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:
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/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
> ctrl)/DV2_N15 ctrl (Fab26 not bound) J282 chimerax session.cxs"
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)/DV2_N15 ctrl (Fab26 not bound) J282 chimerax session.cxs" format
> session
Error opening map "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
Fabs/DV2_N15_Fab26 (No Fab ctrl)/DV2_N15 ctrl (Fab26 not bound) J282 chimerax
session.cxs": File DV2_N15 ctrl (Fab26 not bound) J282 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)/DV2_N15 ctrl (Fab26 not bound) J282 chimerax session.cxs" format
> session
Error opening map "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
Fabs/DV2_N15_Fab26 (No Fab ctrl)/DV2_N15 ctrl (Fab26 not bound) J282 chimerax
session.cxs": File DV2_N15 ctrl (Fab26 not bound) J282 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)/DV2_N15 ctrl (Fab26 not bound) J282 chimerax session.cxs" format
> session
Error opening map "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
Fabs/DV2_N15_Fab26 (No Fab ctrl)/DV2_N15 ctrl (Fab26 not bound) J282 chimerax
session.cxs": File DV2_N15 ctrl (Fab26 not bound) J282 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)/DV2_N15 ctrl (Fab26 not bound) J282 chimerax session.cxs" format
> session
Error opening map "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-
Fabs/DV2_N15_Fab26 (No Fab ctrl)/DV2_N15 ctrl (Fab26 not bound) J282 chimerax
session.cxs": File DV2_N15 ctrl (Fab26 not bound) J282 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 "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/(Bigger Box) DV2_N15 No Fab ctrl (37C)
> cryosparc_P108_J416_011_volume_map_sharp.mrc"
Opened (Bigger Box) DV2_N15 No Fab ctrl (37C)
cryosparc_P108_J416_011_volume_map_sharp.mrc as #1, grid size 512,512,512,
pixel 1.69, shown at level 0.283, step 2, values float32
> ui tool show "Surface Color"
> open "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No
> Fab ctrl)/(Bigger Box) DV2_N15 No Fab ctrl (4C)
> cryosparc_P108_J400_014_volume_map_sharp.mrc"
Opened (Bigger Box) DV2_N15 No Fab ctrl (4C)
cryosparc_P108_J400_014_volume_map_sharp.mrc as #2, grid size 512,512,512,
pixel 1.69, shown at level 0.234, step 2, values float32
> open "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15 (No Fab
> ctrl)/cryosparc_P108_J282_009_volume_map_sharp.mrc"
Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #3, grid size
512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32
> hide #!1 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> show #!2 models
> volume #2 level 0.2
> volume #3 level 0.2
> volume #2 step 1
Error processing trigger "graphics update":
You deleted or moved a volume file that is still open in ChimeraX.
/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
ctrl)/(Bigger Box) DV2_N15 No Fab ctrl (4C)
cryosparc_P108_J400_014_volume_map_sharp.mrc
To allow fast initial display of volume data ChimeraX does not read all data
from the file when it is first opened, and will later read more data when
needed. ChimeraX got an error trying to read the above file.
> volume #3 step 1
> hide #!2 models
> show #!2 models
> fitmap #2 inMap #3
You deleted or moved a volume file that is still open in ChimeraX.
/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
ctrl)/(Bigger Box) DV2_N15 No Fab ctrl (4C)
cryosparc_P108_J400_014_volume_map_sharp.mrc To allow fast initial display of
volume data ChimeraX does not read all data from the file when it is first
opened, and will later read more data when needed. ChimeraX got an error
trying to read the above file.
> select add #2
2 models selected
> fitmap #2 inMap #3
You deleted or moved a volume file that is still open in ChimeraX.
/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
ctrl)/(Bigger Box) DV2_N15 No Fab ctrl (4C)
cryosparc_P108_J400_014_volume_map_sharp.mrc To allow fast initial display of
volume data ChimeraX does not read all data from the file when it is first
opened, and will later read more data when needed. ChimeraX got an error
trying to read the above file.
> select add #3
4 models selected
> fitmap #2 inMap #3
You deleted or moved a volume file that is still open in ChimeraX.
/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab
ctrl)/(Bigger Box) DV2_N15 No Fab ctrl (4C)
cryosparc_P108_J400_014_volume_map_sharp.mrc To allow fast initial display of
volume data ChimeraX does not read all data from the file when it is first
opened, and will later read more data when needed. ChimeraX got an error
trying to read the above file.
> close #1
> close #2
> close #3
> open "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15 (No Fab
> ctrl)/(Bigger Box) DV2_N15 No Fab ctrl (37C)
> cryosparc_P108_J416_011_volume_map_sharp.mrc"
Opened (Bigger Box) DV2_N15 No Fab ctrl (37C)
cryosparc_P108_J416_011_volume_map_sharp.mrc as #1, grid size 512,512,512,
pixel 1.69, shown at level 0.283, step 2, values float32
> open "/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15 (No Fab
> ctrl)/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
> select add #1
2 models selected
> select add #2
4 models selected
> fitmap #1 inMap #2
Fit map (Bigger Box) DV2_N15 No Fab ctrl (37C)
cryosparc_P108_J416_011_volume_map_sharp.mrc in map
cryosparc_P108_J282_009_volume_map_sharp.mrc using 167632 points
correlation = 0.512, correlation about mean = 0.06285, overlap = 1.969e+04
steps = 28, shift = 0.0213, angle = 0.0014 degrees
Position of (Bigger Box) DV2_N15 No Fab ctrl (37C)
cryosparc_P108_J416_011_volume_map_sharp.mrc (#1) relative to
cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
1.00000000 -0.00000378 -0.00001624 -0.00868428
0.00000378 1.00000000 -0.00001792 -0.00625538
0.00001624 0.00001792 1.00000000 -0.01537649
Axis 0.73199547 -0.66355340 0.15452996
Axis point 0.00000000 818.76335435 -518.89216129
Rotation angle (degrees) 0.00140228
Shift along axis -0.00458220
> volume flip #1
Opened (Bigger Box) DV2_N15 No Fab ctrl (37C)
cryosparc_P108_J416_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.69, shown at step 1, values float32
Traceback (most recent call last):
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
See log for complete Python traceback.
> select subtract #1
2 models selected
> select subtract #2
Nothing selected
Traceback (most recent call last):
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
See log for complete Python traceback.
> color #3 blue models
> hide #!2 models
> hide #!3 models
Traceback (most recent call last):
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
See log for complete Python traceback.
> close #3
> volume flip #1
Opened (Bigger Box) DV2_N15 No Fab ctrl (37C)
cryosparc_P108_J416_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.69, shown at step 1, values float32
Traceback (most recent call last):
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
See log for complete Python traceback.
> close #3
> show #!1 models
> volume flip #1
Opened (Bigger Box) DV2_N15 No Fab ctrl (37C)
cryosparc_P108_J416_011_volume_map_sharp.mrc z flip as #3, grid size
512,512,512, pixel 1.69, shown at step 1, values float32
Traceback (most recent call last):
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
See log for complete Python traceback.
> volume #3
Traceback (most recent call last):
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2751, in update_cb
s.update_histogram(rm, m, rz, delay = 0)
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume_viewer.py", line 2759, in update_histogram
s = v.matrix_value_statistics(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1736, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1771, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1254, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1278, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 41, in matrix
mf = flip_matrix(m, self.axes)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
TypeError: 'NoneType' object is not subscriptable
TypeError: 'NoneType' object is not subscriptable
File "/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_filter/flip.py", line 87, in flip_matrix
m = m[::-1,:,:]
~^^^^^^^^^^
See log for complete Python traceback.
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 16Gi 12Gi 423Mi 35Gi 46Gi
Swap: 8.0Gi 363Mi 7.6Gi
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
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Duplicate of #17378