Restore coloring on non-existent surface: bad error message

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-38-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Replace this text with list of actions that caused this problem to occur

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

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/J158_009 DV2_N15_Fab24 chimerax session.cxs"

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.2, step 1, values float32  
Log from Mon Apr 14 19:50:11 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.1, step 1, values float32  
Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.17, step 2, values float32  
Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at level 0.0843, step 1, values float32  
Log from Mon Apr 14 19:17:23 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb
> format pdb

current_fittingE7kv8_DENV2Fab13_20250330.pdb title:  
Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more
info...]  
  
Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
Chain | Description  
A B C | envelope protein E  
a b c | matrix protein M  
  
Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl
dihydrogen phosphate  
6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-
propan-2-yl] (~{Z})-octadec-9-enoate  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 13/cryosparc_P108_J123_011_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32  

> volume #1 level 0.17

> volume #1 level 0.13

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.15

> volume #1 level 0.16

> volume #1 level 0.17

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> hide #!2 models

> volume #1

> ui tool show "Surface Color"

> color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center
> 340.99,340.99,340.99

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

[Repeated 1 time(s)]

> volume #1 level 0.13

> volume #1 level 0.12

> volume #1 level 0.11

> volume #1 level 0.1

> volume #1 level 0.0843

> volume #1 step 1

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45

> view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653

> view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468

> ui mousemode right "translate selected models"

> select subtract #2

Nothing selected  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> select add #2

2 models selected  

> view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383

> view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477

> view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62

> view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41

> view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901

> view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853

> view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068

> select add #1

4 models selected  

> fitmap #1 inMap #2

Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points  
correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05  
steps = 56, shift = 7.96, angle = 0.00238 degrees  
  
Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00003026 0.00002609 91.91389849  
0.00003026 1.00000000 -0.00001109 91.89891079  
-0.00002609 0.00001109 1.00000000 91.91922251  
Axis 0.26746273 0.62926682 0.72971704  
Axis point 71695.94102549 1716204.69448452 0.00000000  
Rotation angle (degrees) 0.00237592  
Shift along axis 149.48750038  
  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> volume #2 step 1

> show #!1 models

> color #2 #f5c211ff models

> color #1 white models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.17

> select add #2

2 models selected  

> surface dust #2 size 16.9

> volume #2 level 0.0843

> select subtract #2

Nothing selected  

> volume flip #1

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> hide #!2 models

> show #!2 models

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> show #!1 models

> hide #!3 models

> surface undust #2

> volume #2 level 0.1844

> volume #2 level 0.2

> volume #2 level 0.25

> volume #2 level 0.27

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.3

> volume #2 level 0.35

> view

> view orient

> show #!1 models

> surface undust #1

> volume #1 level 0.2

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

> hide #!1 models

> color radial #2.1 palette
> 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

Surface Color: surface has no bounding box  

[Repeated 2 time(s)]

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> color radial #1.1 palette
> 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

> color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> hide #!1 models

> show #!2 models

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

[Repeated 2 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> select add #2

2 models selected  

> select add #1

4 models selected  

> show #!1 models

> hide #!1 models

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144

> view matrix models
> #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785

> select subtract #1

2 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "rotate selected models"

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> show #!1 models

> hide #!2 models

Surface Color: surface has no bounding box  

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> volume #1 level 0.17

> volume #1 level 0.13

> volume #1 level 0.1

> volume #1 level 0.09

> volume #1 level 0.08

> volume #1 level 0.09

> hide #!1 models

> show #!2 models

> set bgColor white

> set bgColor #ffffff00

> surface dust #2 size 16.9

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> surface undust #1

> volume #2 level 0.3

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.2

> surface dust #2 size 16.9

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key size 0.24000,0.05000

> key size 0.24000,0.04000

> key size 0.24000,0.03000

> key size 0.23000,0.03000

> key size 0.22000,0.03000

> key size 0.21000,0.03000

> key size 0.20000,0.03000

> key pos 0.671038,0.107382

> key pos 0,0.10738

> key pos 0.7000,0.10738

> key pos 0.70000,0.10738

> key pos 0.70000,0.10

> key pos 0.70000,0.10000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> key pos 0.70000,0.11000

> key pos 0.70000,0.10000

> key pos 0.70000,0.09000

> key pos 0.70000,0.08000

> key pos 0.70000,0.07000

> key pos 0.70000,0.06000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> surface dust #2 size 16.9

> select subtract #2

Nothing selected  

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).png" width 1243 height 913
> supersample 3

> volume #2 step 2

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> volume #2 step 1

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> hide #!2 models

> show #!1 models

> select add #1

2 models selected  

Surface Color: surface has no bounding box  

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> ui mousemode right "rotate selected models"

> hide #4 models

> show #4 models

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> volume #1 level 0.08

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png" width 1243 height 913
> supersample 3

> volume #1 step 2

> volume #1 level 0.07

> volume #1 level 0.06

> volume #1 level 0.05

> volume #1 level 0.06

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png" width 1243 height 913
> supersample 3

> surface undust #2

> select add #1

2 models selected  

> surface undust #1

> volume #1 level 0.2

> volume #1 step 1

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> hide #!1 models

> show #!2 models

> volume #2 step 1

> volume #2 level 0.2

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> surface dust #2 size 16.9

> key #0cf0fa:200 blue:235 #9141ac:270 showTool true

> ui mousemode right "color key"

> key fontSize 17

> key fontSize 16

Could not find palette custom at COLOURlovers.com using keyword search  

> ui mousemode right "rotate selected models"

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).tif" width 1243 height 913
> supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step1).tif" width 1243 height 913 supersample 3

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step2).tif" width 1243 height 913 supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"

——— End of log from Mon Apr 14 19:17:23 2025 ———

opened ChimeraX session  

> close #1

> close #3

> ui tool show "Surface Color"

> color radial #2.1 palette 210,#0cf0fa:240,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette
> 160,#ff0000:180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff
> center 304.1,346.73,364.43

> color radial #2.1 palette 120,#00ffff:160,#00ff00:200,#ffff00:240,#ff0000
> center 304.1,346.73,364.43

> color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff
> center 304.1,346.73,364.43

> volume #2 step 1

> volume #2 level 0.2

> color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff
> center 304.1,346.73,364.43

> color radial #2.1 palette 150,#ff0000:200,#f4f735:250,#0000ff center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 150,#ff0000:200,#ffff00:250,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ffff00:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ff7f7f:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ffffff center 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ffffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#ff0000:160,#ffffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#0000ff:160,#ffffff:240,#ff0000 center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#ff0000:220,#ffffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> key red:200 #f4f735:220 blue:240 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/f-fold.tif" width 1243 height 913 supersample 3

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/3-fold.tif" width 1243 height 913 supersample 3

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> view matrix models
> #2,0.93097,-0.36237,0.044589,38.647,0.36152,0.932,0.026031,-224.51,-0.05099,-0.0081145,0.99867,-42.311

> view matrix models
> #2,0.83884,-0.53188,-0.11599,221.43,0.49449,0.83358,-0.24622,-121.6,0.22765,0.14919,0.96225,-215.26

> select subtract #2

Nothing selected  

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/Assymmetric unit.tif" width 1243 height 913 supersample 3

> hide #!2 models

> show #!2 models

> color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center
> 304.1,346.73,364.43

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/Assymmetric unit.tif" width 1243 height 913 supersample 3

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"

——— End of log from Mon Apr 14 19:50:11 2025 ———

opened ChimeraX session  

> surface dust #2 size 16.9

> select add #2

2 models selected  

> surface dust #2 size 16.9

> select subtract #2

Nothing selected  

> surface undust #2

> ui tool show "Surface Color"

> color single #2.1

> hide #4 models

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 24/cryosparc_P108_J158_009_volume_map_sharp.mrc"

Opened cryosparc_P108_J158_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.386, step 2, values float32  

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-32.618,0,1,0,13.707,0,0,1,10.371

> fitmap #1 inMap #2

Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 167700 points  
correlation = 0.5909, correlation about mean = 0.04444, overlap = 2.124e+04  
steps = 108, shift = 15.8, angle = 1.5 degrees  
  
Position of cryosparc_P108_J158_009_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.82826999 0.50750099 0.23751120 -103.66917651  
-0.54459400 0.82886053 0.12809214 292.18437852  
-0.13185677 -0.23544205 0.96290230 229.66009928  
Axis -0.30996736 0.31494153 -0.89706860  
Axis point 455.51638490 408.41445019 0.00000000  
Rotation angle (degrees) 35.90246553  
Shift along axis -81.86580633  
  

> select subtract #1

Nothing selected  

> color #1 white models

> volume #1 level 0.2

> volume #2 level 0.35

> volume #1 step 1

> volume flip #1

Opened cryosparc_P108_J158_009_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 0 atomic models, 3 maps.  

> hide #!1 models

> select add #2

2 models selected  

> select add #3

4 models selected  

> fitmap #2 inMap #3

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J158_009_volume_map_sharp.mrc z flip using 1224990 points  
correlation = 0.4719, correlation about mean = 0.03672, overlap = 9.85e+04  
steps = 116, shift = 1.69, angle = 0.594 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.82440776 -0.55126619 -0.12828656 278.80177895  
0.51577977 0.82504786 -0.23079699 -139.73648527  
0.23307313 0.12410322 0.96450781 -232.57749077  
Axis 0.30046933 -0.30593812 0.90339363  
Axis point 458.01985432 405.41639473 0.00000000  
Rotation angle (degrees) 36.19792378  
Shift along axis -83.58692045  
  

> select subtract #2

2 models selected  

> fitmap #3 inMap #2

Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 2898868 points  
correlation = 0.5655, correlation about mean = 0.08721, overlap = 2.415e+05  
steps = 60, shift = 0.153, angle = 0.119 degrees  
  
Position of cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) relative
to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.82325634 0.51741968 0.23350775 -103.92052940  
-0.55299279 0.82391286 0.12396201 298.82318541  
-0.12824965 -0.23118061 0.96442084 228.12552688  
Axis -0.29985300 0.30543796 -0.90376758  
Axis point 457.46220141 405.63522711 0.00000000  
Rotation angle (degrees) 36.31289551  
Shift along axis -83.73962720  
  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select add #1

2 models selected  

> fitmap #1 inMap #2

Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 2898868 points  
correlation = 0.5676, correlation about mean = 0.08856, overlap = 2.442e+05  
steps = 96, shift = 2.74, angle = 2.89 degrees  
  
Position of cryosparc_P108_J158_009_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.80124001 0.54981568 0.23604484 -108.18277230  
-0.58085609 0.80941657 0.08631926 326.28552381  
-0.14359893 -0.20627052 0.96790073 220.80698867  
Axis -0.23825164 0.30913845 -0.92068973  
Axis point 471.18219773 400.31151980 0.00000000  
Rotation angle (degrees) 37.88184834  
Shift along axis -76.65260251  
  

> select subtract #1

Nothing selected  

> hide #!1 models

> show #!3 models

> select add #3

2 models selected  

> fitmap #3 inMap #2

Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 2898868 points  
correlation = 0.5655, correlation about mean = 0.08723, overlap = 2.415e+05  
steps = 48, shift = 0.0274, angle = 0.00425 degrees  
  
Position of cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) relative
to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.82323369 0.51746639 0.23348408 -103.91850196  
-0.55302628 0.82389895 0.12390503 298.88529905  
-0.12825060 -0.23112562 0.96443389 228.09655392  
Axis -0.29975036 0.30541053 -0.90381089  
Axis point 457.53098412 405.61244531 0.00000000  
Rotation angle (degrees) 36.31403235  
Shift along axis -83.72382245  
  

> select subtract #3

Nothing selected  

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> volume #1 level 0.17

> volume #3 level 0.17

> show #!2 models

> hide #!3 models

> show #!1 models

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.99805,0.046255,0.041868,32.884,-0.044429,0.99806,-0.04355,17.666,-0.043802,0.041605,0.99817,-81.943

> view matrix models
> #1,0.99805,0.046255,0.041868,-69.1,-0.044429,0.99806,-0.04355,39.541,-0.043802,0.041605,0.99817,47.309

> view matrix models
> #1,0.99805,0.046255,0.041868,-73.936,-0.044429,0.99806,-0.04355,48.258,-0.043802,0.041605,0.99817,58.928

> view matrix models
> #1,0.99805,0.046255,0.041868,-101.06,-0.044429,0.99806,-0.04355,35.094,-0.043802,0.041605,0.99817,89.448

> volume #1 step 2

> volume #3 step 2

> select subtract #1

Nothing selected  

> select add #1

2 models selected  

> view matrix models
> #1,0.99805,0.046255,0.041868,-130.74,-0.044429,0.99806,-0.04355,35.361,-0.043802,0.041605,0.99817,149.68

> view matrix models
> #1,0.99805,0.046255,0.041868,-69.833,-0.044429,0.99806,-0.04355,44.93,-0.043802,0.041605,0.99817,9.4144

> view matrix models
> #1,0.99805,0.046255,0.041868,-62.46,-0.044429,0.99806,-0.04355,29.075,-0.043802,0.041605,0.99817,20.457

> view matrix models
> #1,0.99805,0.046255,0.041868,-70.431,-0.044429,0.99806,-0.04355,38.526,-0.043802,0.041605,0.99817,21.185

> view matrix models
> #1,0.99805,0.046255,0.041868,-67.43,-0.044429,0.99806,-0.04355,36.724,-0.043802,0.041605,0.99817,18.018

> fitmap #1 inMap #2

Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 483066 points  
correlation = 0.5662, correlation about mean = 0.108, overlap = 3.368e+04  
steps = 96, shift = 5.09, angle = 0.678 degrees  
  
Position of cryosparc_P108_J158_009_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.80244809 0.54431606 0.24453441 -109.89788491  
-0.57639398 0.81308990 0.08157691 324.68718543  
-0.15442484 -0.20640940 0.96620294 226.16867801  
Axis -0.23528924 0.32595585 -0.91563735  
Axis point 474.10721900 406.56300724 0.00000000  
Rotation angle (degrees) 37.73306737  
Shift along axis -75.39701273  
  

> select subtract #1

Nothing selected  

> select add #2

2 models selected  

> hide #!1 models

> select subtract #2

Nothing selected  

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> show #!2 models

> select add #3

2 models selected  

> fitmap #3 inMap #2

Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 483066 points  
correlation = 0.5636, correlation about mean = 0.105, overlap = 3.332e+04  
steps = 80, shift = 1.55, angle = 0.291 degrees  
  
Position of cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) relative
to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.82193668 0.51916630 0.23427858 -103.85961463  
-0.55425965 0.82379183 0.11900950 301.09583720  
-0.13121106 -0.22766943 0.96485765 229.25518153  
Axis -0.29237006 0.30823398 -0.90526878  
Axis point 461.16745780 405.73160388 0.00000000  
Rotation angle (degrees) 36.36143070  
Shift along axis -84.36414673  
  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!1 models

> select add #1

2 models selected  

> fitmap #1 inMap #2

Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 483066 points  
correlation = 0.5662, correlation about mean = 0.1079, overlap = 3.368e+04  
steps = 64, shift = 0.00365, angle = 0.00186 degrees  
  
Position of cryosparc_P108_J158_009_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.80245947 0.54429775 0.24453784 -109.89308018  
-0.57637330 0.81310636 0.08155894 324.68091838  
-0.15444292 -0.20639283 0.96620359 226.16847760  
Axis -0.23526811 0.32598323 -0.91563303  
Axis point 474.12689577 406.56019298 0.00000000  
Rotation angle (degrees) 37.73173349  
Shift along axis -75.39245955  
  

> select subtract #1

Nothing selected  

> volume #2 step 2

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!2 models

> show #!1 models

> hide #!3 models

> set bgColor black

> show #!2 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> volume #2 step 1

> volume #1 step 1

> volume #3 step 1

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> select add #1

2 models selected  

> show #!1 models

> hide #!1 models

> select subtract #1

Nothing selected  

> show #!3 models

> select add #3

2 models selected  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!2 models

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.3,346.69,362.54

> volume #1 level 0.08

> volume #1 level 0.02

> volume #1 level 0.2

> select add #1

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.95191,0.09858,0.29008,496.36,0.24685,0.80761,0.53557,-195.49,-0.18148,0.58142,-0.7931,496.6

> view matrix models
> #1,-0.77579,-0.24624,-0.58097,850.91,-0.19351,0.96919,-0.1524,134.16,0.60059,-0.0058085,-0.79953,432.36

> view matrix models
> #1,-0.97041,-0.063267,-0.23305,736.24,-0.17223,0.85779,0.48429,-52.215,0.16927,0.51009,-0.8433,418.44

> view matrix models
> #1,-0.74657,-0.28223,-0.60247,860.55,-0.25742,0.95757,-0.12959,152.14,0.61348,0.058338,-0.78755,402

> view matrix models
> #1,0.53758,-0.51729,-0.66589,524.44,-0.36157,0.572,-0.73626,526,0.76175,0.63657,0.12046,-155.36

> view matrix models
> #1,0.90405,0.13598,0.40521,-188.52,0.32873,0.38469,-0.86253,397.54,-0.27317,0.91298,0.30307,41.023

> view matrix models
> #1,0.26478,-0.065154,0.9621,-91.843,-0.18904,0.97485,0.11804,38.487,-0.9456,-0.21313,0.24581,673.84

> view matrix models
> #1,0.15833,-0.82302,0.5455,344.94,-0.96164,-0.0031878,0.27431,582.15,-0.22402,-0.568,-0.79195,902.66

> view matrix models
> #1,0.1655,-0.7938,0.58523,318.98,-0.97218,-0.23105,-0.038469,770.1,0.16575,-0.56258,-0.80995,774.04

> view matrix models
> #1,0.33756,-0.73388,0.58946,238.44,-0.24501,-0.67314,-0.69775,897.7,0.90886,0.091111,-0.40703,160.35

> view matrix models
> #1,0.36854,-0.60045,0.70967,141.39,0.74671,-0.26351,-0.61073,390.18,0.55372,0.755,0.35125,-203.5

> view matrix models
> #1,0.45752,-0.30661,0.83466,-31.776,0.59427,-0.59281,-0.54352,531.53,0.66145,0.74469,-0.089016,-86.59

> view matrix models
> #1,0.78637,-0.043221,0.61625,-159.24,-0.36796,-0.83405,0.41104,616.41,0.49622,-0.54999,-0.67178,609.94

> view matrix models
> #1,0.15045,-0.032599,0.98808,-72.814,-0.58249,-0.81047,0.061951,800.56,0.79879,-0.58487,-0.14092,337.65

> view matrix models
> #1,0.68695,-0.048745,0.72507,-160.57,-0.47958,-0.78003,0.40193,639.16,0.54598,-0.62384,-0.55922,579.78

> view matrix models
> #1,0.99307,-0.11115,-0.03828,16.624,-0.06368,-0.78235,0.61957,423.92,-0.098812,-0.61284,-0.78401,872.54

> view matrix models
> #1,0.91661,-0.081071,0.39148,-114.11,-0.28859,-0.81185,0.50757,548.86,0.27668,-0.57822,-0.76754,727.09

> show #!2 models

> select subtract #1

Nothing selected  

> hide #!1 models

> show #!3 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> select add #2

2 models selected  

> select add #3

4 models selected  

> fitmap #2 inMap #3

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J158_009_volume_map_sharp.mrc z flip using 1224990 points  
correlation = 0.4719, correlation about mean = 0.03672, overlap = 9.85e+04  
steps = 64, shift = 1.64, angle = 0.349 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
0.82440332 -0.55125818 -0.12834945 278.83507123  
0.51574920 0.82505024 -0.23085680 -139.69053927  
0.23315644 0.12412299 0.96448513 -232.63085066  
Axis 0.30052811 -0.30605314 0.90333511  
Axis point 458.00533281 405.49590281 0.00000000  
Rotation angle (degrees) 36.19912394  
Shift along axis -83.59311116  
  

> select subtract #3

2 models selected  

> select subtract #2

Nothing selected  

> hide #!3 models

> hide #!2 models

> show #!3 models

> volume #3 level 0.2

> show #!2 models

> hide #!3 models

> show #!3 models

> select add #3

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.99962,0.015323,0.023126,108.14,-0.014942,0.99975,-0.016573,-74.72,-0.023374,0.016222,0.9996,23.791

> view matrix models
> #3,0.99962,0.015323,0.023126,-119.77,-0.014942,0.99975,-0.016573,56.77,-0.023374,0.016222,0.9996,28.703

> hide #!2 models

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!3 models

> show #!2 models

> select add #3

2 models selected  

> view matrix models
> #3,0.99962,0.015323,0.023126,-18.743,-0.014942,0.99975,-0.016573,-1.8357,-0.023374,0.016222,0.9996,32.646

> view matrix models
> #3,0.99962,0.015323,0.023126,-123.99,-0.014942,0.99975,-0.016573,58.473,-0.023374,0.016222,0.9996,42.804

> view matrix models
> #3,0.99962,0.015323,0.023126,-231.56,-0.014942,0.99975,-0.016573,122.37,-0.023374,0.016222,0.9996,10.005

> view matrix models
> #3,0.99962,0.015323,0.023126,-64.602,-0.014942,0.99975,-0.016573,25.245,-0.023374,0.016222,0.9996,21.704

> view matrix models
> #3,0.99962,0.015323,0.023126,-51.943,-0.014942,0.99975,-0.016573,17.659,-0.023374,0.016222,0.9996,26.845

> view matrix models
> #3,0.99962,0.015323,0.023126,-31.446,-0.014942,0.99975,-0.016573,5.6759,-0.023374,0.016222,0.9996,29.429

> view matrix models
> #3,0.99962,0.015323,0.023126,-40.045,-0.014942,0.99975,-0.016573,7.1083,-0.023374,0.016222,0.9996,29.415

> view matrix models
> #3,0.99962,0.015323,0.023126,-35.996,-0.014942,0.99975,-0.016573,6.2978,-0.023374,0.016222,0.9996,30.791

> fitmap #3 inMap #2

Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 2898868 points  
correlation = 0.5666, correlation about mean = 0.08887, overlap = 2.429e+05  
steps = 136, shift = 16.9, angle = 2.9 degrees  
  
Position of cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) relative
to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.80500069 0.55278763 0.21540594 -103.09258307  
-0.58050912 0.80883882 0.09374930 323.28594379  
-0.12240524 -0.20051336 0.97201407 212.67451568  
Axis -0.24146930 0.27720483 -0.92997315  
Axis point 468.81479847 388.24792077 0.00000000  
Rotation angle (degrees) 37.54012796  
Shift along axis -83.27147151  
  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!3 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!1 models

> hide #!2 models

> volume #1 level 0.08

> volume #1 level 0.2

> hide #!1 models

> show #!2 models

> select add #2

2 models selected  

> close #2

> close #3

> show #!1 models

> ui mousemode right select

> select #1

2 models selected  
Drag select of 1 cryosparc_P108_J158_009_volume_map_sharp.mrc  
[Repeated 1 time(s)]

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> volume #1 level 0.08

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.3,346.69,362.54

> show #4 models

> hide #4 models

> key cyan:200 blue:235 #9141ac:270 showTool true

> ui mousemode right "color key"

> key delete

> ui mousemode right select

> key cyan:200 blue:235 #9141ac:270 showTool true

> ui mousemode right "color key"

> key pos 0.70000,0.07000

> key pos 0.70000,0.06000

> key pos 0.70000,0.05000

> key pos 0.70000,0.06000

> key size 0.24000,0.05000

> key size 0.23000,0.05000

> key size 0.22000,0.05000

> key size 0.21000,0.05000

> key size 0.20000,0.05000

> key size 0.20000,0.04000

> key size 0.20000,0.03000

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> ui mousemode right select

> hide #2 models

> show #2 models

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> set bgColor white

> hide #2 models

> show #2 models

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.07

> volume #1 level 0.06

> volume #1 level 0.05

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1).tif" width 1243 height 913
> supersample 3

> volume #1 level 0.08

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1)2.tif" width 1243 height 913
> supersample 3

> volume #1 step 2

> volume #1 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step2).tif" width 1243 height 913
> supersample 3

> volume #1 level 0.03

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step2)2.tif" width 1243 height 913
> supersample 3

> volume #1 step 1

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1)3.tif" width 1243 height 913
> supersample 3

> volume #1 level 0.2

> volume #1 level 0.08

> volume #1 level 0.05

> volume #1 level 0.08

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1_3fold).tif" width 1243 height 913
> supersample 3

> volume #1 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1_3fold)2.tif" width 1243 height 913
> supersample 3

> volume #1 level 0.2

> unhide dust #1

Unknown command: unhide dust #1  

> help help:user

> surface undust #1

> volume flip #1

Opened cryosparc_P108_J158_009_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> color radial #3.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 303.78,346.02,363.56

> volume #3 level 0.03

> volume #3 level 0.08

> volume #3 level 0.2

> volume #3 level 0.08

> surface dust #3 size 13.3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1_3fold)_map flipped.tif" width 1207
> height 913 supersample 3

> volume #3 level 0.05

> volume #3 level 0.03

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1_3fold)_map flipped2.tif" width 1207
> height 913 supersample 3

> volume #3 level 0.2

> surface undust #3

> surface undust #1

> show #!1 models

> color single #3.1

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!1 models

> show #!1 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab24/J158_009 DV2_N15_Fab24 chimerax session.cxs"

> hide #!1 models

> hide #2 models

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab13/J123
> DV2_Fab13 chimerax session.cxs"

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at level 0.05, step 2, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  
  
Log from Mon Apr 14 20:39:34 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> set bgColor #ffffff00

Log from Mon Apr 14 19:17:23 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb
> format pdb

current_fittingE7kv8_DENV2Fab13_20250330.pdb title:  
Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more
info...]  
  
Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
Chain | Description  
A B C | envelope protein E  
a b c | matrix protein M  
  
Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl
dihydrogen phosphate  
6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-
propan-2-yl] (~{Z})-octadec-9-enoate  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 13/cryosparc_P108_J123_011_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32  

> volume #1 level 0.17

> volume #1 level 0.13

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.15

> volume #1 level 0.16

> volume #1 level 0.17

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> hide #!2 models

> volume #1

> ui tool show "Surface Color"

> color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center
> 340.99,340.99,340.99

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

[Repeated 1 time(s)]

> volume #1 level 0.13

> volume #1 level 0.12

> volume #1 level 0.11

> volume #1 level 0.1

> volume #1 level 0.0843

> volume #1 step 1

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45

> view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653

> view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468

> ui mousemode right "translate selected models"

> select subtract #2

Nothing selected  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> select add #2

2 models selected  

> view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383

> view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477

> view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62

> view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41

> view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901

> view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853

> view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068

> select add #1

4 models selected  

> fitmap #1 inMap #2

Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points  
correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05  
steps = 56, shift = 7.96, angle = 0.00238 degrees  
  
Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00003026 0.00002609 91.91389849  
0.00003026 1.00000000 -0.00001109 91.89891079  
-0.00002609 0.00001109 1.00000000 91.91922251  
Axis 0.26746273 0.62926682 0.72971704  
Axis point 71695.94102549 1716204.69448452 0.00000000  
Rotation angle (degrees) 0.00237592  
Shift along axis 149.48750038  
  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> volume #2 step 1

> show #!1 models

> color #2 #f5c211ff models

> color #1 white models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.17

> select add #2

2 models selected  

> surface dust #2 size 16.9

> volume #2 level 0.0843

> select subtract #2

Nothing selected  

> volume flip #1

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> hide #!2 models

> show #!2 models

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> show #!1 models

> hide #!3 models

> surface undust #2

> volume #2 level 0.1844

> volume #2 level 0.2

> volume #2 level 0.25

> volume #2 level 0.27

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.3

> volume #2 level 0.35

> view

> view orient

> show #!1 models

> surface undust #1

> volume #1 level 0.2

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

> hide #!1 models

> color radial #2.1 palette
> 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

Surface Color: surface has no bounding box  

[Repeated 2 time(s)]

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> color radial #1.1 palette
> 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

> color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> hide #!1 models

> show #!2 models

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

[Repeated 2 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> select add #2

2 models selected  

> select add #1

4 models selected  

> show #!1 models

> hide #!1 models

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144

> view matrix models
> #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785

> select subtract #1

2 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "rotate selected models"

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> show #!1 models

> hide #!2 models

Surface Color: surface has no bounding box  

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> volume #1 level 0.17

> volume #1 level 0.13

> volume #1 level 0.1

> volume #1 level 0.09

> volume #1 level 0.08

> volume #1 level 0.09

> hide #!1 models

> show #!2 models

> set bgColor white

> set bgColor #ffffff00

> surface dust #2 size 16.9

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> surface undust #1

> volume #2 level 0.3

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.2

> surface dust #2 size 16.9

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key size 0.24000,0.05000

> key size 0.24000,0.04000

> key size 0.24000,0.03000

> key size 0.23000,0.03000

> key size 0.22000,0.03000

> key size 0.21000,0.03000

> key size 0.20000,0.03000

> key pos 0.671038,0.107382

> key pos 0,0.10738

> key pos 0.7000,0.10738

> key pos 0.70000,0.10738

> key pos 0.70000,0.10

> key pos 0.70000,0.10000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> key pos 0.70000,0.11000

> key pos 0.70000,0.10000

> key pos 0.70000,0.09000

> key pos 0.70000,0.08000

> key pos 0.70000,0.07000

> key pos 0.70000,0.06000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> surface dust #2 size 16.9

> select subtract #2

Nothing selected  

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).png" width 1243 height 913
> supersample 3

> volume #2 step 2

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> volume #2 step 1

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> hide #!2 models

> show #!1 models

> select add #1

2 models selected  

Surface Color: surface has no bounding box  

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> ui mousemode right "rotate selected models"

> hide #4 models

> show #4 models

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> volume #1 level 0.08

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png" width 1243 height 913
> supersample 3

> volume #1 step 2

> volume #1 level 0.07

> volume #1 level 0.06

> volume #1 level 0.05

> volume #1 level 0.06

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png" width 1243 height 913
> supersample 3

> surface undust #2

> select add #1

2 models selected  

> surface undust #1

> volume #1 level 0.2

> volume #1 step 1

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> hide #!1 models

> show #!2 models

> volume #2 step 1

> volume #2 level 0.2

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> surface dust #2 size 16.9

> key #0cf0fa:200 blue:235 #9141ac:270 showTool true

> ui mousemode right "color key"

> key fontSize 17

> key fontSize 16

Could not find palette custom at COLOURlovers.com using keyword search  

> ui mousemode right "rotate selected models"

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).tif" width 1243 height 913
> supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step1).tif" width 1243 height 913 supersample 3

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step2).tif" width 1243 height 913 supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"

——— End of log from Mon Apr 14 19:17:23 2025 ———

opened ChimeraX session  

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> select add #1

2 models selected  

> close #1

> hide #4 models

> show #!3 models

> select add #3

2 models selected  

> close #3

> show #!2 models

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32  

> volume #2 level 0.35

> volume #2 step 1

> volume #1 level 0.2

> volume #1 step 1

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-48.634,0,1,0,1.6656,0,0,1,33.287

> view matrix models #1,1,0,0,13.61,0,1,0,6.7723,0,0,1,18.375

> view matrix models #1,1,0,0,13.668,0,1,0,6.639,0,0,1,17.833

> view matrix models #1,1,0,0,-17.789,0,1,0,2.819,0,0,1,20.629

> view matrix models #1,1,0,0,-39.187,0,1,0,0.34575,0,0,1,23.009

> select add #2

4 models selected  

> select subtract #2

2 models selected  

> view matrix models #1,1,0,0,-34.176,0,1,0,3.1709,0,0,1,20.524

> select add #2

4 models selected  

> fitmap #2 inMap #1

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J123_011_volume_map_sharp.mrc using 1224990 points  
correlation = 0.5927, correlation about mean = 0.05969, overlap = 8.84e+04  
steps = 124, shift = 4.73, angle = 4.44 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J123_011_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000934 -0.00000606 -91.91551273  
-0.00000934 1.00000000 -0.00001788 -91.90278947  
0.00000606 0.00001788 1.00000000 -91.91231745  
Axis 0.84889746 -0.28787388 -0.44328516  
Axis point 0.00000000 5408246.84963320 -5313748.61359478  
Rotation angle (degrees) 0.00120694  
Shift along axis -10.82706671  
  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> hide #!2 models

> volume flip #1

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> show #!2 models

> fitmap #2 inMap #3

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points  
correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05  
steps = 28, shift = 1.34, angle = 0.000137 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000760 -0.00000484 -91.89861891  
-0.00000760 1.00000000 -0.00001899 -91.89997565  
0.00000483 0.00001899 1.00000000 -93.24973991  
Axis 0.90349284 -0.23008647 -0.36160876  
Axis point 0.00000000 5447828.04621494 -5181752.87000347  
Rotation angle (degrees) 0.00120402  
Shift along axis -28.16488010  
  

> select add #2

2 models selected  

> select add #3

4 models selected  

> fitmap #2 inMap #3

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points  
correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05  
steps = 24, shift = 0.0063, angle = 0.000111 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000613 -0.00000381 -91.89742078  
-0.00000613 1.00000000 -0.00001975 -91.89877679  
0.00000381 0.00001975 1.00000000 -93.25566971  
Axis 0.93921386 -0.18128033 -0.29157292  
Axis point 0.00000000 5347267.65743666 -5041635.74047945  
Rotation angle (degrees) 0.00120513  
Shift along axis -42.46106316  
  

> select subtract #2

2 models selected  

> select subtract #3

Nothing selected  

> ui tool show "Surface Color"

Surface Color: surface has no bounding box  

> hide #!2 models

> hide #!3 models

> show #!2 models

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.83,344.16,360.18

> hide #!2 models

> show #!3 models

> color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.82,344.16,360.18

[Repeated 1 time(s)]

> set bgColor black

> set bgColor transparent

> volume #1 level 0.08

> hide #!3 models

> show #!3 models

> close #1

> volume #2 level 0.2

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> volume #3 level 0.08

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> color single #3.1

> color single #2.1

> color #3 white models

> show #!3 models

> volume #2 level 0.1

> volume #2 level 0.2

> color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.82,344.16,360.18

Drag select of 3 cryosparc_P108_J123_011_volume_map_sharp.mrc z flip  

> hide #!3 models

> show #!3 models

> select subtract #3

Nothing selected  

> set bgColor white

> set bgColor #ffffff00

> select add #3

2 models selected  

> surface dust #3 size 13.3

> select subtract #3

Nothing selected  

> show #4 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1).tif" width 1273 height 945
> supersample 3

> volume #3 step 2

> volume #3 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2).tif" width 1273 height 945
> supersample 3

> hide #!3 models

> show #!2 models

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.83,344.16,360.18

> show #!3 models

> hide #!2 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold).tif" width 1273 height 945
> supersample 3

> volume #3 level 0.08

> volume #3 step 1

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold).tif" width 1273 height 945
> supersample 3

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!3 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold)2.tif" width 1273 height 945
> supersample 3

> volume #3 step 2

> volume #3 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold)2.tif" width 1273 height 945
> supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"

——— End of log from Mon Apr 14 20:39:34 2025 ———

opened ChimeraX session  

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab13/J123
> DV2_Fab13 chimerax session.cxs" format session

Error opening map "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs": File J123 DV2_Fab13
chimerax session.cxs, format mrc  
MRC header value nsymbt (912209460) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at level 0.05, step 2, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  
  
Log from Mon Apr 14 20:39:34 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> set bgColor #ffffff00

Log from Mon Apr 14 19:17:23 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb
> format pdb

current_fittingE7kv8_DENV2Fab13_20250330.pdb title:  
Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more
info...]  
  
Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
Chain | Description  
A B C | envelope protein E  
a b c | matrix protein M  
  
Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl
dihydrogen phosphate  
6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-
propan-2-yl] (~{Z})-octadec-9-enoate  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 13/cryosparc_P108_J123_011_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32  

> volume #1 level 0.17

> volume #1 level 0.13

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.15

> volume #1 level 0.16

> volume #1 level 0.17

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> hide #!2 models

> volume #1

> ui tool show "Surface Color"

> color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center
> 340.99,340.99,340.99

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

[Repeated 1 time(s)]

> volume #1 level 0.13

> volume #1 level 0.12

> volume #1 level 0.11

> volume #1 level 0.1

> volume #1 level 0.0843

> volume #1 step 1

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45

> view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653

> view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468

> ui mousemode right "translate selected models"

> select subtract #2

Nothing selected  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> select add #2

2 models selected  

> view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383

> view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477

> view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62

> view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41

> view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901

> view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853

> view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068

> select add #1

4 models selected  

> fitmap #1 inMap #2

Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points  
correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05  
steps = 56, shift = 7.96, angle = 0.00238 degrees  
  
Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00003026 0.00002609 91.91389849  
0.00003026 1.00000000 -0.00001109 91.89891079  
-0.00002609 0.00001109 1.00000000 91.91922251  
Axis 0.26746273 0.62926682 0.72971704  
Axis point 71695.94102549 1716204.69448452 0.00000000  
Rotation angle (degrees) 0.00237592  
Shift along axis 149.48750038  
  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> volume #2 step 1

> show #!1 models

> color #2 #f5c211ff models

> color #1 white models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.17

> select add #2

2 models selected  

> surface dust #2 size 16.9

> volume #2 level 0.0843

> select subtract #2

Nothing selected  

> volume flip #1

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> hide #!2 models

> show #!2 models

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> show #!1 models

> hide #!3 models

> surface undust #2

> volume #2 level 0.1844

> volume #2 level 0.2

> volume #2 level 0.25

> volume #2 level 0.27

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.3

> volume #2 level 0.35

> view

> view orient

> show #!1 models

> surface undust #1

> volume #1 level 0.2

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

> hide #!1 models

> color radial #2.1 palette
> 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

Surface Color: surface has no bounding box  

[Repeated 2 time(s)]

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> color radial #1.1 palette
> 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

> color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> hide #!1 models

> show #!2 models

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

[Repeated 2 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> select add #2

2 models selected  

> select add #1

4 models selected  

> show #!1 models

> hide #!1 models

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144

> view matrix models
> #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785

> select subtract #1

2 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "rotate selected models"

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> show #!1 models

> hide #!2 models

Surface Color: surface has no bounding box  

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> volume #1 level 0.17

> volume #1 level 0.13

> volume #1 level 0.1

> volume #1 level 0.09

> volume #1 level 0.08

> volume #1 level 0.09

> hide #!1 models

> show #!2 models

> set bgColor white

> set bgColor #ffffff00

> surface dust #2 size 16.9

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> surface undust #1

> volume #2 level 0.3

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.2

> surface dust #2 size 16.9

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key size 0.24000,0.05000

> key size 0.24000,0.04000

> key size 0.24000,0.03000

> key size 0.23000,0.03000

> key size 0.22000,0.03000

> key size 0.21000,0.03000

> key size 0.20000,0.03000

> key pos 0.671038,0.107382

> key pos 0,0.10738

> key pos 0.7000,0.10738

> key pos 0.70000,0.10738

> key pos 0.70000,0.10

> key pos 0.70000,0.10000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> key pos 0.70000,0.11000

> key pos 0.70000,0.10000

> key pos 0.70000,0.09000

> key pos 0.70000,0.08000

> key pos 0.70000,0.07000

> key pos 0.70000,0.06000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> surface dust #2 size 16.9

> select subtract #2

Nothing selected  

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).png" width 1243 height 913
> supersample 3

> volume #2 step 2

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> volume #2 step 1

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> hide #!2 models

> show #!1 models

> select add #1

2 models selected  

Surface Color: surface has no bounding box  

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> ui mousemode right "rotate selected models"

> hide #4 models

> show #4 models

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> volume #1 level 0.08

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png" width 1243 height 913
> supersample 3

> volume #1 step 2

> volume #1 level 0.07

> volume #1 level 0.06

> volume #1 level 0.05

> volume #1 level 0.06

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png" width 1243 height 913
> supersample 3

> surface undust #2

> select add #1

2 models selected  

> surface undust #1

> volume #1 level 0.2

> volume #1 step 1

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> hide #!1 models

> show #!2 models

> volume #2 step 1

> volume #2 level 0.2

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> surface dust #2 size 16.9

> key #0cf0fa:200 blue:235 #9141ac:270 showTool true

> ui mousemode right "color key"

> key fontSize 17

> key fontSize 16

Could not find palette custom at COLOURlovers.com using keyword search  

> ui mousemode right "rotate selected models"

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).tif" width 1243 height 913
> supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step1).tif" width 1243 height 913 supersample 3

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step2).tif" width 1243 height 913 supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"

——— End of log from Mon Apr 14 19:17:23 2025 ———

opened ChimeraX session  

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> select add #1

2 models selected  

> close #1

> hide #4 models

> show #!3 models

> select add #3

2 models selected  

> close #3

> show #!2 models

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32  

> volume #2 level 0.35

> volume #2 step 1

> volume #1 level 0.2

> volume #1 step 1

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-48.634,0,1,0,1.6656,0,0,1,33.287

> view matrix models #1,1,0,0,13.61,0,1,0,6.7723,0,0,1,18.375

> view matrix models #1,1,0,0,13.668,0,1,0,6.639,0,0,1,17.833

> view matrix models #1,1,0,0,-17.789,0,1,0,2.819,0,0,1,20.629

> view matrix models #1,1,0,0,-39.187,0,1,0,0.34575,0,0,1,23.009

> select add #2

4 models selected  

> select subtract #2

2 models selected  

> view matrix models #1,1,0,0,-34.176,0,1,0,3.1709,0,0,1,20.524

> select add #2

4 models selected  

> fitmap #2 inMap #1

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J123_011_volume_map_sharp.mrc using 1224990 points  
correlation = 0.5927, correlation about mean = 0.05969, overlap = 8.84e+04  
steps = 124, shift = 4.73, angle = 4.44 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J123_011_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000934 -0.00000606 -91.91551273  
-0.00000934 1.00000000 -0.00001788 -91.90278947  
0.00000606 0.00001788 1.00000000 -91.91231745  
Axis 0.84889746 -0.28787388 -0.44328516  
Axis point 0.00000000 5408246.84963320 -5313748.61359478  
Rotation angle (degrees) 0.00120694  
Shift along axis -10.82706671  
  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> hide #!2 models

> volume flip #1

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> show #!2 models

> fitmap #2 inMap #3

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points  
correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05  
steps = 28, shift = 1.34, angle = 0.000137 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000760 -0.00000484 -91.89861891  
-0.00000760 1.00000000 -0.00001899 -91.89997565  
0.00000483 0.00001899 1.00000000 -93.24973991  
Axis 0.90349284 -0.23008647 -0.36160876  
Axis point 0.00000000 5447828.04621494 -5181752.87000347  
Rotation angle (degrees) 0.00120402  
Shift along axis -28.16488010  
  

> select add #2

2 models selected  

> select add #3

4 models selected  

> fitmap #2 inMap #3

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points  
correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05  
steps = 24, shift = 0.0063, angle = 0.000111 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000613 -0.00000381 -91.89742078  
-0.00000613 1.00000000 -0.00001975 -91.89877679  
0.00000381 0.00001975 1.00000000 -93.25566971  
Axis 0.93921386 -0.18128033 -0.29157292  
Axis point 0.00000000 5347267.65743666 -5041635.74047945  
Rotation angle (degrees) 0.00120513  
Shift along axis -42.46106316  
  

> select subtract #2

2 models selected  

> select subtract #3

Nothing selected  

> ui tool show "Surface Color"

Surface Color: surface has no bounding box  

> hide #!2 models

> hide #!3 models

> show #!2 models

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.83,344.16,360.18

> hide #!2 models

> show #!3 models

> color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.82,344.16,360.18

[Repeated 1 time(s)]

> set bgColor black

> set bgColor transparent

> volume #1 level 0.08

> hide #!3 models

> show #!3 models

> close #1

> volume #2 level 0.2

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> volume #3 level 0.08

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> color single #3.1

> color single #2.1

> color #3 white models

> show #!3 models

> volume #2 level 0.1

> volume #2 level 0.2

> color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.82,344.16,360.18

Drag select of 3 cryosparc_P108_J123_011_volume_map_sharp.mrc z flip  

> hide #!3 models

> show #!3 models

> select subtract #3

Nothing selected  

> set bgColor white

> set bgColor #ffffff00

> select add #3

2 models selected  

> surface dust #3 size 13.3

> select subtract #3

Nothing selected  

> show #4 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1).tif" width 1273 height 945
> supersample 3

> volume #3 step 2

> volume #3 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2).tif" width 1273 height 945
> supersample 3

> hide #!3 models

> show #!2 models

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.83,344.16,360.18

> show #!3 models

> hide #!2 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold).tif" width 1273 height 945
> supersample 3

> volume #3 level 0.08

> volume #3 step 1

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold).tif" width 1273 height 945
> supersample 3

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!3 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold)2.tif" width 1273 height 945
> supersample 3

> volume #3 step 2

> volume #3 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold)2.tif" width 1273 height 945
> supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"

——— End of log from Mon Apr 14 20:39:34 2025 ———

opened ChimeraX session  

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab13/J123
> DV2_Fab13 chimerax session.cxs" format session

Error opening map "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs": File J123 DV2_Fab13
chimerax session.cxs, format mrc  
MRC header value nsymbt (912209460) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at level 0.05, step 2, values float32  
Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  
  
Log from Mon Apr 14 20:39:34 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> set bgColor #ffffff00

Log from Mon Apr 14 19:17:23 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb
> format pdb

current_fittingE7kv8_DENV2Fab13_20250330.pdb title:  
Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more
info...]  
  
Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
Chain | Description  
A B C | envelope protein E  
a b c | matrix protein M  
  
Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl
dihydrogen phosphate  
6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-
propan-2-yl] (~{Z})-octadec-9-enoate  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 13/cryosparc_P108_J123_011_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32  

> volume #1 level 0.17

> volume #1 level 0.13

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.15

> volume #1 level 0.16

> volume #1 level 0.17

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> hide #!2 models

> volume #1

> ui tool show "Surface Color"

> color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center
> 340.99,340.99,340.99

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

[Repeated 1 time(s)]

> volume #1 level 0.13

> volume #1 level 0.12

> volume #1 level 0.11

> volume #1 level 0.1

> volume #1 level 0.0843

> volume #1 step 1

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45

> view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653

> view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468

> ui mousemode right "translate selected models"

> select subtract #2

Nothing selected  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> select add #2

2 models selected  

> view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383

> view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477

> view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62

> view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41

> view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901

> view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853

> view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068

> select add #1

4 models selected  

> fitmap #1 inMap #2

Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points  
correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05  
steps = 56, shift = 7.96, angle = 0.00238 degrees  
  
Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00003026 0.00002609 91.91389849  
0.00003026 1.00000000 -0.00001109 91.89891079  
-0.00002609 0.00001109 1.00000000 91.91922251  
Axis 0.26746273 0.62926682 0.72971704  
Axis point 71695.94102549 1716204.69448452 0.00000000  
Rotation angle (degrees) 0.00237592  
Shift along axis 149.48750038  
  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> volume #2 step 1

> show #!1 models

> color #2 #f5c211ff models

> color #1 white models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.17

> select add #2

2 models selected  

> surface dust #2 size 16.9

> volume #2 level 0.0843

> select subtract #2

Nothing selected  

> volume flip #1

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> hide #!2 models

> show #!2 models

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> show #!1 models

> hide #!3 models

> surface undust #2

> volume #2 level 0.1844

> volume #2 level 0.2

> volume #2 level 0.25

> volume #2 level 0.27

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.3

> volume #2 level 0.35

> view

> view orient

> show #!1 models

> surface undust #1

> volume #1 level 0.2

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

> hide #!1 models

> color radial #2.1 palette
> 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

Surface Color: surface has no bounding box  

[Repeated 2 time(s)]

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> color radial #1.1 palette
> 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

> color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> hide #!1 models

> show #!2 models

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

[Repeated 2 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> select add #2

2 models selected  

> select add #1

4 models selected  

> show #!1 models

> hide #!1 models

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144

> view matrix models
> #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785

> select subtract #1

2 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "rotate selected models"

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> show #!1 models

> hide #!2 models

Surface Color: surface has no bounding box  

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> volume #1 level 0.17

> volume #1 level 0.13

> volume #1 level 0.1

> volume #1 level 0.09

> volume #1 level 0.08

> volume #1 level 0.09

> hide #!1 models

> show #!2 models

> set bgColor white

> set bgColor #ffffff00

> surface dust #2 size 16.9

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> surface undust #1

> volume #2 level 0.3

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.2

> surface dust #2 size 16.9

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key size 0.24000,0.05000

> key size 0.24000,0.04000

> key size 0.24000,0.03000

> key size 0.23000,0.03000

> key size 0.22000,0.03000

> key size 0.21000,0.03000

> key size 0.20000,0.03000

> key pos 0.671038,0.107382

> key pos 0,0.10738

> key pos 0.7000,0.10738

> key pos 0.70000,0.10738

> key pos 0.70000,0.10

> key pos 0.70000,0.10000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> key pos 0.70000,0.11000

> key pos 0.70000,0.10000

> key pos 0.70000,0.09000

> key pos 0.70000,0.08000

> key pos 0.70000,0.07000

> key pos 0.70000,0.06000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> surface dust #2 size 16.9

> select subtract #2

Nothing selected  

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).png" width 1243 height 913
> supersample 3

> volume #2 step 2

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> volume #2 step 1

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> hide #!2 models

> show #!1 models

> select add #1

2 models selected  

Surface Color: surface has no bounding box  

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> ui mousemode right "rotate selected models"

> hide #4 models

> show #4 models

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> volume #1 level 0.08

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png" width 1243 height 913
> supersample 3

> volume #1 step 2

> volume #1 level 0.07

> volume #1 level 0.06

> volume #1 level 0.05

> volume #1 level 0.06

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png" width 1243 height 913
> supersample 3

> surface undust #2

> select add #1

2 models selected  

> surface undust #1

> volume #1 level 0.2

> volume #1 step 1

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> hide #!1 models

> show #!2 models

> volume #2 step 1

> volume #2 level 0.2

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> surface dust #2 size 16.9

> key #0cf0fa:200 blue:235 #9141ac:270 showTool true

> ui mousemode right "color key"

> key fontSize 17

> key fontSize 16

Could not find palette custom at COLOURlovers.com using keyword search  

> ui mousemode right "rotate selected models"

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).tif" width 1243 height 913
> supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step1).tif" width 1243 height 913 supersample 3

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step2).tif" width 1243 height 913 supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"

——— End of log from Mon Apr 14 19:17:23 2025 ———

opened ChimeraX session  

> hide #!2 models

> show #!2 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> hide #!3 models

> select add #1

2 models selected  

> close #1

> hide #4 models

> show #!3 models

> select add #3

2 models selected  

> close #3

> show #!2 models

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32  

> volume #2 level 0.35

> volume #2 step 1

> volume #1 level 0.2

> volume #1 step 1

> select add #1

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-48.634,0,1,0,1.6656,0,0,1,33.287

> view matrix models #1,1,0,0,13.61,0,1,0,6.7723,0,0,1,18.375

> view matrix models #1,1,0,0,13.668,0,1,0,6.639,0,0,1,17.833

> view matrix models #1,1,0,0,-17.789,0,1,0,2.819,0,0,1,20.629

> view matrix models #1,1,0,0,-39.187,0,1,0,0.34575,0,0,1,23.009

> select add #2

4 models selected  

> select subtract #2

2 models selected  

> view matrix models #1,1,0,0,-34.176,0,1,0,3.1709,0,0,1,20.524

> select add #2

4 models selected  

> fitmap #2 inMap #1

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J123_011_volume_map_sharp.mrc using 1224990 points  
correlation = 0.5927, correlation about mean = 0.05969, overlap = 8.84e+04  
steps = 124, shift = 4.73, angle = 4.44 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J123_011_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000934 -0.00000606 -91.91551273  
-0.00000934 1.00000000 -0.00001788 -91.90278947  
0.00000606 0.00001788 1.00000000 -91.91231745  
Axis 0.84889746 -0.28787388 -0.44328516  
Axis point 0.00000000 5408246.84963320 -5313748.61359478  
Rotation angle (degrees) 0.00120694  
Shift along axis -10.82706671  
  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> hide #!2 models

> volume flip #1

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> show #!2 models

> fitmap #2 inMap #3

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points  
correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05  
steps = 28, shift = 1.34, angle = 0.000137 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000760 -0.00000484 -91.89861891  
-0.00000760 1.00000000 -0.00001899 -91.89997565  
0.00000483 0.00001899 1.00000000 -93.24973991  
Axis 0.90349284 -0.23008647 -0.36160876  
Axis point 0.00000000 5447828.04621494 -5181752.87000347  
Rotation angle (degrees) 0.00120402  
Shift along axis -28.16488010  
  

> select add #2

2 models selected  

> select add #3

4 models selected  

> fitmap #2 inMap #3

Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points  
correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05  
steps = 24, shift = 0.0063, angle = 0.000111 degrees  
  
Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to
cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates:  
Matrix rotation and translation  
1.00000000 0.00000613 -0.00000381 -91.89742078  
-0.00000613 1.00000000 -0.00001975 -91.89877679  
0.00000381 0.00001975 1.00000000 -93.25566971  
Axis 0.93921386 -0.18128033 -0.29157292  
Axis point 0.00000000 5347267.65743666 -5041635.74047945  
Rotation angle (degrees) 0.00120513  
Shift along axis -42.46106316  
  

> select subtract #2

2 models selected  

> select subtract #3

Nothing selected  

> ui tool show "Surface Color"

Surface Color: surface has no bounding box  

> hide #!2 models

> hide #!3 models

> show #!2 models

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.83,344.16,360.18

> hide #!2 models

> show #!3 models

> color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.82,344.16,360.18

[Repeated 1 time(s)]

> set bgColor black

> set bgColor transparent

> volume #1 level 0.08

> hide #!3 models

> show #!3 models

> close #1

> volume #2 level 0.2

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> volume #3 level 0.08

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> color single #3.1

> color single #2.1

> color #3 white models

> show #!3 models

> volume #2 level 0.1

> volume #2 level 0.2

> color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.82,344.16,360.18

Drag select of 3 cryosparc_P108_J123_011_volume_map_sharp.mrc z flip  

> hide #!3 models

> show #!3 models

> select subtract #3

Nothing selected  

> set bgColor white

> set bgColor #ffffff00

> select add #3

2 models selected  

> surface dust #3 size 13.3

> select subtract #3

Nothing selected  

> show #4 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1).tif" width 1273 height 945
> supersample 3

> volume #3 step 2

> volume #3 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2).tif" width 1273 height 945
> supersample 3

> hide #!3 models

> show #!2 models

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 306.83,344.16,360.18

> show #!3 models

> hide #!2 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold).tif" width 1273 height 945
> supersample 3

> volume #3 level 0.08

> volume #3 step 1

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold).tif" width 1273 height 945
> supersample 3

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!3 models

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold)2.tif" width 1273 height 945
> supersample 3

> volume #3 step 2

> volume #3 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold)2.tif" width 1273 height 945
> supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"

——— End of log from Mon Apr 14 20:39:34 2025 ———

opened ChimeraX session  

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs" format
> session

Error opening map "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs": File J123 DV2_Fab13
chimerax session.cxs, format mrc  
MRC header value nsymbt (912209460) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Redust" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  
  
Log from Mon Apr 14 19:50:11 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.1, step 1, values float32  
Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.17, step 2, values float32  
Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at level 0.0843, step 1, values float32  
Log from Mon Apr 14 19:17:23 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb
> format pdb

current_fittingE7kv8_DENV2Fab13_20250330.pdb title:  
Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more
info...]  
  
Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
Chain | Description  
A B C | envelope protein E  
a b c | matrix protein M  
  
Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl
dihydrogen phosphate  
6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-
propan-2-yl] (~{Z})-octadec-9-enoate  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 13/cryosparc_P108_J123_011_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32  

> volume #1 level 0.17

> volume #1 level 0.13

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.15

> volume #1 level 0.16

> volume #1 level 0.17

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> hide #!2 models

> volume #1

> ui tool show "Surface Color"

> color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center
> 340.99,340.99,340.99

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

[Repeated 1 time(s)]

> volume #1 level 0.13

> volume #1 level 0.12

> volume #1 level 0.11

> volume #1 level 0.1

> volume #1 level 0.0843

> volume #1 step 1

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45

> view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653

> view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468

> ui mousemode right "translate selected models"

> select subtract #2

Nothing selected  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> select add #2

2 models selected  

> view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383

> view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477

> view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62

> view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41

> view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901

> view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853

> view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068

> select add #1

4 models selected  

> fitmap #1 inMap #2

Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points  
correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05  
steps = 56, shift = 7.96, angle = 0.00238 degrees  
  
Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00003026 0.00002609 91.91389849  
0.00003026 1.00000000 -0.00001109 91.89891079  
-0.00002609 0.00001109 1.00000000 91.91922251  
Axis 0.26746273 0.62926682 0.72971704  
Axis point 71695.94102549 1716204.69448452 0.00000000  
Rotation angle (degrees) 0.00237592  
Shift along axis 149.48750038  
  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> volume #2 step 1

> show #!1 models

> color #2 #f5c211ff models

> color #1 white models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.17

> select add #2

2 models selected  

> surface dust #2 size 16.9

> volume #2 level 0.0843

> select subtract #2

Nothing selected  

> volume flip #1

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> hide #!2 models

> show #!2 models

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> show #!1 models

> hide #!3 models

> surface undust #2

> volume #2 level 0.1844

> volume #2 level 0.2

> volume #2 level 0.25

> volume #2 level 0.27

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.3

> volume #2 level 0.35

> view

> view orient

> show #!1 models

> surface undust #1

> volume #1 level 0.2

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

> hide #!1 models

> color radial #2.1 palette
> 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

Surface Color: surface has no bounding box  

[Repeated 2 time(s)]

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> color radial #1.1 palette
> 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

> color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> hide #!1 models

> show #!2 models

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

[Repeated 2 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> select add #2

2 models selected  

> select add #1

4 models selected  

> show #!1 models

> hide #!1 models

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144

> view matrix models
> #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785

> select subtract #1

2 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "rotate selected models"

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> show #!1 models

> hide #!2 models

Surface Color: surface has no bounding box  

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> volume #1 level 0.17

> volume #1 level 0.13

> volume #1 level 0.1

> volume #1 level 0.09

> volume #1 level 0.08

> volume #1 level 0.09

> hide #!1 models

> show #!2 models

> set bgColor white

> set bgColor #ffffff00

> surface dust #2 size 16.9

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> surface undust #1

> volume #2 level 0.3

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.2

> surface dust #2 size 16.9

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key size 0.24000,0.05000

> key size 0.24000,0.04000

> key size 0.24000,0.03000

> key size 0.23000,0.03000

> key size 0.22000,0.03000

> key size 0.21000,0.03000

> key size 0.20000,0.03000

> key pos 0.671038,0.107382

> key pos 0,0.10738

> key pos 0.7000,0.10738

> key pos 0.70000,0.10738

> key pos 0.70000,0.10

> key pos 0.70000,0.10000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> key pos 0.70000,0.11000

> key pos 0.70000,0.10000

> key pos 0.70000,0.09000

> key pos 0.70000,0.08000

> key pos 0.70000,0.07000

> key pos 0.70000,0.06000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> surface dust #2 size 16.9

> select subtract #2

Nothing selected  

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).png" width 1243 height 913
> supersample 3

> volume #2 step 2

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> volume #2 step 1

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> hide #!2 models

> show #!1 models

> select add #1

2 models selected  

Surface Color: surface has no bounding box  

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> ui mousemode right "rotate selected models"

> hide #4 models

> show #4 models

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> volume #1 level 0.08

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png" width 1243 height 913
> supersample 3

> volume #1 step 2

> volume #1 level 0.07

> volume #1 level 0.06

> volume #1 level 0.05

> volume #1 level 0.06

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png" width 1243 height 913
> supersample 3

> surface undust #2

> select add #1

2 models selected  

> surface undust #1

> volume #1 level 0.2

> volume #1 step 1

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> hide #!1 models

> show #!2 models

> volume #2 step 1

> volume #2 level 0.2

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> surface dust #2 size 16.9

> key #0cf0fa:200 blue:235 #9141ac:270 showTool true

> ui mousemode right "color key"

> key fontSize 17

> key fontSize 16

Could not find palette custom at COLOURlovers.com using keyword search  

> ui mousemode right "rotate selected models"

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).tif" width 1243 height 913
> supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step1).tif" width 1243 height 913 supersample 3

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step2).tif" width 1243 height 913 supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"

——— End of log from Mon Apr 14 19:17:23 2025 ———

opened ChimeraX session  

> close #1

> close #3

> ui tool show "Surface Color"

> color radial #2.1 palette 210,#0cf0fa:240,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette
> 160,#ff0000:180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff
> center 304.1,346.73,364.43

> color radial #2.1 palette 120,#00ffff:160,#00ff00:200,#ffff00:240,#ff0000
> center 304.1,346.73,364.43

> color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff
> center 304.1,346.73,364.43

> volume #2 step 1

> volume #2 level 0.2

> color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff
> center 304.1,346.73,364.43

> color radial #2.1 palette 150,#ff0000:200,#f4f735:250,#0000ff center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 150,#ff0000:200,#ffff00:250,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ffff00:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ff7f7f:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ffffff center 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ffffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#ff0000:160,#ffffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#0000ff:160,#ffffff:240,#ff0000 center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#ff0000:220,#ffffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> key red:200 #f4f735:220 blue:240 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/f-fold.tif" width 1243 height 913 supersample 3

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/3-fold.tif" width 1243 height 913 supersample 3

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> view matrix models
> #2,0.93097,-0.36237,0.044589,38.647,0.36152,0.932,0.026031,-224.51,-0.05099,-0.0081145,0.99867,-42.311

> view matrix models
> #2,0.83884,-0.53188,-0.11599,221.43,0.49449,0.83358,-0.24622,-121.6,0.22765,0.14919,0.96225,-215.26

> select subtract #2

Nothing selected  

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/Assymmetric unit.tif" width 1243 height 913 supersample 3

> hide #!2 models

> show #!2 models

> color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center
> 304.1,346.73,364.43

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/Assymmetric unit.tif" width 1243 height 913 supersample 3

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"

——— End of log from Mon Apr 14 19:50:11 2025 ———

opened ChimeraX session  

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs" format
> session

Error opening map "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs": File J123 DV2_Fab13
chimerax session.cxs, format mrc  
MRC header value nsymbt (912209460) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Redust" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  
  
Log from Mon Apr 14 19:50:11 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.1, step 1, values float32  
Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.17, step 2, values float32  
Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at level 0.0843, step 1, values float32  
Log from Mon Apr 14 19:17:23 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb
> format pdb

current_fittingE7kv8_DENV2Fab13_20250330.pdb title:  
Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more
info...]  
  
Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
Chain | Description  
A B C | envelope protein E  
a b c | matrix protein M  
  
Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1  
---  
1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl
dihydrogen phosphate  
6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-
propan-2-yl] (~{Z})-octadec-9-enoate  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
  
4 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 13/cryosparc_P108_J123_011_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc" format mrc

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> close session

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size
512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32  

> volume #1 level 0.17

> volume #1 level 0.13

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.15

> volume #1 level 0.16

> volume #1 level 0.17

> open "/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab
> 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"

Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32  

> hide #!2 models

> volume #1

> ui tool show "Surface Color"

> color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center
> 340.99,340.99,340.99

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

[Repeated 1 time(s)]

> volume #1 level 0.13

> volume #1 level 0.12

> volume #1 level 0.11

> volume #1 level 0.1

> volume #1 level 0.0843

> volume #1 step 1

> select add #2

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45

> view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653

> view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468

> ui mousemode right "translate selected models"

> select subtract #2

Nothing selected  

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> select add #2

2 models selected  

> view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383

> view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477

> view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62

> view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41

> view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901

> view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853

> view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068

> select add #1

4 models selected  

> fitmap #1 inMap #2

Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points  
correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05  
steps = 56, shift = 7.96, angle = 0.00238 degrees  
  
Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
1.00000000 -0.00003026 0.00002609 91.91389849  
0.00003026 1.00000000 -0.00001109 91.89891079  
-0.00002609 0.00001109 1.00000000 91.91922251  
Axis 0.26746273 0.62926682 0.72971704  
Axis point 71695.94102549 1716204.69448452 0.00000000  
Rotation angle (degrees) 0.00237592  
Shift along axis 149.48750038  
  

> select subtract #2

2 models selected  

> select subtract #1

Nothing selected  

> hide #!1 models

> volume #2 step 1

> show #!1 models

> color #2 #f5c211ff models

> color #1 white models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> volume #2 level 0.17

> select add #2

2 models selected  

> surface dust #2 size 16.9

> volume #2 level 0.0843

> select subtract #2

Nothing selected  

> volume flip #1

Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.33, shown at step 1, values float32  

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> hide #!2 models

> show #!2 models

> surface dust #2 size 16.9

> surface dust #3 size 13.3

> show #!1 models

> hide #!3 models

> surface undust #2

> volume #2 level 0.1844

> volume #2 level 0.2

> volume #2 level 0.25

> volume #2 level 0.27

> hide #!2 models

> show #!2 models

> hide #!1 models

> volume #2 level 0.3

> volume #2 level 0.35

> view

> view orient

> show #!1 models

> surface undust #1

> volume #1 level 0.2

> color radial #1.1 palette
> 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 340.99,340.99,340.99

> hide #!1 models

> color radial #2.1 palette
> 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

Surface Color: surface has no bounding box  

[Repeated 2 time(s)]

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!1 models

> show #!1 models

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette
> 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> color radial #1.1 palette
> 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

[Repeated 2 time(s)]

> color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb
> center 337.1,346.56,336.84

> color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.84

> hide #!1 models

> show #!2 models

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

[Repeated 2 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

[Repeated 1 time(s)]

> color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 337.1,346.56,336.83

> select add #2

2 models selected  

> select add #1

4 models selected  

> show #!1 models

> hide #!1 models

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203

> view matrix models
> #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144

> view matrix models
> #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785

> select subtract #1

2 models selected  

> select subtract #2

Nothing selected  

> ui mousemode right "rotate selected models"

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> show #!1 models

> hide #!2 models

Surface Color: surface has no bounding box  

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> volume #1 level 0.17

> volume #1 level 0.13

> volume #1 level 0.1

> volume #1 level 0.09

> volume #1 level 0.08

> volume #1 level 0.09

> hide #!1 models

> show #!2 models

> set bgColor white

> set bgColor #ffffff00

> surface dust #2 size 16.9

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> surface undust #1

> volume #2 level 0.3

> set bgColor black

> set bgColor transparent

> set bgColor white

> set bgColor #ffffff00

> color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> volume #2 level 0.2

> surface dust #2 size 16.9

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> key fontSize 23

> key fontSize 22

> key fontSize 21

> key fontSize 20

> key fontSize 19

> key fontSize 18

> key fontSize 17

> key fontSize 16

> key size 0.24000,0.05000

> key size 0.24000,0.04000

> key size 0.24000,0.03000

> key size 0.23000,0.03000

> key size 0.22000,0.03000

> key size 0.21000,0.03000

> key size 0.20000,0.03000

> key pos 0.671038,0.107382

> key pos 0,0.10738

> key pos 0.7000,0.10738

> key pos 0.70000,0.10738

> key pos 0.70000,0.10

> key pos 0.70000,0.10000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> key pos 0.70000,0.11000

> key pos 0.70000,0.10000

> key pos 0.70000,0.09000

> key pos 0.70000,0.08000

> key pos 0.70000,0.07000

> key pos 0.70000,0.06000

> hide #!2 models

> show #!1 models

> hide #!1 models

> show #!2 models

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> surface dust #2 size 16.9

> select subtract #2

Nothing selected  

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).png" width 1243 height 913
> supersample 3

> volume #2 step 2

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> volume #2 step 1

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step2).png" width 1243 height 913
> supersample 3

> hide #!2 models

> show #!1 models

> select add #1

2 models selected  

Surface Color: surface has no bounding box  

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> key cyan:200 blue:235 #c061cb:270 showTool true

> ui mousemode right "color key"

> ui mousemode right "rotate selected models"

> hide #4 models

> show #4 models

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> volume #1 level 0.08

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png" width 1243 height 913
> supersample 3

> volume #1 step 2

> volume #1 level 0.07

> volume #1 level 0.06

> volume #1 level 0.05

> volume #1 level 0.06

> select add #1

2 models selected  

> surface dust #1 size 13.3

> select subtract #1

Nothing selected  

> volume #1 level 0.05

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png" width 1243 height 913
> supersample 3

> surface undust #2

> select add #1

2 models selected  

> surface undust #1

> volume #1 level 0.2

> volume #1 step 1

> select subtract #1

Nothing selected  

> volume #1 level 0.1

> hide #!1 models

> show #!2 models

> volume #2 step 1

> volume #2 level 0.2

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> surface dust #2 size 16.9

> key #0cf0fa:200 blue:235 #9141ac:270 showTool true

> ui mousemode right "color key"

> key fontSize 17

> key fontSize 16

Could not find palette custom at COLOURlovers.com using keyword search  

> ui mousemode right "rotate selected models"

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J282 control map (step1).tif" width 1243 height 913
> supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step1).tif" width 1243 height 913 supersample 3

> volume #2 step 2

> volume #2 level 0.17

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/J282 control map (step2).tif" width 1243 height 913 supersample 3

> save "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
> Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"

——— End of log from Mon Apr 14 19:17:23 2025 ———

opened ChimeraX session  

> close #1

> close #3

> ui tool show "Surface Color"

> color radial #2.1 palette 210,#0cf0fa:240,#0000ff:270,#9141ac center
> 304.1,346.73,364.43

> color radial #2.1 palette
> 160,#ff0000:180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff
> center 304.1,346.73,364.43

> color radial #2.1 palette 120,#00ffff:160,#00ff00:200,#ffff00:240,#ff0000
> center 304.1,346.73,364.43

> color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff
> center 304.1,346.73,364.43

> volume #2 step 1

> volume #2 level 0.2

> color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff
> center 304.1,346.73,364.43

> color radial #2.1 palette 150,#ff0000:200,#f4f735:250,#0000ff center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> color radial #2.1 palette 150,#ff0000:200,#ffff00:250,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ffff00:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ff7f7f:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ffffff center 304.1,346.73,364.43

> color radial #2.1 palette 160,#ff0000:200,#ffffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#ff0000:160,#ffffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#0000ff:160,#ffffff:240,#ff0000 center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#ff0000:220,#ffffff:240,#0000ff center
> 304.1,346.73,364.43

> color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center
> 304.1,346.73,364.43

[Repeated 1 time(s)]

> key red:200 #f4f735:220 blue:240 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/f-fold.tif" width 1243 height 913 supersample 3

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/3-fold.tif" width 1243 height 913 supersample 3

> ui mousemode right "rotate selected models"

> select add #2

2 models selected  

> view matrix models
> #2,0.93097,-0.36237,0.044589,38.647,0.36152,0.932,0.026031,-224.51,-0.05099,-0.0081145,0.99867,-42.311

> view matrix models
> #2,0.83884,-0.53188,-0.11599,221.43,0.49449,0.83358,-0.24622,-121.6,0.22765,0.14919,0.96225,-215.26

> select subtract #2

Nothing selected  

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/Assymmetric unit.tif" width 1243 height 913 supersample 3

> hide #!2 models

> show #!2 models

> color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center
> 304.1,346.73,364.43

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/Assymmetric unit.tif" width 1243 height 913 supersample 3

> save "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"

——— End of log from Mon Apr 14 19:50:11 2025 ———

opened ChimeraX session  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA GeForce GTX 750 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: Super Server
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        19Gi        16Gi       414Mi        28Gi        43Gi
	Swap:          8.0Gi       171Mi       7.8Gi

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 [GeForce GTX 750 Ti] [10de:1380] (rev a2)	
	Subsystem: eVga.com. Corp. GM107 [GeForce GTX 750 Ti] [3842:3751]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13

[Tom Goddard]

I am not sure if this is the bug they are trying to report since it does not appear at the end of the log.

> open "/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs" format
> session

Error opening map "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs": File J123 DV2_Fab13
chimerax session.cxs, format mrc  
MRC header value nsymbt (912209460) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

restore_snapshot for "Redust" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 873, in restore  
obj = sm.restore_snapshot(self, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/surface/colorgeom.py", line 236, in restore_snapshot  
% '.'.join('%d' % i for i in id))  
^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'builtin_function_or_method' object is not iterable  

But this error should be fixed if the problem still present in ChimeraX. It appears the user opened a session that references an MRC file that is corrupted. They don't replace the file and then surface coloring code raises this error.

[Tom Goddard]

Fixed.

The error message when restoring surface coloring on a surface that did not get restored contained old code trying to print the id number of the surface. But the id number is no longer saved (probably comes from original Chimera code). So I took out reporting the missing surface id.