17 to 'R'  
Remapping chain ID 'I' in dimer_one.pdb #17 to 'S'  
Remapping chain ID 'J' in dimer_one.pdb #17 to 'T'  
Remapping chain ID 'A' in dimer_one.pdb #18 to 'U'  
Remapping chain ID 'B' in dimer_one.pdb #18 to 'V'  
Remapping chain ID 'C' in dimer_one.pdb #18 to 'W'  
Remapping chain ID 'D' in dimer_one.pdb #18 to 'X'  
Remapping chain ID 'E' in dimer_one.pdb #18 to 'Y'  
Remapping chain ID 'F' in dimer_one.pdb #18 to 'Z'  
Remapping chain ID 'G' in dimer_one.pdb #18 to 'a'  
Remapping chain ID 'H' in dimer_one.pdb #18 to 'b'  
Remapping chain ID 'I' in dimer_one.pdb #18 to 'c'  
Remapping chain ID 'J' in dimer_one.pdb #18 to 'd'  
Remapping chain ID 'A' in dimer_one.pdb #19 to 'e'  
Remapping chain ID 'B' in dimer_one.pdb #19 to 'f'  
Remapping chain ID 'C' in dimer_one.pdb #19 to 'g'  
Remapping chain ID 'D' in dimer_one.pdb #19 to 'h'  
Remapping chain ID 'E' in dimer_one.pdb #19 to 'i'  
Remapping chain ID 'F' in dimer_one.pdb #19 to 'j'  
Remapping chain ID 'G' in dimer_one.pdb #19 to 'k'  
Remapping chain ID 'H' in dimer_one.pdb #19 to 'l'  
Remapping chain ID 'I' in dimer_one.pdb #19 to 'm'  
Remapping chain ID 'J' in dimer_one.pdb #19 to 'n'  
Remapping chain ID 'A' in dimer_one.pdb #20 to 'o'  
Remapping chain ID 'B' in dimer_one.pdb #20 to 'p'  
Remapping chain ID 'C' in dimer_one.pdb #20 to 'q'  
Remapping chain ID 'D' in dimer_one.pdb #20 to 'r'  
Remapping chain ID 'E' in dimer_one.pdb #20 to 's'  
Remapping chain ID 'F' in dimer_one.pdb #20 to 't'  
Remapping chain ID 'G' in dimer_one.pdb #20 to 'u'  
Remapping chain ID 'H' in dimer_one.pdb #20 to 'v'  
Remapping chain ID 'I' in dimer_one.pdb #20 to 'w'  
Remapping chain ID 'J' in dimer_one.pdb #20 to 'x'  
Remapping chain ID 'A' in dimer_one.pdb #21 to 'y'  
Remapping chain ID 'B' in dimer_one.pdb #21 to 'z'  
Remapping chain ID 'C' in dimer_one.pdb #21 to '1'  
Remapping chain ID 'D' in dimer_one.pdb #21 to '2'  
Remapping chain ID 'E' in dimer_one.pdb #21 to '3'  
Remapping chain ID 'F' in dimer_one.pdb #21 to '4'  
Remapping chain ID 'G' in dimer_one.pdb #21 to '5'  
Remapping chain ID 'H' in dimer_one.pdb #21 to '6'  
Remapping chain ID 'I' in dimer_one.pdb #21 to '7'  
Remapping chain ID 'J' in dimer_one.pdb #21 to '8'  

> hide #!28 models

> show #!28 models

> combine #22 #23 #24 #25 #26 #27

Remapping chain ID 'A' in dimer_one.pdb #23 to 'K'  
Remapping chain ID 'B' in dimer_one.pdb #23 to 'L'  
Remapping chain ID 'C' in dimer_one.pdb #23 to 'M'  
Remapping chain ID 'D' in dimer_one.pdb #23 to 'N'  
Remapping chain ID 'E' in dimer_one.pdb #23 to 'O'  
Remapping chain ID 'F' in dimer_one.pdb #23 to 'P'  
Remapping chain ID 'G' in dimer_one.pdb #23 to 'Q'  
Remapping chain ID 'H' in dimer_one.pdb #23 to 'R'  
Remapping chain ID 'I' in dimer_one.pdb #23 to 'S'  
Remapping chain ID 'J' in dimer_one.pdb #23 to 'T'  
Remapping chain ID 'A' in dimer_one.pdb #24 to 'U'  
Remapping chain ID 'B' in dimer_one.pdb #24 to 'V'  
Remapping chain ID 'C' in dimer_one.pdb #24 to 'W'  
Remapping chain ID 'D' in dimer_one.pdb #24 to 'X'  
Remapping chain ID 'E' in dimer_one.pdb #24 to 'Y'  
Remapping chain ID 'F' in dimer_one.pdb #24 to 'Z'  
Remapping chain ID 'G' in dimer_one.pdb #24 to 'a'  
Remapping chain ID 'H' in dimer_one.pdb #24 to 'b'  
Remapping chain ID 'I' in dimer_one.pdb #24 to 'c'  
Remapping chain ID 'J' in dimer_one.pdb #24 to 'd'  
Remapping chain ID 'A' in dimer_one.pdb #25 to 'e'  
Remapping chain ID 'B' in dimer_one.pdb #25 to 'f'  
Remapping chain ID 'C' in dimer_one.pdb #25 to 'g'  
Remapping chain ID 'D' in dimer_one.pdb #25 to 'h'  
Remapping chain ID 'E' in dimer_one.pdb #25 to 'i'  
Remapping chain ID 'F' in dimer_one.pdb #25 to 'j'  
Remapping chain ID 'G' in dimer_one.pdb #25 to 'k'  
Remapping chain ID 'H' in dimer_one.pdb #25 to 'l'  
Remapping chain ID 'I' in dimer_one.pdb #25 to 'm'  
Remapping chain ID 'J' in dimer_one.pdb #25 to 'n'  
Remapping chain ID 'A' in dimer_one.pdb #26 to 'o'  
Remapping chain ID 'B' in dimer_one.pdb #26 to 'p'  
Remapping chain ID 'C' in dimer_one.pdb #26 to 'q'  
Remapping chain ID 'D' in dimer_one.pdb #26 to 'r'  
Remapping chain ID 'E' in dimer_one.pdb #26 to 's'  
Remapping chain ID 'F' in dimer_one.pdb #26 to 't'  
Remapping chain ID 'G' in dimer_one.pdb #26 to 'u'  
Remapping chain ID 'H' in dimer_one.pdb #26 to 'v'  
Remapping chain ID 'I' in dimer_one.pdb #26 to 'w'  
Remapping chain ID 'J' in dimer_one.pdb #26 to 'x'  
Remapping chain ID 'A' in dimer_one.pdb #27 to 'y'  
Remapping chain ID 'B' in dimer_one.pdb #27 to 'z'  
Remapping chain ID 'C' in dimer_one.pdb #27 to '1'  
Remapping chain ID 'D' in dimer_one.pdb #27 to '2'  
Remapping chain ID 'E' in dimer_one.pdb #27 to '3'  
Remapping chain ID 'F' in dimer_one.pdb #27 to '4'  
Remapping chain ID 'G' in dimer_one.pdb #27 to '5'  
Remapping chain ID 'H' in dimer_one.pdb #27 to '6'  
Remapping chain ID 'I' in dimer_one.pdb #27 to '7'  
Remapping chain ID 'J' in dimer_one.pdb #27 to '8'  

> hide #!30 models

> select add #31

39234 atoms, 40428 bonds, 102 pseudobonds, 5100 residues, 3 models selected  

> select add #29

85007 atoms, 87594 bonds, 221 pseudobonds, 11050 residues, 6 models selected  

> select add #28

130780 atoms, 134760 bonds, 340 pseudobonds, 17000 residues, 9 models selected  

> show #!30 models

> select add #30

170014 atoms, 175188 bonds, 442 pseudobonds, 22100 residues, 12 models
selected  

> view matrix models
> #28,0.14171,0.98979,0.015142,-31.079,-0.95897,0.14105,-0.24594,452.29,-0.24556,0.02033,0.96917,55.833,#29,-0.97354,-0.22813,0.013479,477.91,0.21735,-0.9425,-0.25387,442.95,0.070621,-0.24423,0.96714,9.4514,#30,0.042995,-0.99906,-0.0055863,431.51,0.96876,0.043057,-0.24423,19.559,0.24424,0.0050889,0.9697,84.828,#31,0.89602,-0.44388,0.01091,115.98,0.43239,0.86672,-0.24869,20.883,0.10093,0.22755,0.96852,-184.76

> ui mousemode right "translate selected models"

> view matrix models
> #28,0.14171,0.98979,0.015142,-224.17,-0.95897,0.14105,-0.24594,639.03,-0.24556,0.02033,0.96917,71.417,#29,-0.97354,-0.22813,0.013479,284.82,0.21735,-0.9425,-0.25387,629.69,0.070621,-0.24423,0.96714,25.035,#30,0.042995,-0.99906,-0.0055863,238.41,0.96876,0.043057,-0.24423,206.3,0.24424,0.0050889,0.9697,100.41,#31,0.89602,-0.44388,0.01091,-77.115,0.43239,0.86672,-0.24869,207.62,0.10093,0.22755,0.96852,-169.17

> combine #28 #29 #30 #31

Remapping chain ID '0' in combination #29 to 'AI'  
Remapping chain ID '1' in combination #29 to 'AJ'  
Remapping chain ID '2' in combination #29 to 'AK'  
Remapping chain ID '3' in combination #29 to 'AL'  
Remapping chain ID '4' in combination #29 to 'AM'  
Remapping chain ID '5' in combination #29 to 'AN'  
Remapping chain ID '6' in combination #29 to 'AO'  
Remapping chain ID '7' in combination #29 to 'AP'  
Remapping chain ID '8' in combination #29 to 'AQ'  
Remapping chain ID '9' in combination #29 to 'AR'  
Remapping chain ID 'A' in combination #29 to 'AS'  
Remapping chain ID 'AA' in combination #29 to 'AT'  
Remapping chain ID 'AB' in combination #29 to 'AU'  
Remapping chain ID 'AC' in combination #29 to 'AV'  
Remapping chain ID 'AD' in combination #29 to 'AW'  
Remapping chain ID 'AE' in combination #29 to 'AX'  
Remapping chain ID 'AF' in combination #29 to 'AY'  
Remapping chain ID 'AG' in combination #29 to 'AZ'  
Remapping chain ID 'AH' in combination #29 to 'Aa'  
Remapping chain ID 'B' in combination #29 to 'Ab'  
Remapping chain ID 'C' in combination #29 to 'Ac'  
Remapping chain ID 'D' in combination #29 to 'Ad'  
Remapping chain ID 'E' in combination #29 to 'Ae'  
Remapping chain ID 'F' in combination #29 to 'Af'  
Remapping chain ID 'G' in combination #29 to 'Ag'  
Remapping chain ID 'H' in combination #29 to 'Ah'  
Remapping chain ID 'I' in combination #29 to 'Ai'  
Remapping chain ID 'J' in combination #29 to 'Aj'  
Remapping chain ID 'K' in combination #29 to 'Ak'  
Remapping chain ID 'L' in combination #29 to 'Al'  
Remapping chain ID 'M' in combination #29 to 'Am'  
Remapping chain ID 'N' in combination #29 to 'An'  
Remapping chain ID 'O' in combination #29 to 'Ao'  
Remapping chain ID 'P' in combination #29 to 'Ap'  
Remapping chain ID 'Q' in combination #29 to 'Aq'  
Remapping chain ID 'R' in combination #29 to 'Ar'  
Remapping chain ID 'S' in combination #29 to 'As'  
Remapping chain ID 'T' in combination #29 to 'At'  
Remapping chain ID 'U' in combination #29 to 'Au'  
Remapping chain ID 'V' in combination #29 to 'Av'  
Remapping chain ID 'W' in combination #29 to 'Aw'  
Remapping chain ID 'X' in combination #29 to 'Ax'  
Remapping chain ID 'Y' in combination #29 to 'Ay'  
Remapping chain ID 'Z' in combination #29 to 'Az'  
Remapping chain ID 'a' in combination #29 to 'A1'  
Remapping chain ID 'b' in combination #29 to 'A2'  
Remapping chain ID 'c' in combination #29 to 'A3'  
Remapping chain ID 'd' in combination #29 to 'A4'  
Remapping chain ID 'e' in combination #29 to 'A5'  
Remapping chain ID 'f' in combination #29 to 'A6'  
Remapping chain ID 'g' in combination #29 to 'A7'  
Remapping chain ID 'h' in combination #29 to 'A8'  
Remapping chain ID 'i' in combination #29 to 'A9'  
Remapping chain ID 'j' in combination #29 to 'A0'  
Remapping chain ID 'k' in combination #29 to 'BA'  
Remapping chain ID 'l' in combination #29 to 'BB'  
Remapping chain ID 'm' in combination #29 to 'BC'  
Remapping chain ID 'n' in combination #29 to 'BD'  
Remapping chain ID 'o' in combination #29 to 'BE'  
Remapping chain ID 'p' in combination #29 to 'BF'  
Remapping chain ID 'q' in combination #29 to 'BG'  
Remapping chain ID 'r' in combination #29 to 'BH'  
Remapping chain ID 's' in combination #29 to 'BI'  
Remapping chain ID 't' in combination #29 to 'BJ'  
Remapping chain ID 'u' in combination #29 to 'BK'  
Remapping chain ID 'v' in combination #29 to 'BL'  
Remapping chain ID 'w' in combination #29 to 'BM'  
Remapping chain ID 'x' in combination #29 to 'BN'  
Remapping chain ID 'y' in combination #29 to 'BO'  
Remapping chain ID 'z' in combination #29 to 'BP'  
Remapping chain ID '1' in combination #30 to 'BQ'  
Remapping chain ID '2' in combination #30 to 'BR'  
Remapping chain ID '3' in combination #30 to 'BS'  
Remapping chain ID '4' in combination #30 to 'BT'  
Remapping chain ID '5' in combination #30 to 'BU'  
Remapping chain ID '6' in combination #30 to 'BV'  
Remapping chain ID '7' in combination #30 to 'BW'  
Remapping chain ID '8' in combination #30 to 'BX'  
Remapping chain ID 'A' in combination #30 to 'BY'  
Remapping chain ID 'B' in combination #30 to 'BZ'  
Remapping chain ID 'C' in combination #30 to 'Ba'  
Remapping chain ID 'D' in combination #30 to 'Bb'  
Remapping chain ID 'E' in combination #30 to 'Bc'  
Remapping chain ID 'F' in combination #30 to 'Bd'  
Remapping chain ID 'G' in combination #30 to 'Be'  
Remapping chain ID 'H' in combination #30 to 'Bf'  
Remapping chain ID 'I' in combination #30 to 'Bg'  
Remapping chain ID 'J' in combination #30 to 'Bh'  
Remapping chain ID 'K' in combination #30 to 'Bi'  
Remapping chain ID 'L' in combination #30 to 'Bj'  
Remapping chain ID 'M' in combination #30 to 'Bk'  
Remapping chain ID 'N' in combination #30 to 'Bl'  
Remapping chain ID 'O' in combination #30 to 'Bm'  
Remapping chain ID 'P' in combination #30 to 'Bn'  
Remapping chain ID 'Q' in combination #30 to 'Bo'  
Remapping chain ID 'R' in combination #30 to 'Bp'  
Remapping chain ID 'S' in combination #30 to 'Bq'  
Remapping chain ID 'T' in combination #30 to 'Br'  
Remapping chain ID 'U' in combination #30 to 'Bs'  
Remapping chain ID 'V' in combination #30 to 'Bt'  
Remapping chain ID 'W' in combination #30 to 'Bu'  
Remapping chain ID 'X' in combination #30 to 'Bv'  
Remapping chain ID 'Y' in combination #30 to 'Bw'  
Remapping chain ID 'Z' in combination #30 to 'Bx'  
Remapping chain ID 'a' in combination #30 to 'By'  
Remapping chain ID 'b' in combination #30 to 'Bz'  
Remapping chain ID 'c' in combination #30 to 'B1'  
Remapping chain ID 'd' in combination #30 to 'B2'  
Remapping chain ID 'e' in combination #30 to 'B3'  
Remapping chain ID 'f' in combination #30 to 'B4'  
Remapping chain ID 'g' in combination #30 to 'B5'  
Remapping chain ID 'h' in combination #30 to 'B6'  
Remapping chain ID 'i' in combination #30 to 'B7'  
Remapping chain ID 'j' in combination #30 to 'B8'  
Remapping chain ID 'k' in combination #30 to 'B9'  
Remapping chain ID 'l' in combination #30 to 'B0'  
Remapping chain ID 'm' in combination #30 to 'CA'  
Remapping chain ID 'n' in combination #30 to 'CB'  
Remapping chain ID 'o' in combination #30 to 'CC'  
Remapping chain ID 'p' in combination #30 to 'CD'  
Remapping chain ID 'q' in combination #30 to 'CE'  
Remapping chain ID 'r' in combination #30 to 'CF'  
Remapping chain ID 's' in combination #30 to 'CG'  
Remapping chain ID 't' in combination #30 to 'CH'  
Remapping chain ID 'u' in combination #30 to 'CI'  
Remapping chain ID 'v' in combination #30 to 'CJ'  
Remapping chain ID 'w' in combination #30 to 'CK'  
Remapping chain ID 'x' in combination #30 to 'CL'  
Remapping chain ID 'y' in combination #30 to 'CM'  
Remapping chain ID 'z' in combination #30 to 'CN'  
Remapping chain ID '1' in combination #31 to 'CO'  
Remapping chain ID '2' in combination #31 to 'CP'  
Remapping chain ID '3' in combination #31 to 'CQ'  
Remapping chain ID '4' in combination #31 to 'CR'  
Remapping chain ID '5' in combination #31 to 'CS'  
Remapping chain ID '6' in combination #31 to 'CT'  
Remapping chain ID '7' in combination #31 to 'CU'  
Remapping chain ID '8' in combination #31 to 'CV'  
Remapping chain ID 'A' in combination #31 to 'CW'  
Remapping chain ID 'B' in combination #31 to 'CX'  
Remapping chain ID 'C' in combination #31 to 'CY'  
Remapping chain ID 'D' in combination #31 to 'CZ'  
Remapping chain ID 'E' in combination #31 to 'Ca'  
Remapping chain ID 'F' in combination #31 to 'Cb'  
Remapping chain ID 'G' in combination #31 to 'Cc'  
Remapping chain ID 'H' in combination #31 to 'Cd'  
Remapping chain ID 'I' in combination #31 to 'Ce'  
Remapping chain ID 'J' in combination #31 to 'Cf'  
Remapping chain ID 'K' in combination #31 to 'Cg'  
Remapping chain ID 'L' in combination #31 to 'Ch'  
Remapping chain ID 'M' in combination #31 to 'Ci'  
Remapping chain ID 'N' in combination #31 to 'Cj'  
Remapping chain ID 'O' in combination #31 to 'Ck'  
Remapping chain ID 'P' in combination #31 to 'Cl'  
Remapping chain ID 'Q' in combination #31 to 'Cm'  
Remapping chain ID 'R' in combination #31 to 'Cn'  
Remapping chain ID 'S' in combination #31 to 'Co'  
Remapping chain ID 'T' in combination #31 to 'Cp'  
Remapping chain ID 'U' in combination #31 to 'Cq'  
Remapping chain ID 'V' in combination #31 to 'Cr'  
Remapping chain ID 'W' in combination #31 to 'Cs'  
Remapping chain ID 'X' in combination #31 to 'Ct'  
Remapping chain ID 'Y' in combination #31 to 'Cu'  
Remapping chain ID 'Z' in combination #31 to 'Cv'  
Remapping chain ID 'a' in combination #31 to 'Cw'  
Remapping chain ID 'b' in combination #31 to 'Cx'  
Remapping chain ID 'c' in combination #31 to 'Cy'  
Remapping chain ID 'd' in combination #31 to 'Cz'  
Remapping chain ID 'e' in combination #31 to 'C1'  
Remapping chain ID 'f' in combination #31 to 'C2'  
Remapping chain ID 'g' in combination #31 to 'C3'  
Remapping chain ID 'h' in combination #31 to 'C4'  
Remapping chain ID 'i' in combination #31 to 'C5'  
Remapping chain ID 'j' in combination #31 to 'C6'  
Remapping chain ID 'k' in combination #31 to 'C7'  
Remapping chain ID 'l' in combination #31 to 'C8'  
Remapping chain ID 'm' in combination #31 to 'C9'  
Remapping chain ID 'n' in combination #31 to 'C0'  
Remapping chain ID 'o' in combination #31 to 'DA'  
Remapping chain ID 'p' in combination #31 to 'DB'  
Remapping chain ID 'q' in combination #31 to 'DC'  
Remapping chain ID 'r' in combination #31 to 'DD'  
Remapping chain ID 's' in combination #31 to 'DE'  
Remapping chain ID 't' in combination #31 to 'DF'  
Remapping chain ID 'u' in combination #31 to 'DG'  
Remapping chain ID 'v' in combination #31 to 'DH'  
Remapping chain ID 'w' in combination #31 to 'DI'  
Remapping chain ID 'x' in combination #31 to 'DJ'  
Remapping chain ID 'y' in combination #31 to 'DK'  
Remapping chain ID 'z' in combination #31 to 'DL'  

> select subtract #31

130780 atoms, 134760 bonds, 340 pseudobonds, 17000 residues, 9 models selected  

> select subtract #30

91546 atoms, 94332 bonds, 238 pseudobonds, 11900 residues, 6 models selected  

> select subtract #29

45773 atoms, 47166 bonds, 119 pseudobonds, 5950 residues, 3 models selected  

> select subtract #28

Nothing selected  

> select add #32

170014 atoms, 175188 bonds, 442 pseudobonds, 22100 residues, 3 models selected  

> view matrix models
> #32,0.14171,0.98979,0.015142,-390.11,-0.95897,0.14105,-0.24594,527.86,-0.24556,0.02033,0.96917,50.867

> view matrix models
> #32,0.14171,0.98979,0.015142,-377.76,-0.95897,0.14105,-0.24594,430.55,-0.24556,0.02033,0.96917,-18.718

> view matrix models
> #32,0.14171,0.98979,0.015142,-283.82,-0.95897,0.14105,-0.24594,399.95,-0.24556,0.02033,0.96917,18.109

> select subtract #32

Nothing selected  

> save /home/pauline/Desktop/map316_modelbuilding/4sheets_7lrf.cif models #32
> relModel #1

> save /home/pauline/Desktop/map316_modelbuilding/sheet_one_7lrf.pdb models
> #31 relModel #1

> save /home/pauline/Desktop/map316_modelbuilding/sheet_two_7lrf.pdb models
> #30 relModel #1

> save /home/pauline/Desktop/map316_modelbuilding/sheet_three_7lrf.pdb models
> #29 relModel #1

> save /home/pauline/Desktop/map316_modelbuilding/sheet_four_7lrf.pdb models
> #28 relModel #1

> save /home/pauline/Desktop/map316_modelbuilding/sheet_one_7lrf.pdb models
> #28 relModel #1

> save /home/pauline/Desktop/map316_modelbuilding/sheet_two_7lrf.pdb models
> #29 relModel #1

> save /home/pauline/Desktop/map316_modelbuilding/sheet_three_7lrf.pdb models
> #30 relModel #1

> save /home/pauline/Desktop/map316_modelbuilding/sheet_four_7lrf.pdb models
> #31 relModel #1

> hide #!32 models

> hide #!31 models

> hide #!30 models

> hide #!29 models

> hide #!28 models

> hide #!27 models

> hide #!26 models

> hide #!25 models

> hide #!24 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> ui mousemode right "tape measure"

> marker segment #33 position 99.8,221,339.3 toPosition 112.9,172.9,391.5
> color yellow radius 0.1 label 72.22 labelHeight 7.222 labelColor yellow

> marker segment #33 position 178.7,240,330.1 toPosition 175.7,235.8,343.7
> color yellow radius 0.1 label 14.54 labelHeight 1.454 labelColor yellow

> marker segment #33 position 178.7,240,330.1 toPosition 180.5,239.7,336.2
> color yellow radius 0.1 label 6.308 labelHeight 0.6308 labelColor yellow

> marker delete #33

> marker segment #33 position 178.7,240,330.1 toPosition 178.6,240.6,343 color
> yellow radius 0.1 label 12.9 labelHeight 1.29 labelColor yellow

> marker delete #33

> marker segment #33 position 100.7,228.2,344.4 toPosition 147.8,176,365.1
> color yellow radius 0.1 label 73.28 labelHeight 7.328 labelColor yellow

> marker delete #33

> marker segment #33 position 100.7,228.2,344.4 toPosition 99,184.3,389.2
> color yellow radius 0.1 label 62.74 labelHeight 6.274 labelColor yellow

> marker segment #33 position 116.8,176.3,393.7 toPosition 128.7,226.6,371.6
> color yellow radius 0.1 label 56.17 labelHeight 5.617 labelColor yellow

> marker delete #33

> marker segment #33 position 100.9,224.6,339.2 toPosition 109.9,169,388.6
> color yellow radius 0.1 label 75 labelHeight 7.5 labelColor yellow

> marker delete #33

> hide #!9 models

> hide #!10 models

> hide #!11 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> show #!9 models

> show #!10 models

> show #!11 models

> show #!12 models

> show #!13 models

> show #!14 models

> show #!15 models

> save /home/pauline/Desktop/map316_modelbuilding/sheets.cxs

——— End of log from Fri Nov 17 14:43:17 2023 ———

opened ChimeraX session  

> close session

> open /home/pauline/Desktop/map316_modelbuilding/sheet_four_7lrf.pdb

Chain information for sheet_four_7lrf.pdb #1  
---  
Chain | Description  
A B K U e o y | No description available  
L V f p z | No description available  
  

> ui tool show "Show Sequence Viewer"

QXcbConnection: XCB error: 3 (BadWindow), sequence: 14416, resource id:
13394325, major code: 40 (TranslateCoords), minor code: 0  

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B /K /U /e /o /y

Alignment identifier is 1  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 18168, resource id:
13398854, major code: 40 (TranslateCoords), minor code: 0  

> select clear

[Repeated 1 time(s)]

> select /A-B,K,U,e,o,y:40-111

3697 atoms, 3822 bonds, 504 residues, 1 model selected  

> hide sel atoms

> select clear

> select

39234 atoms, 40428 bonds, 72 pseudobonds, 5100 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select clear

[Repeated 1 time(s)]

> select /A-B,K,U,e,o,y:40-181

7703 atoms, 7975 bonds, 994 residues, 1 model selected  

> hide sel cartoons

> select clear

> select /A-B,K,U,e,o,y:40-256

11723 atoms, 12086 bonds, 1519 residues, 1 model selected  

> select clear

> select /A,K,U,e,o,y:40-269/B:40-262

12396 atoms, 12772 bonds, 1603 residues, 1 model selected  

> select clear

> select /A-B,K,U,e,o,y:40-277

12880 atoms, 13276 bonds, 1659 residues, 1 model selected  

> hide sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain /L /V /f /p /z

Alignment identifier is 1  

> select /L,V,f,p,z:40

35 atoms, 35 bonds, 5 residues, 1 model selected  

> select /L,V,f,p,z:40-276

8755 atoms, 9025 bonds, 1150 residues, 1 model selected  

> hide sel cartoons

> delete atoms sel

> delete bonds sel

> ui tool show "Show Sequence Viewer"

> sequence chain /A /B /K /U /e /o /y

Alignment identifier is 1  

> select clear

> select /A-B,K,U,e,o,y:40-276

12845 atoms, 13241 bonds, 1652 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

No map chosen to save  

QXcbConnection: XCB error: 3 (BadWindow), sequence: 63904, resource id:
13349911, major code: 40 (TranslateCoords), minor code: 0  

> save /home/pauline/Desktop/map316_modelbuilding/tails_277Y_1sheet.cif
> displayedOnly true bestGuess true relModel #1

Traceback (most recent call last):  
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 127, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 62, in display  
run(session, cmd)  
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "/usr/lib64/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/mmcif/__init__.py", line 123, in save  
mmcif_write.write_mmcif(session, path, **kw)  
File "src/mmcif_write.pyx", line 160, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 167, in
chimerax.mmcif.mmcif_write.write_mmcif  
File "src/mmcif_write.pyx", line 899, in
chimerax.mmcif.mmcif_write.save_structure  
AttributeError: 'Residue' object has no attribute 'display'  
  
AttributeError: 'Residue' object has no attribute 'display'  
  
File "src/mmcif_write.pyx", line 899, in
chimerax.mmcif.mmcif_write.save_structure  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 525.85.05
OpenGL renderer: Quadro RTX 4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_CA.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xfce
XDG_SESSION_DESKTOP=xfce
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: Dell Inc.
Model: Precision 7820 Tower
OS: Gentoo 2.14 n/a
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 Intel(R) Xeon(R) Silver 4110 CPU @ 2.10GHz
Cache Size: 11264 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           157Gi       7.1Gi       146Gi        70Mi       3.5Gi       148Gi
	Swap:          159Gi       2.5Gi       157Gi

Graphics:
	0000:5b:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP106 [GeForce GTX 1060 6GB] [10de:1c03] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] GP106 [GeForce GTX 1060 6GB] [1462:3283]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

[Greg Couch]

Fixed in daily build. Consider a residue displayed if it's ribbon depiction is displayed or if any of the atoms are displayed.