id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17378 Restore coloring on non-existent surface: bad error message chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-6.8.0-38-generic-x86_64-with-glibc2.39 ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/home/kuhn/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/J158_009 DV2_N15_Fab24 chimerax session.cxs"" Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.2, step 1, values float32 Log from Mon Apr 14 19:50:11 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"" Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.1, step 1, values float32 Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.17, step 2, values float32 Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at level 0.0843, step 1, values float32 Log from Mon Apr 14 19:17:23 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb > format pdb current_fittingE7kv8_DENV2Fab13_20250330.pdb title: Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more info...] Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- Chain | Description A B C | envelope protein E a b c | matrix protein M Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- 1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"" Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32 > volume #1 level 0.17 > volume #1 level 0.13 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.15 > volume #1 level 0.16 > volume #1 level 0.17 > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > hide #!2 models > volume #1 > ui tool show ""Surface Color"" > color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center > 340.99,340.99,340.99 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 [Repeated 1 time(s)] > volume #1 level 0.13 > volume #1 level 0.12 > volume #1 level 0.11 > volume #1 level 0.1 > volume #1 level 0.0843 > volume #1 step 1 > select add #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45 > view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653 > view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468 > ui mousemode right ""translate selected models"" > select subtract #2 Nothing selected > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > select add #2 2 models selected > view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383 > view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477 > view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62 > view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41 > view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901 > view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853 > view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068 > select add #1 4 models selected > fitmap #1 inMap #2 Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05 steps = 56, shift = 7.96, angle = 0.00238 degrees Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00003026 0.00002609 91.91389849 0.00003026 1.00000000 -0.00001109 91.89891079 -0.00002609 0.00001109 1.00000000 91.91922251 Axis 0.26746273 0.62926682 0.72971704 Axis point 71695.94102549 1716204.69448452 0.00000000 Rotation angle (degrees) 0.00237592 Shift along axis 149.48750038 > select subtract #2 2 models selected > select subtract #1 Nothing selected > hide #!1 models > volume #2 step 1 > show #!1 models > color #2 #f5c211ff models > color #1 white models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.17 > select add #2 2 models selected > surface dust #2 size 16.9 > volume #2 level 0.0843 > select subtract #2 Nothing selected > volume flip #1 Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > surface dust #2 size 16.9 > surface dust #3 size 13.3 > hide #!2 models > show #!2 models > surface dust #2 size 16.9 > surface dust #3 size 13.3 > show #!1 models > hide #!3 models > surface undust #2 > volume #2 level 0.1844 > volume #2 level 0.2 > volume #2 level 0.25 > volume #2 level 0.27 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.3 > volume #2 level 0.35 > view > view orient > show #!1 models > surface undust #1 > volume #1 level 0.2 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 > hide #!1 models > color radial #2.1 palette > 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] Surface Color: surface has no bounding box [Repeated 2 time(s)] > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > color radial #1.1 palette > 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 > color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > hide #!1 models > show #!2 models > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 [Repeated 2 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > select add #2 2 models selected > select add #1 4 models selected > show #!1 models > hide #!1 models > view matrix models > #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144 > view matrix models > #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785 > select subtract #1 2 models selected > select subtract #2 Nothing selected > ui mousemode right ""rotate selected models"" > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > show #!1 models > hide #!2 models Surface Color: surface has no bounding box > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > volume #1 level 0.17 > volume #1 level 0.13 > volume #1 level 0.1 > volume #1 level 0.09 > volume #1 level 0.08 > volume #1 level 0.09 > hide #!1 models > show #!2 models > set bgColor white > set bgColor #ffffff00 > surface dust #2 size 16.9 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > surface undust #1 > volume #2 level 0.3 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > volume #2 level 0.2 > surface dust #2 size 16.9 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 19 > key fontSize 18 > key fontSize 17 > key fontSize 16 > key size 0.24000,0.05000 > key size 0.24000,0.04000 > key size 0.24000,0.03000 > key size 0.23000,0.03000 > key size 0.22000,0.03000 > key size 0.21000,0.03000 > key size 0.20000,0.03000 > key pos 0.671038,0.107382 > key pos 0,0.10738 > key pos 0.7000,0.10738 > key pos 0.70000,0.10738 > key pos 0.70000,0.10 > key pos 0.70000,0.10000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > key pos 0.70000,0.11000 > key pos 0.70000,0.10000 > key pos 0.70000,0.09000 > key pos 0.70000,0.08000 > key pos 0.70000,0.07000 > key pos 0.70000,0.06000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > surface dust #2 size 16.9 > select subtract #2 Nothing selected > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).png"" width 1243 height 913 > supersample 3 > volume #2 step 2 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > volume #2 step 1 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > hide #!2 models > show #!1 models > select add #1 2 models selected Surface Color: surface has no bounding box > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > ui mousemode right ""rotate selected models"" > hide #4 models > show #4 models > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.1 > volume #1 level 0.08 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png"" width 1243 height 913 > supersample 3 > volume #1 step 2 > volume #1 level 0.07 > volume #1 level 0.06 > volume #1 level 0.05 > volume #1 level 0.06 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png"" width 1243 height 913 > supersample 3 > surface undust #2 > select add #1 2 models selected > surface undust #1 > volume #1 level 0.2 > volume #1 step 1 > select subtract #1 Nothing selected > volume #1 level 0.1 > hide #!1 models > show #!2 models > volume #2 step 1 > volume #2 level 0.2 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > surface dust #2 size 16.9 > key #0cf0fa:200 blue:235 #9141ac:270 showTool true > ui mousemode right ""color key"" > key fontSize 17 > key fontSize 16 Could not find palette custom at COLOURlovers.com using keyword search > ui mousemode right ""rotate selected models"" > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).tif"" width 1243 height 913 > supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step1).tif"" width 1243 height 913 supersample 3 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step2).tif"" width 1243 height 913 supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"" ——— End of log from Mon Apr 14 19:17:23 2025 ——— opened ChimeraX session > close #1 > close #3 > ui tool show ""Surface Color"" > color radial #2.1 palette 210,#0cf0fa:240,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette > 160,#ff0000:180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff > center 304.1,346.73,364.43 > color radial #2.1 palette 120,#00ffff:160,#00ff00:200,#ffff00:240,#ff0000 > center 304.1,346.73,364.43 > color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff > center 304.1,346.73,364.43 > volume #2 step 1 > volume #2 level 0.2 > color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff > center 304.1,346.73,364.43 > color radial #2.1 palette 150,#ff0000:200,#f4f735:250,#0000ff center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 150,#ff0000:200,#ffff00:250,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ffff00:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ff7f7f:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ffffff center 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ffffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#ff0000:160,#ffffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#0000ff:160,#ffffff:240,#ff0000 center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#ff0000:220,#ffffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center > 304.1,346.73,364.43 [Repeated 1 time(s)] > key red:200 #f4f735:220 blue:240 showTool true > ui mousemode right ""color key"" > ui mousemode right translate > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/f-fold.tif"" width 1243 height 913 supersample 3 > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/3-fold.tif"" width 1243 height 913 supersample 3 > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > view matrix models > #2,0.93097,-0.36237,0.044589,38.647,0.36152,0.932,0.026031,-224.51,-0.05099,-0.0081145,0.99867,-42.311 > view matrix models > #2,0.83884,-0.53188,-0.11599,221.43,0.49449,0.83358,-0.24622,-121.6,0.22765,0.14919,0.96225,-215.26 > select subtract #2 Nothing selected > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/Assymmetric unit.tif"" width 1243 height 913 supersample 3 > hide #!2 models > show #!2 models > color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center > 304.1,346.73,364.43 > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/Assymmetric unit.tif"" width 1243 height 913 supersample 3 > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"" ——— End of log from Mon Apr 14 19:50:11 2025 ——— opened ChimeraX session > surface dust #2 size 16.9 > select add #2 2 models selected > surface dust #2 size 16.9 > select subtract #2 Nothing selected > surface undust #2 > ui tool show ""Surface Color"" > color single #2.1 > hide #4 models > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 24/cryosparc_P108_J158_009_volume_map_sharp.mrc"" Opened cryosparc_P108_J158_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.386, step 2, values float32 > select add #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-32.618,0,1,0,13.707,0,0,1,10.371 > fitmap #1 inMap #2 Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 167700 points correlation = 0.5909, correlation about mean = 0.04444, overlap = 2.124e+04 steps = 108, shift = 15.8, angle = 1.5 degrees Position of cryosparc_P108_J158_009_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.82826999 0.50750099 0.23751120 -103.66917651 -0.54459400 0.82886053 0.12809214 292.18437852 -0.13185677 -0.23544205 0.96290230 229.66009928 Axis -0.30996736 0.31494153 -0.89706860 Axis point 455.51638490 408.41445019 0.00000000 Rotation angle (degrees) 35.90246553 Shift along axis -81.86580633 > select subtract #1 Nothing selected > color #1 white models > volume #1 level 0.2 > volume #2 level 0.35 > volume #1 step 1 > volume flip #1 Opened cryosparc_P108_J158_009_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 0 atomic models, 3 maps. > hide #!1 models > select add #2 2 models selected > select add #3 4 models selected > fitmap #2 inMap #3 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip using 1224990 points correlation = 0.4719, correlation about mean = 0.03672, overlap = 9.85e+04 steps = 116, shift = 1.69, angle = 0.594 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 0.82440776 -0.55126619 -0.12828656 278.80177895 0.51577977 0.82504786 -0.23079699 -139.73648527 0.23307313 0.12410322 0.96450781 -232.57749077 Axis 0.30046933 -0.30593812 0.90339363 Axis point 458.01985432 405.41639473 0.00000000 Rotation angle (degrees) 36.19792378 Shift along axis -83.58692045 > select subtract #2 2 models selected > fitmap #3 inMap #2 Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 2898868 points correlation = 0.5655, correlation about mean = 0.08721, overlap = 2.415e+05 steps = 60, shift = 0.153, angle = 0.119 degrees Position of cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.82325634 0.51741968 0.23350775 -103.92052940 -0.55299279 0.82391286 0.12396201 298.82318541 -0.12824965 -0.23118061 0.96442084 228.12552688 Axis -0.29985300 0.30543796 -0.90376758 Axis point 457.46220141 405.63522711 0.00000000 Rotation angle (degrees) 36.31289551 Shift along axis -83.73962720 > select subtract #3 Nothing selected > hide #!3 models > show #!1 models > hide #!1 models > show #!1 models > select add #1 2 models selected > fitmap #1 inMap #2 Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 2898868 points correlation = 0.5676, correlation about mean = 0.08856, overlap = 2.442e+05 steps = 96, shift = 2.74, angle = 2.89 degrees Position of cryosparc_P108_J158_009_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.80124001 0.54981568 0.23604484 -108.18277230 -0.58085609 0.80941657 0.08631926 326.28552381 -0.14359893 -0.20627052 0.96790073 220.80698867 Axis -0.23825164 0.30913845 -0.92068973 Axis point 471.18219773 400.31151980 0.00000000 Rotation angle (degrees) 37.88184834 Shift along axis -76.65260251 > select subtract #1 Nothing selected > hide #!1 models > show #!3 models > select add #3 2 models selected > fitmap #3 inMap #2 Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 2898868 points correlation = 0.5655, correlation about mean = 0.08723, overlap = 2.415e+05 steps = 48, shift = 0.0274, angle = 0.00425 degrees Position of cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.82323369 0.51746639 0.23348408 -103.91850196 -0.55302628 0.82389895 0.12390503 298.88529905 -0.12825060 -0.23112562 0.96443389 228.09655392 Axis -0.29975036 0.30541053 -0.90381089 Axis point 457.53098412 405.61244531 0.00000000 Rotation angle (degrees) 36.31403235 Shift along axis -83.72382245 > select subtract #3 Nothing selected > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > volume #1 level 0.17 > volume #3 level 0.17 > show #!2 models > hide #!3 models > show #!1 models > select add #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,0.99805,0.046255,0.041868,32.884,-0.044429,0.99806,-0.04355,17.666,-0.043802,0.041605,0.99817,-81.943 > view matrix models > #1,0.99805,0.046255,0.041868,-69.1,-0.044429,0.99806,-0.04355,39.541,-0.043802,0.041605,0.99817,47.309 > view matrix models > #1,0.99805,0.046255,0.041868,-73.936,-0.044429,0.99806,-0.04355,48.258,-0.043802,0.041605,0.99817,58.928 > view matrix models > #1,0.99805,0.046255,0.041868,-101.06,-0.044429,0.99806,-0.04355,35.094,-0.043802,0.041605,0.99817,89.448 > volume #1 step 2 > volume #3 step 2 > select subtract #1 Nothing selected > select add #1 2 models selected > view matrix models > #1,0.99805,0.046255,0.041868,-130.74,-0.044429,0.99806,-0.04355,35.361,-0.043802,0.041605,0.99817,149.68 > view matrix models > #1,0.99805,0.046255,0.041868,-69.833,-0.044429,0.99806,-0.04355,44.93,-0.043802,0.041605,0.99817,9.4144 > view matrix models > #1,0.99805,0.046255,0.041868,-62.46,-0.044429,0.99806,-0.04355,29.075,-0.043802,0.041605,0.99817,20.457 > view matrix models > #1,0.99805,0.046255,0.041868,-70.431,-0.044429,0.99806,-0.04355,38.526,-0.043802,0.041605,0.99817,21.185 > view matrix models > #1,0.99805,0.046255,0.041868,-67.43,-0.044429,0.99806,-0.04355,36.724,-0.043802,0.041605,0.99817,18.018 > fitmap #1 inMap #2 Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 483066 points correlation = 0.5662, correlation about mean = 0.108, overlap = 3.368e+04 steps = 96, shift = 5.09, angle = 0.678 degrees Position of cryosparc_P108_J158_009_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.80244809 0.54431606 0.24453441 -109.89788491 -0.57639398 0.81308990 0.08157691 324.68718543 -0.15442484 -0.20640940 0.96620294 226.16867801 Axis -0.23528924 0.32595585 -0.91563735 Axis point 474.10721900 406.56300724 0.00000000 Rotation angle (degrees) 37.73306737 Shift along axis -75.39701273 > select subtract #1 Nothing selected > select add #2 2 models selected > hide #!1 models > select subtract #2 Nothing selected > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!3 models > hide #!2 models > show #!2 models > select add #3 2 models selected > fitmap #3 inMap #2 Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 483066 points correlation = 0.5636, correlation about mean = 0.105, overlap = 3.332e+04 steps = 80, shift = 1.55, angle = 0.291 degrees Position of cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.82193668 0.51916630 0.23427858 -103.85961463 -0.55425965 0.82379183 0.11900950 301.09583720 -0.13121106 -0.22766943 0.96485765 229.25518153 Axis -0.29237006 0.30823398 -0.90526878 Axis point 461.16745780 405.73160388 0.00000000 Rotation angle (degrees) 36.36143070 Shift along axis -84.36414673 > select subtract #3 Nothing selected > hide #!3 models > show #!1 models > select add #1 2 models selected > fitmap #1 inMap #2 Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 483066 points correlation = 0.5662, correlation about mean = 0.1079, overlap = 3.368e+04 steps = 64, shift = 0.00365, angle = 0.00186 degrees Position of cryosparc_P108_J158_009_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.80245947 0.54429775 0.24453784 -109.89308018 -0.57637330 0.81310636 0.08155894 324.68091838 -0.15444292 -0.20639283 0.96620359 226.16847760 Axis -0.23526811 0.32598323 -0.91563303 Axis point 474.12689577 406.56019298 0.00000000 Rotation angle (degrees) 37.73173349 Shift along axis -75.39245955 > select subtract #1 Nothing selected > volume #2 step 2 > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > hide #!2 models > show #!1 models > hide #!3 models > set bgColor black > show #!2 models > hide #!1 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > volume #2 step 1 > volume #1 step 1 > volume #3 step 1 > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > select add #1 2 models selected > show #!1 models > hide #!1 models > select subtract #1 Nothing selected > show #!3 models > select add #3 2 models selected > select subtract #3 Nothing selected > hide #!3 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!1 models > hide #!2 models > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.3,346.69,362.54 > volume #1 level 0.08 > volume #1 level 0.02 > volume #1 level 0.2 > select add #1 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.95191,0.09858,0.29008,496.36,0.24685,0.80761,0.53557,-195.49,-0.18148,0.58142,-0.7931,496.6 > view matrix models > #1,-0.77579,-0.24624,-0.58097,850.91,-0.19351,0.96919,-0.1524,134.16,0.60059,-0.0058085,-0.79953,432.36 > view matrix models > #1,-0.97041,-0.063267,-0.23305,736.24,-0.17223,0.85779,0.48429,-52.215,0.16927,0.51009,-0.8433,418.44 > view matrix models > #1,-0.74657,-0.28223,-0.60247,860.55,-0.25742,0.95757,-0.12959,152.14,0.61348,0.058338,-0.78755,402 > view matrix models > #1,0.53758,-0.51729,-0.66589,524.44,-0.36157,0.572,-0.73626,526,0.76175,0.63657,0.12046,-155.36 > view matrix models > #1,0.90405,0.13598,0.40521,-188.52,0.32873,0.38469,-0.86253,397.54,-0.27317,0.91298,0.30307,41.023 > view matrix models > #1,0.26478,-0.065154,0.9621,-91.843,-0.18904,0.97485,0.11804,38.487,-0.9456,-0.21313,0.24581,673.84 > view matrix models > #1,0.15833,-0.82302,0.5455,344.94,-0.96164,-0.0031878,0.27431,582.15,-0.22402,-0.568,-0.79195,902.66 > view matrix models > #1,0.1655,-0.7938,0.58523,318.98,-0.97218,-0.23105,-0.038469,770.1,0.16575,-0.56258,-0.80995,774.04 > view matrix models > #1,0.33756,-0.73388,0.58946,238.44,-0.24501,-0.67314,-0.69775,897.7,0.90886,0.091111,-0.40703,160.35 > view matrix models > #1,0.36854,-0.60045,0.70967,141.39,0.74671,-0.26351,-0.61073,390.18,0.55372,0.755,0.35125,-203.5 > view matrix models > #1,0.45752,-0.30661,0.83466,-31.776,0.59427,-0.59281,-0.54352,531.53,0.66145,0.74469,-0.089016,-86.59 > view matrix models > #1,0.78637,-0.043221,0.61625,-159.24,-0.36796,-0.83405,0.41104,616.41,0.49622,-0.54999,-0.67178,609.94 > view matrix models > #1,0.15045,-0.032599,0.98808,-72.814,-0.58249,-0.81047,0.061951,800.56,0.79879,-0.58487,-0.14092,337.65 > view matrix models > #1,0.68695,-0.048745,0.72507,-160.57,-0.47958,-0.78003,0.40193,639.16,0.54598,-0.62384,-0.55922,579.78 > view matrix models > #1,0.99307,-0.11115,-0.03828,16.624,-0.06368,-0.78235,0.61957,423.92,-0.098812,-0.61284,-0.78401,872.54 > view matrix models > #1,0.91661,-0.081071,0.39148,-114.11,-0.28859,-0.81185,0.50757,548.86,0.27668,-0.57822,-0.76754,727.09 > show #!2 models > select subtract #1 Nothing selected > hide #!1 models > show #!3 models > hide #!3 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > select add #2 2 models selected > select add #3 4 models selected > fitmap #2 inMap #3 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip using 1224990 points correlation = 0.4719, correlation about mean = 0.03672, overlap = 9.85e+04 steps = 64, shift = 1.64, angle = 0.349 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 0.82440332 -0.55125818 -0.12834945 278.83507123 0.51574920 0.82505024 -0.23085680 -139.69053927 0.23315644 0.12412299 0.96448513 -232.63085066 Axis 0.30052811 -0.30605314 0.90333511 Axis point 458.00533281 405.49590281 0.00000000 Rotation angle (degrees) 36.19912394 Shift along axis -83.59311116 > select subtract #3 2 models selected > select subtract #2 Nothing selected > hide #!3 models > hide #!2 models > show #!3 models > volume #3 level 0.2 > show #!2 models > hide #!3 models > show #!3 models > select add #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.99962,0.015323,0.023126,108.14,-0.014942,0.99975,-0.016573,-74.72,-0.023374,0.016222,0.9996,23.791 > view matrix models > #3,0.99962,0.015323,0.023126,-119.77,-0.014942,0.99975,-0.016573,56.77,-0.023374,0.016222,0.9996,28.703 > hide #!2 models > select subtract #3 Nothing selected > hide #!3 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!3 models > show #!2 models > select add #3 2 models selected > view matrix models > #3,0.99962,0.015323,0.023126,-18.743,-0.014942,0.99975,-0.016573,-1.8357,-0.023374,0.016222,0.9996,32.646 > view matrix models > #3,0.99962,0.015323,0.023126,-123.99,-0.014942,0.99975,-0.016573,58.473,-0.023374,0.016222,0.9996,42.804 > view matrix models > #3,0.99962,0.015323,0.023126,-231.56,-0.014942,0.99975,-0.016573,122.37,-0.023374,0.016222,0.9996,10.005 > view matrix models > #3,0.99962,0.015323,0.023126,-64.602,-0.014942,0.99975,-0.016573,25.245,-0.023374,0.016222,0.9996,21.704 > view matrix models > #3,0.99962,0.015323,0.023126,-51.943,-0.014942,0.99975,-0.016573,17.659,-0.023374,0.016222,0.9996,26.845 > view matrix models > #3,0.99962,0.015323,0.023126,-31.446,-0.014942,0.99975,-0.016573,5.6759,-0.023374,0.016222,0.9996,29.429 > view matrix models > #3,0.99962,0.015323,0.023126,-40.045,-0.014942,0.99975,-0.016573,7.1083,-0.023374,0.016222,0.9996,29.415 > view matrix models > #3,0.99962,0.015323,0.023126,-35.996,-0.014942,0.99975,-0.016573,6.2978,-0.023374,0.016222,0.9996,30.791 > fitmap #3 inMap #2 Fit map cryosparc_P108_J158_009_volume_map_sharp.mrc z flip in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 2898868 points correlation = 0.5666, correlation about mean = 0.08887, overlap = 2.429e+05 steps = 136, shift = 16.9, angle = 2.9 degrees Position of cryosparc_P108_J158_009_volume_map_sharp.mrc z flip (#3) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.80500069 0.55278763 0.21540594 -103.09258307 -0.58050912 0.80883882 0.09374930 323.28594379 -0.12240524 -0.20051336 0.97201407 212.67451568 Axis -0.24146930 0.27720483 -0.92997315 Axis point 468.81479847 388.24792077 0.00000000 Rotation angle (degrees) 37.54012796 Shift along axis -83.27147151 > select subtract #3 Nothing selected > hide #!3 models > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > show #!1 models > hide #!2 models > volume #1 level 0.08 > volume #1 level 0.2 > hide #!1 models > show #!2 models > select add #2 2 models selected > close #2 > close #3 > show #!1 models > ui mousemode right select > select #1 2 models selected Drag select of 1 cryosparc_P108_J158_009_volume_map_sharp.mrc [Repeated 1 time(s)] > select add #1 2 models selected > select subtract #1 Nothing selected > volume #1 level 0.08 > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.3,346.69,362.54 > show #4 models > hide #4 models > key cyan:200 blue:235 #9141ac:270 showTool true > ui mousemode right ""color key"" > key delete > ui mousemode right select > key cyan:200 blue:235 #9141ac:270 showTool true > ui mousemode right ""color key"" > key pos 0.70000,0.07000 > key pos 0.70000,0.06000 > key pos 0.70000,0.05000 > key pos 0.70000,0.06000 > key size 0.24000,0.05000 > key size 0.23000,0.05000 > key size 0.22000,0.05000 > key size 0.21000,0.05000 > key size 0.20000,0.05000 > key size 0.20000,0.04000 > key size 0.20000,0.03000 > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 19 > key fontSize 18 > key fontSize 17 > key fontSize 16 > ui mousemode right select > hide #2 models > show #2 models > select add #1 2 models selected > select subtract #1 Nothing selected > set bgColor white > hide #2 models > show #2 models > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.07 > volume #1 level 0.06 > volume #1 level 0.05 > select add #1 2 models selected > select subtract #1 Nothing selected > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1).tif"" width 1243 height 913 > supersample 3 > volume #1 level 0.08 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1)2.tif"" width 1243 height 913 > supersample 3 > volume #1 step 2 > volume #1 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step2).tif"" width 1243 height 913 > supersample 3 > volume #1 level 0.03 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step2)2.tif"" width 1243 height 913 > supersample 3 > volume #1 step 1 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1)3.tif"" width 1243 height 913 > supersample 3 > volume #1 level 0.2 > volume #1 level 0.08 > volume #1 level 0.05 > volume #1 level 0.08 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1_3fold).tif"" width 1243 height 913 > supersample 3 > volume #1 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1_3fold)2.tif"" width 1243 height 913 > supersample 3 > volume #1 level 0.2 > unhide dust #1 Unknown command: unhide dust #1 > help help:user > surface undust #1 > volume flip #1 Opened cryosparc_P108_J158_009_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > color radial #3.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 303.78,346.02,363.56 > volume #3 level 0.03 > volume #3 level 0.08 > volume #3 level 0.2 > volume #3 level 0.08 > surface dust #3 size 13.3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1_3fold)_map flipped.tif"" width 1207 > height 913 supersample 3 > volume #3 level 0.05 > volume #3 level 0.03 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/DV2_N15_Fab24 (step1_3fold)_map flipped2.tif"" width 1207 > height 913 supersample 3 > volume #3 level 0.2 > surface undust #3 > surface undust #1 > show #!1 models > color single #3.1 > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!1 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab24/J158_009 DV2_N15_Fab24 chimerax session.cxs"" > hide #!1 models > hide #2 models > open ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab13/J123 > DV2_Fab13 chimerax session.cxs"" restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at level 0.05, step 2, values float32 Unable to restore session, resetting. Traceback (most recent call last): File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/session.py"", line 873, in restore obj = sm.restore_snapshot(self, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/surface/colorgeom.py"", line 236, in restore_snapshot % '.'.join('%d' % i for i in id)) ^^^^^^^^^^^^^^^^^^^^^^ TypeError: 'builtin_function_or_method' object is not iterable Log from Mon Apr 14 20:39:34 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > set bgColor #ffffff00 Log from Mon Apr 14 19:17:23 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb > format pdb current_fittingE7kv8_DENV2Fab13_20250330.pdb title: Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more info...] Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- Chain | Description A B C | envelope protein E a b c | matrix protein M Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- 1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"" Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32 > volume #1 level 0.17 > volume #1 level 0.13 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.15 > volume #1 level 0.16 > volume #1 level 0.17 > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > hide #!2 models > volume #1 > ui tool show ""Surface Color"" > color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center > 340.99,340.99,340.99 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 [Repeated 1 time(s)] > volume #1 level 0.13 > volume #1 level 0.12 > volume #1 level 0.11 > volume #1 level 0.1 > volume #1 level 0.0843 > volume #1 step 1 > select add #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45 > view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653 > view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468 > ui mousemode right ""translate selected models"" > select subtract #2 Nothing selected > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > select add #2 2 models selected > view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383 > view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477 > view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62 > view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41 > view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901 > view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853 > view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068 > select add #1 4 models selected > fitmap #1 inMap #2 Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05 steps = 56, shift = 7.96, angle = 0.00238 degrees Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00003026 0.00002609 91.91389849 0.00003026 1.00000000 -0.00001109 91.89891079 -0.00002609 0.00001109 1.00000000 91.91922251 Axis 0.26746273 0.62926682 0.72971704 Axis point 71695.94102549 1716204.69448452 0.00000000 Rotation angle (degrees) 0.00237592 Shift along axis 149.48750038 > select subtract #2 2 models selected > select subtract #1 Nothing selected > hide #!1 models > volume #2 step 1 > show #!1 models > color #2 #f5c211ff models > color #1 white models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.17 > select add #2 2 models selected > surface dust #2 size 16.9 > volume #2 level 0.0843 > select subtract #2 Nothing selected > volume flip #1 Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > surface dust #2 size 16.9 > surface dust #3 size 13.3 > hide #!2 models > show #!2 models > surface dust #2 size 16.9 > surface dust #3 size 13.3 > show #!1 models > hide #!3 models > surface undust #2 > volume #2 level 0.1844 > volume #2 level 0.2 > volume #2 level 0.25 > volume #2 level 0.27 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.3 > volume #2 level 0.35 > view > view orient > show #!1 models > surface undust #1 > volume #1 level 0.2 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 > hide #!1 models > color radial #2.1 palette > 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] Surface Color: surface has no bounding box [Repeated 2 time(s)] > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > color radial #1.1 palette > 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 > color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > hide #!1 models > show #!2 models > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 [Repeated 2 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > select add #2 2 models selected > select add #1 4 models selected > show #!1 models > hide #!1 models > view matrix models > #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144 > view matrix models > #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785 > select subtract #1 2 models selected > select subtract #2 Nothing selected > ui mousemode right ""rotate selected models"" > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > show #!1 models > hide #!2 models Surface Color: surface has no bounding box > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > volume #1 level 0.17 > volume #1 level 0.13 > volume #1 level 0.1 > volume #1 level 0.09 > volume #1 level 0.08 > volume #1 level 0.09 > hide #!1 models > show #!2 models > set bgColor white > set bgColor #ffffff00 > surface dust #2 size 16.9 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > surface undust #1 > volume #2 level 0.3 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > volume #2 level 0.2 > surface dust #2 size 16.9 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 19 > key fontSize 18 > key fontSize 17 > key fontSize 16 > key size 0.24000,0.05000 > key size 0.24000,0.04000 > key size 0.24000,0.03000 > key size 0.23000,0.03000 > key size 0.22000,0.03000 > key size 0.21000,0.03000 > key size 0.20000,0.03000 > key pos 0.671038,0.107382 > key pos 0,0.10738 > key pos 0.7000,0.10738 > key pos 0.70000,0.10738 > key pos 0.70000,0.10 > key pos 0.70000,0.10000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > key pos 0.70000,0.11000 > key pos 0.70000,0.10000 > key pos 0.70000,0.09000 > key pos 0.70000,0.08000 > key pos 0.70000,0.07000 > key pos 0.70000,0.06000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > surface dust #2 size 16.9 > select subtract #2 Nothing selected > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).png"" width 1243 height 913 > supersample 3 > volume #2 step 2 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > volume #2 step 1 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > hide #!2 models > show #!1 models > select add #1 2 models selected Surface Color: surface has no bounding box > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > ui mousemode right ""rotate selected models"" > hide #4 models > show #4 models > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.1 > volume #1 level 0.08 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png"" width 1243 height 913 > supersample 3 > volume #1 step 2 > volume #1 level 0.07 > volume #1 level 0.06 > volume #1 level 0.05 > volume #1 level 0.06 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png"" width 1243 height 913 > supersample 3 > surface undust #2 > select add #1 2 models selected > surface undust #1 > volume #1 level 0.2 > volume #1 step 1 > select subtract #1 Nothing selected > volume #1 level 0.1 > hide #!1 models > show #!2 models > volume #2 step 1 > volume #2 level 0.2 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > surface dust #2 size 16.9 > key #0cf0fa:200 blue:235 #9141ac:270 showTool true > ui mousemode right ""color key"" > key fontSize 17 > key fontSize 16 Could not find palette custom at COLOURlovers.com using keyword search > ui mousemode right ""rotate selected models"" > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).tif"" width 1243 height 913 > supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step1).tif"" width 1243 height 913 supersample 3 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step2).tif"" width 1243 height 913 supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"" ——— End of log from Mon Apr 14 19:17:23 2025 ——— opened ChimeraX session > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > select add #1 2 models selected > close #1 > hide #4 models > show #!3 models > select add #3 2 models selected > close #3 > show #!2 models > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"" Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32 > volume #2 level 0.35 > volume #2 step 1 > volume #1 level 0.2 > volume #1 step 1 > select add #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-48.634,0,1,0,1.6656,0,0,1,33.287 > view matrix models #1,1,0,0,13.61,0,1,0,6.7723,0,0,1,18.375 > view matrix models #1,1,0,0,13.668,0,1,0,6.639,0,0,1,17.833 > view matrix models #1,1,0,0,-17.789,0,1,0,2.819,0,0,1,20.629 > view matrix models #1,1,0,0,-39.187,0,1,0,0.34575,0,0,1,23.009 > select add #2 4 models selected > select subtract #2 2 models selected > view matrix models #1,1,0,0,-34.176,0,1,0,3.1709,0,0,1,20.524 > select add #2 4 models selected > fitmap #2 inMap #1 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J123_011_volume_map_sharp.mrc using 1224990 points correlation = 0.5927, correlation about mean = 0.05969, overlap = 8.84e+04 steps = 124, shift = 4.73, angle = 4.44 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J123_011_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 0.00000934 -0.00000606 -91.91551273 -0.00000934 1.00000000 -0.00001788 -91.90278947 0.00000606 0.00001788 1.00000000 -91.91231745 Axis 0.84889746 -0.28787388 -0.44328516 Axis point 0.00000000 5408246.84963320 -5313748.61359478 Rotation angle (degrees) 0.00120694 Shift along axis -10.82706671 > select subtract #2 2 models selected > select subtract #1 Nothing selected > hide #!2 models > volume flip #1 Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > show #!2 models > fitmap #2 inMap #3 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05 steps = 28, shift = 1.34, angle = 0.000137 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 1.00000000 0.00000760 -0.00000484 -91.89861891 -0.00000760 1.00000000 -0.00001899 -91.89997565 0.00000483 0.00001899 1.00000000 -93.24973991 Axis 0.90349284 -0.23008647 -0.36160876 Axis point 0.00000000 5447828.04621494 -5181752.87000347 Rotation angle (degrees) 0.00120402 Shift along axis -28.16488010 > select add #2 2 models selected > select add #3 4 models selected > fitmap #2 inMap #3 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05 steps = 24, shift = 0.0063, angle = 0.000111 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 1.00000000 0.00000613 -0.00000381 -91.89742078 -0.00000613 1.00000000 -0.00001975 -91.89877679 0.00000381 0.00001975 1.00000000 -93.25566971 Axis 0.93921386 -0.18128033 -0.29157292 Axis point 0.00000000 5347267.65743666 -5041635.74047945 Rotation angle (degrees) 0.00120513 Shift along axis -42.46106316 > select subtract #2 2 models selected > select subtract #3 Nothing selected > ui tool show ""Surface Color"" Surface Color: surface has no bounding box > hide #!2 models > hide #!3 models > show #!2 models > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.83,344.16,360.18 > hide #!2 models > show #!3 models > color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.82,344.16,360.18 [Repeated 1 time(s)] > set bgColor black > set bgColor transparent > volume #1 level 0.08 > hide #!3 models > show #!3 models > close #1 > volume #2 level 0.2 > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > volume #3 level 0.08 > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > color single #3.1 > color single #2.1 > color #3 white models > show #!3 models > volume #2 level 0.1 > volume #2 level 0.2 > color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.82,344.16,360.18 Drag select of 3 cryosparc_P108_J123_011_volume_map_sharp.mrc z flip > hide #!3 models > show #!3 models > select subtract #3 Nothing selected > set bgColor white > set bgColor #ffffff00 > select add #3 2 models selected > surface dust #3 size 13.3 > select subtract #3 Nothing selected > show #4 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1).tif"" width 1273 height 945 > supersample 3 > volume #3 step 2 > volume #3 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2).tif"" width 1273 height 945 > supersample 3 > hide #!3 models > show #!2 models > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.83,344.16,360.18 > show #!3 models > hide #!2 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold).tif"" width 1273 height 945 > supersample 3 > volume #3 level 0.08 > volume #3 step 1 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold).tif"" width 1273 height 945 > supersample 3 > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold)2.tif"" width 1273 height 945 > supersample 3 > volume #3 step 2 > volume #3 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold)2.tif"" width 1273 height 945 > supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"" ——— End of log from Mon Apr 14 20:39:34 2025 ——— opened ChimeraX session > open ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab13/J123 > DV2_Fab13 chimerax session.cxs"" format session Error opening map ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"": File J123 DV2_Fab13 chimerax session.cxs, format mrc MRC header value nsymbt (912209460) is invalid restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at level 0.05, step 2, values float32 Unable to restore session, resetting. Traceback (most recent call last): File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/session.py"", line 873, in restore obj = sm.restore_snapshot(self, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/surface/colorgeom.py"", line 236, in restore_snapshot % '.'.join('%d' % i for i in id)) ^^^^^^^^^^^^^^^^^^^^^^ TypeError: 'builtin_function_or_method' object is not iterable Log from Mon Apr 14 20:39:34 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > set bgColor #ffffff00 Log from Mon Apr 14 19:17:23 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb > format pdb current_fittingE7kv8_DENV2Fab13_20250330.pdb title: Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more info...] Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- Chain | Description A B C | envelope protein E a b c | matrix protein M Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- 1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"" Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32 > volume #1 level 0.17 > volume #1 level 0.13 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.15 > volume #1 level 0.16 > volume #1 level 0.17 > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > hide #!2 models > volume #1 > ui tool show ""Surface Color"" > color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center > 340.99,340.99,340.99 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 [Repeated 1 time(s)] > volume #1 level 0.13 > volume #1 level 0.12 > volume #1 level 0.11 > volume #1 level 0.1 > volume #1 level 0.0843 > volume #1 step 1 > select add #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45 > view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653 > view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468 > ui mousemode right ""translate selected models"" > select subtract #2 Nothing selected > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > select add #2 2 models selected > view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383 > view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477 > view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62 > view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41 > view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901 > view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853 > view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068 > select add #1 4 models selected > fitmap #1 inMap #2 Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05 steps = 56, shift = 7.96, angle = 0.00238 degrees Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00003026 0.00002609 91.91389849 0.00003026 1.00000000 -0.00001109 91.89891079 -0.00002609 0.00001109 1.00000000 91.91922251 Axis 0.26746273 0.62926682 0.72971704 Axis point 71695.94102549 1716204.69448452 0.00000000 Rotation angle (degrees) 0.00237592 Shift along axis 149.48750038 > select subtract #2 2 models selected > select subtract #1 Nothing selected > hide #!1 models > volume #2 step 1 > show #!1 models > color #2 #f5c211ff models > color #1 white models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.17 > select add #2 2 models selected > surface dust #2 size 16.9 > volume #2 level 0.0843 > select subtract #2 Nothing selected > volume flip #1 Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > surface dust #2 size 16.9 > surface dust #3 size 13.3 > hide #!2 models > show #!2 models > surface dust #2 size 16.9 > surface dust #3 size 13.3 > show #!1 models > hide #!3 models > surface undust #2 > volume #2 level 0.1844 > volume #2 level 0.2 > volume #2 level 0.25 > volume #2 level 0.27 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.3 > volume #2 level 0.35 > view > view orient > show #!1 models > surface undust #1 > volume #1 level 0.2 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 > hide #!1 models > color radial #2.1 palette > 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] Surface Color: surface has no bounding box [Repeated 2 time(s)] > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > color radial #1.1 palette > 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 > color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > hide #!1 models > show #!2 models > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 [Repeated 2 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > select add #2 2 models selected > select add #1 4 models selected > show #!1 models > hide #!1 models > view matrix models > #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144 > view matrix models > #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785 > select subtract #1 2 models selected > select subtract #2 Nothing selected > ui mousemode right ""rotate selected models"" > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > show #!1 models > hide #!2 models Surface Color: surface has no bounding box > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > volume #1 level 0.17 > volume #1 level 0.13 > volume #1 level 0.1 > volume #1 level 0.09 > volume #1 level 0.08 > volume #1 level 0.09 > hide #!1 models > show #!2 models > set bgColor white > set bgColor #ffffff00 > surface dust #2 size 16.9 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > surface undust #1 > volume #2 level 0.3 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > volume #2 level 0.2 > surface dust #2 size 16.9 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 19 > key fontSize 18 > key fontSize 17 > key fontSize 16 > key size 0.24000,0.05000 > key size 0.24000,0.04000 > key size 0.24000,0.03000 > key size 0.23000,0.03000 > key size 0.22000,0.03000 > key size 0.21000,0.03000 > key size 0.20000,0.03000 > key pos 0.671038,0.107382 > key pos 0,0.10738 > key pos 0.7000,0.10738 > key pos 0.70000,0.10738 > key pos 0.70000,0.10 > key pos 0.70000,0.10000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > key pos 0.70000,0.11000 > key pos 0.70000,0.10000 > key pos 0.70000,0.09000 > key pos 0.70000,0.08000 > key pos 0.70000,0.07000 > key pos 0.70000,0.06000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > surface dust #2 size 16.9 > select subtract #2 Nothing selected > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).png"" width 1243 height 913 > supersample 3 > volume #2 step 2 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > volume #2 step 1 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > hide #!2 models > show #!1 models > select add #1 2 models selected Surface Color: surface has no bounding box > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > ui mousemode right ""rotate selected models"" > hide #4 models > show #4 models > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.1 > volume #1 level 0.08 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png"" width 1243 height 913 > supersample 3 > volume #1 step 2 > volume #1 level 0.07 > volume #1 level 0.06 > volume #1 level 0.05 > volume #1 level 0.06 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png"" width 1243 height 913 > supersample 3 > surface undust #2 > select add #1 2 models selected > surface undust #1 > volume #1 level 0.2 > volume #1 step 1 > select subtract #1 Nothing selected > volume #1 level 0.1 > hide #!1 models > show #!2 models > volume #2 step 1 > volume #2 level 0.2 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > surface dust #2 size 16.9 > key #0cf0fa:200 blue:235 #9141ac:270 showTool true > ui mousemode right ""color key"" > key fontSize 17 > key fontSize 16 Could not find palette custom at COLOURlovers.com using keyword search > ui mousemode right ""rotate selected models"" > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).tif"" width 1243 height 913 > supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step1).tif"" width 1243 height 913 supersample 3 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step2).tif"" width 1243 height 913 supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"" ——— End of log from Mon Apr 14 19:17:23 2025 ——— opened ChimeraX session > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > select add #1 2 models selected > close #1 > hide #4 models > show #!3 models > select add #3 2 models selected > close #3 > show #!2 models > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"" Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32 > volume #2 level 0.35 > volume #2 step 1 > volume #1 level 0.2 > volume #1 step 1 > select add #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-48.634,0,1,0,1.6656,0,0,1,33.287 > view matrix models #1,1,0,0,13.61,0,1,0,6.7723,0,0,1,18.375 > view matrix models #1,1,0,0,13.668,0,1,0,6.639,0,0,1,17.833 > view matrix models #1,1,0,0,-17.789,0,1,0,2.819,0,0,1,20.629 > view matrix models #1,1,0,0,-39.187,0,1,0,0.34575,0,0,1,23.009 > select add #2 4 models selected > select subtract #2 2 models selected > view matrix models #1,1,0,0,-34.176,0,1,0,3.1709,0,0,1,20.524 > select add #2 4 models selected > fitmap #2 inMap #1 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J123_011_volume_map_sharp.mrc using 1224990 points correlation = 0.5927, correlation about mean = 0.05969, overlap = 8.84e+04 steps = 124, shift = 4.73, angle = 4.44 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J123_011_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 0.00000934 -0.00000606 -91.91551273 -0.00000934 1.00000000 -0.00001788 -91.90278947 0.00000606 0.00001788 1.00000000 -91.91231745 Axis 0.84889746 -0.28787388 -0.44328516 Axis point 0.00000000 5408246.84963320 -5313748.61359478 Rotation angle (degrees) 0.00120694 Shift along axis -10.82706671 > select subtract #2 2 models selected > select subtract #1 Nothing selected > hide #!2 models > volume flip #1 Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > show #!2 models > fitmap #2 inMap #3 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05 steps = 28, shift = 1.34, angle = 0.000137 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 1.00000000 0.00000760 -0.00000484 -91.89861891 -0.00000760 1.00000000 -0.00001899 -91.89997565 0.00000483 0.00001899 1.00000000 -93.24973991 Axis 0.90349284 -0.23008647 -0.36160876 Axis point 0.00000000 5447828.04621494 -5181752.87000347 Rotation angle (degrees) 0.00120402 Shift along axis -28.16488010 > select add #2 2 models selected > select add #3 4 models selected > fitmap #2 inMap #3 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05 steps = 24, shift = 0.0063, angle = 0.000111 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 1.00000000 0.00000613 -0.00000381 -91.89742078 -0.00000613 1.00000000 -0.00001975 -91.89877679 0.00000381 0.00001975 1.00000000 -93.25566971 Axis 0.93921386 -0.18128033 -0.29157292 Axis point 0.00000000 5347267.65743666 -5041635.74047945 Rotation angle (degrees) 0.00120513 Shift along axis -42.46106316 > select subtract #2 2 models selected > select subtract #3 Nothing selected > ui tool show ""Surface Color"" Surface Color: surface has no bounding box > hide #!2 models > hide #!3 models > show #!2 models > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.83,344.16,360.18 > hide #!2 models > show #!3 models > color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.82,344.16,360.18 [Repeated 1 time(s)] > set bgColor black > set bgColor transparent > volume #1 level 0.08 > hide #!3 models > show #!3 models > close #1 > volume #2 level 0.2 > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > volume #3 level 0.08 > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > color single #3.1 > color single #2.1 > color #3 white models > show #!3 models > volume #2 level 0.1 > volume #2 level 0.2 > color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.82,344.16,360.18 Drag select of 3 cryosparc_P108_J123_011_volume_map_sharp.mrc z flip > hide #!3 models > show #!3 models > select subtract #3 Nothing selected > set bgColor white > set bgColor #ffffff00 > select add #3 2 models selected > surface dust #3 size 13.3 > select subtract #3 Nothing selected > show #4 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1).tif"" width 1273 height 945 > supersample 3 > volume #3 step 2 > volume #3 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2).tif"" width 1273 height 945 > supersample 3 > hide #!3 models > show #!2 models > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.83,344.16,360.18 > show #!3 models > hide #!2 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold).tif"" width 1273 height 945 > supersample 3 > volume #3 level 0.08 > volume #3 step 1 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold).tif"" width 1273 height 945 > supersample 3 > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold)2.tif"" width 1273 height 945 > supersample 3 > volume #3 step 2 > volume #3 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold)2.tif"" width 1273 height 945 > supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"" ——— End of log from Mon Apr 14 20:39:34 2025 ——— opened ChimeraX session > open ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab13/J123 > DV2_Fab13 chimerax session.cxs"" format session Error opening map ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"": File J123 DV2_Fab13 chimerax session.cxs, format mrc MRC header value nsymbt (912209460) is invalid restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at level 0.05, step 2, values float32 Unable to restore session, resetting. Traceback (most recent call last): File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/session.py"", line 873, in restore obj = sm.restore_snapshot(self, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/surface/colorgeom.py"", line 236, in restore_snapshot % '.'.join('%d' % i for i in id)) ^^^^^^^^^^^^^^^^^^^^^^ TypeError: 'builtin_function_or_method' object is not iterable Log from Mon Apr 14 20:39:34 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > set bgColor #ffffff00 Log from Mon Apr 14 19:17:23 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb > format pdb current_fittingE7kv8_DENV2Fab13_20250330.pdb title: Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more info...] Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- Chain | Description A B C | envelope protein E a b c | matrix protein M Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- 1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"" Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32 > volume #1 level 0.17 > volume #1 level 0.13 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.15 > volume #1 level 0.16 > volume #1 level 0.17 > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > hide #!2 models > volume #1 > ui tool show ""Surface Color"" > color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center > 340.99,340.99,340.99 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 [Repeated 1 time(s)] > volume #1 level 0.13 > volume #1 level 0.12 > volume #1 level 0.11 > volume #1 level 0.1 > volume #1 level 0.0843 > volume #1 step 1 > select add #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45 > view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653 > view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468 > ui mousemode right ""translate selected models"" > select subtract #2 Nothing selected > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > select add #2 2 models selected > view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383 > view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477 > view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62 > view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41 > view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901 > view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853 > view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068 > select add #1 4 models selected > fitmap #1 inMap #2 Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05 steps = 56, shift = 7.96, angle = 0.00238 degrees Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00003026 0.00002609 91.91389849 0.00003026 1.00000000 -0.00001109 91.89891079 -0.00002609 0.00001109 1.00000000 91.91922251 Axis 0.26746273 0.62926682 0.72971704 Axis point 71695.94102549 1716204.69448452 0.00000000 Rotation angle (degrees) 0.00237592 Shift along axis 149.48750038 > select subtract #2 2 models selected > select subtract #1 Nothing selected > hide #!1 models > volume #2 step 1 > show #!1 models > color #2 #f5c211ff models > color #1 white models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.17 > select add #2 2 models selected > surface dust #2 size 16.9 > volume #2 level 0.0843 > select subtract #2 Nothing selected > volume flip #1 Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > surface dust #2 size 16.9 > surface dust #3 size 13.3 > hide #!2 models > show #!2 models > surface dust #2 size 16.9 > surface dust #3 size 13.3 > show #!1 models > hide #!3 models > surface undust #2 > volume #2 level 0.1844 > volume #2 level 0.2 > volume #2 level 0.25 > volume #2 level 0.27 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.3 > volume #2 level 0.35 > view > view orient > show #!1 models > surface undust #1 > volume #1 level 0.2 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 > hide #!1 models > color radial #2.1 palette > 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] Surface Color: surface has no bounding box [Repeated 2 time(s)] > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > color radial #1.1 palette > 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 > color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > hide #!1 models > show #!2 models > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 [Repeated 2 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > select add #2 2 models selected > select add #1 4 models selected > show #!1 models > hide #!1 models > view matrix models > #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144 > view matrix models > #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785 > select subtract #1 2 models selected > select subtract #2 Nothing selected > ui mousemode right ""rotate selected models"" > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > show #!1 models > hide #!2 models Surface Color: surface has no bounding box > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > volume #1 level 0.17 > volume #1 level 0.13 > volume #1 level 0.1 > volume #1 level 0.09 > volume #1 level 0.08 > volume #1 level 0.09 > hide #!1 models > show #!2 models > set bgColor white > set bgColor #ffffff00 > surface dust #2 size 16.9 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > surface undust #1 > volume #2 level 0.3 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > volume #2 level 0.2 > surface dust #2 size 16.9 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 19 > key fontSize 18 > key fontSize 17 > key fontSize 16 > key size 0.24000,0.05000 > key size 0.24000,0.04000 > key size 0.24000,0.03000 > key size 0.23000,0.03000 > key size 0.22000,0.03000 > key size 0.21000,0.03000 > key size 0.20000,0.03000 > key pos 0.671038,0.107382 > key pos 0,0.10738 > key pos 0.7000,0.10738 > key pos 0.70000,0.10738 > key pos 0.70000,0.10 > key pos 0.70000,0.10000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > key pos 0.70000,0.11000 > key pos 0.70000,0.10000 > key pos 0.70000,0.09000 > key pos 0.70000,0.08000 > key pos 0.70000,0.07000 > key pos 0.70000,0.06000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > surface dust #2 size 16.9 > select subtract #2 Nothing selected > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).png"" width 1243 height 913 > supersample 3 > volume #2 step 2 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > volume #2 step 1 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > hide #!2 models > show #!1 models > select add #1 2 models selected Surface Color: surface has no bounding box > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > ui mousemode right ""rotate selected models"" > hide #4 models > show #4 models > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.1 > volume #1 level 0.08 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png"" width 1243 height 913 > supersample 3 > volume #1 step 2 > volume #1 level 0.07 > volume #1 level 0.06 > volume #1 level 0.05 > volume #1 level 0.06 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png"" width 1243 height 913 > supersample 3 > surface undust #2 > select add #1 2 models selected > surface undust #1 > volume #1 level 0.2 > volume #1 step 1 > select subtract #1 Nothing selected > volume #1 level 0.1 > hide #!1 models > show #!2 models > volume #2 step 1 > volume #2 level 0.2 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > surface dust #2 size 16.9 > key #0cf0fa:200 blue:235 #9141ac:270 showTool true > ui mousemode right ""color key"" > key fontSize 17 > key fontSize 16 Could not find palette custom at COLOURlovers.com using keyword search > ui mousemode right ""rotate selected models"" > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).tif"" width 1243 height 913 > supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step1).tif"" width 1243 height 913 supersample 3 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step2).tif"" width 1243 height 913 supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"" ——— End of log from Mon Apr 14 19:17:23 2025 ——— opened ChimeraX session > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > select add #1 2 models selected > close #1 > hide #4 models > show #!3 models > select add #3 2 models selected > close #3 > show #!2 models > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"" Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32 > volume #2 level 0.35 > volume #2 step 1 > volume #1 level 0.2 > volume #1 step 1 > select add #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-48.634,0,1,0,1.6656,0,0,1,33.287 > view matrix models #1,1,0,0,13.61,0,1,0,6.7723,0,0,1,18.375 > view matrix models #1,1,0,0,13.668,0,1,0,6.639,0,0,1,17.833 > view matrix models #1,1,0,0,-17.789,0,1,0,2.819,0,0,1,20.629 > view matrix models #1,1,0,0,-39.187,0,1,0,0.34575,0,0,1,23.009 > select add #2 4 models selected > select subtract #2 2 models selected > view matrix models #1,1,0,0,-34.176,0,1,0,3.1709,0,0,1,20.524 > select add #2 4 models selected > fitmap #2 inMap #1 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J123_011_volume_map_sharp.mrc using 1224990 points correlation = 0.5927, correlation about mean = 0.05969, overlap = 8.84e+04 steps = 124, shift = 4.73, angle = 4.44 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J123_011_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 1.00000000 0.00000934 -0.00000606 -91.91551273 -0.00000934 1.00000000 -0.00001788 -91.90278947 0.00000606 0.00001788 1.00000000 -91.91231745 Axis 0.84889746 -0.28787388 -0.44328516 Axis point 0.00000000 5408246.84963320 -5313748.61359478 Rotation angle (degrees) 0.00120694 Shift along axis -10.82706671 > select subtract #2 2 models selected > select subtract #1 Nothing selected > hide #!2 models > volume flip #1 Opened cryosparc_P108_J123_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > show #!2 models > fitmap #2 inMap #3 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05 steps = 28, shift = 1.34, angle = 0.000137 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 1.00000000 0.00000760 -0.00000484 -91.89861891 -0.00000760 1.00000000 -0.00001899 -91.89997565 0.00000483 0.00001899 1.00000000 -93.24973991 Axis 0.90349284 -0.23008647 -0.36160876 Axis point 0.00000000 5447828.04621494 -5181752.87000347 Rotation angle (degrees) 0.00120402 Shift along axis -28.16488010 > select add #2 2 models selected > select add #3 4 models selected > fitmap #2 inMap #3 Fit map cryosparc_P108_J282_009_volume_map_sharp.mrc in map cryosparc_P108_J123_011_volume_map_sharp.mrc z flip using 1224990 points correlation = 0.9699, correlation about mean = 0.8076, overlap = 2.495e+05 steps = 24, shift = 0.0063, angle = 0.000111 degrees Position of cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) relative to cryosparc_P108_J123_011_volume_map_sharp.mrc z flip (#3) coordinates: Matrix rotation and translation 1.00000000 0.00000613 -0.00000381 -91.89742078 -0.00000613 1.00000000 -0.00001975 -91.89877679 0.00000381 0.00001975 1.00000000 -93.25566971 Axis 0.93921386 -0.18128033 -0.29157292 Axis point 0.00000000 5347267.65743666 -5041635.74047945 Rotation angle (degrees) 0.00120513 Shift along axis -42.46106316 > select subtract #2 2 models selected > select subtract #3 Nothing selected > ui tool show ""Surface Color"" Surface Color: surface has no bounding box > hide #!2 models > hide #!3 models > show #!2 models > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.83,344.16,360.18 > hide #!2 models > show #!3 models > color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.82,344.16,360.18 [Repeated 1 time(s)] > set bgColor black > set bgColor transparent > volume #1 level 0.08 > hide #!3 models > show #!3 models > close #1 > volume #2 level 0.2 > show #!2 models > hide #!3 models > hide #!2 models > show #!3 models > volume #3 level 0.08 > show #!2 models > hide #!3 models > show #!3 models > hide #!3 models > color single #3.1 > color single #2.1 > color #3 white models > show #!3 models > volume #2 level 0.1 > volume #2 level 0.2 > color radial #3.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.82,344.16,360.18 Drag select of 3 cryosparc_P108_J123_011_volume_map_sharp.mrc z flip > hide #!3 models > show #!3 models > select subtract #3 Nothing selected > set bgColor white > set bgColor #ffffff00 > select add #3 2 models selected > surface dust #3 size 13.3 > select subtract #3 Nothing selected > show #4 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1).tif"" width 1273 height 945 > supersample 3 > volume #3 step 2 > volume #3 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2).tif"" width 1273 height 945 > supersample 3 > hide #!3 models > show #!2 models > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 306.83,344.16,360.18 > show #!3 models > hide #!2 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold).tif"" width 1273 height 945 > supersample 3 > volume #3 level 0.08 > volume #3 step 1 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold).tif"" width 1273 height 945 > supersample 3 > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step1_3-fold)2.tif"" width 1273 height 945 > supersample 3 > volume #3 step 2 > volume #3 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/DV2_N15_Fab13 (step2_3-fold)2.tif"" width 1273 height 945 > supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"" ——— End of log from Mon Apr 14 20:39:34 2025 ——— opened ChimeraX session > open ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"" format > session Error opening map ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"": File J123 DV2_Fab13 chimerax session.cxs, format mrc MRC header value nsymbt (912209460) is invalid restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Redust"" returned None Unable to restore session, resetting. Traceback (most recent call last): File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/session.py"", line 873, in restore obj = sm.restore_snapshot(self, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/surface/colorgeom.py"", line 236, in restore_snapshot % '.'.join('%d' % i for i in id)) ^^^^^^^^^^^^^^^^^^^^^^ TypeError: 'builtin_function_or_method' object is not iterable Log from Mon Apr 14 19:50:11 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"" Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.1, step 1, values float32 Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.17, step 2, values float32 Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at level 0.0843, step 1, values float32 Log from Mon Apr 14 19:17:23 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb > format pdb current_fittingE7kv8_DENV2Fab13_20250330.pdb title: Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more info...] Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- Chain | Description A B C | envelope protein E a b c | matrix protein M Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- 1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"" Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32 > volume #1 level 0.17 > volume #1 level 0.13 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.15 > volume #1 level 0.16 > volume #1 level 0.17 > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > hide #!2 models > volume #1 > ui tool show ""Surface Color"" > color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center > 340.99,340.99,340.99 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 [Repeated 1 time(s)] > volume #1 level 0.13 > volume #1 level 0.12 > volume #1 level 0.11 > volume #1 level 0.1 > volume #1 level 0.0843 > volume #1 step 1 > select add #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45 > view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653 > view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468 > ui mousemode right ""translate selected models"" > select subtract #2 Nothing selected > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > select add #2 2 models selected > view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383 > view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477 > view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62 > view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41 > view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901 > view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853 > view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068 > select add #1 4 models selected > fitmap #1 inMap #2 Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05 steps = 56, shift = 7.96, angle = 0.00238 degrees Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00003026 0.00002609 91.91389849 0.00003026 1.00000000 -0.00001109 91.89891079 -0.00002609 0.00001109 1.00000000 91.91922251 Axis 0.26746273 0.62926682 0.72971704 Axis point 71695.94102549 1716204.69448452 0.00000000 Rotation angle (degrees) 0.00237592 Shift along axis 149.48750038 > select subtract #2 2 models selected > select subtract #1 Nothing selected > hide #!1 models > volume #2 step 1 > show #!1 models > color #2 #f5c211ff models > color #1 white models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.17 > select add #2 2 models selected > surface dust #2 size 16.9 > volume #2 level 0.0843 > select subtract #2 Nothing selected > volume flip #1 Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > surface dust #2 size 16.9 > surface dust #3 size 13.3 > hide #!2 models > show #!2 models > surface dust #2 size 16.9 > surface dust #3 size 13.3 > show #!1 models > hide #!3 models > surface undust #2 > volume #2 level 0.1844 > volume #2 level 0.2 > volume #2 level 0.25 > volume #2 level 0.27 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.3 > volume #2 level 0.35 > view > view orient > show #!1 models > surface undust #1 > volume #1 level 0.2 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 > hide #!1 models > color radial #2.1 palette > 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] Surface Color: surface has no bounding box [Repeated 2 time(s)] > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > color radial #1.1 palette > 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 > color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > hide #!1 models > show #!2 models > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 [Repeated 2 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > select add #2 2 models selected > select add #1 4 models selected > show #!1 models > hide #!1 models > view matrix models > #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144 > view matrix models > #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785 > select subtract #1 2 models selected > select subtract #2 Nothing selected > ui mousemode right ""rotate selected models"" > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > show #!1 models > hide #!2 models Surface Color: surface has no bounding box > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > volume #1 level 0.17 > volume #1 level 0.13 > volume #1 level 0.1 > volume #1 level 0.09 > volume #1 level 0.08 > volume #1 level 0.09 > hide #!1 models > show #!2 models > set bgColor white > set bgColor #ffffff00 > surface dust #2 size 16.9 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > surface undust #1 > volume #2 level 0.3 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > volume #2 level 0.2 > surface dust #2 size 16.9 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 19 > key fontSize 18 > key fontSize 17 > key fontSize 16 > key size 0.24000,0.05000 > key size 0.24000,0.04000 > key size 0.24000,0.03000 > key size 0.23000,0.03000 > key size 0.22000,0.03000 > key size 0.21000,0.03000 > key size 0.20000,0.03000 > key pos 0.671038,0.107382 > key pos 0,0.10738 > key pos 0.7000,0.10738 > key pos 0.70000,0.10738 > key pos 0.70000,0.10 > key pos 0.70000,0.10000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > key pos 0.70000,0.11000 > key pos 0.70000,0.10000 > key pos 0.70000,0.09000 > key pos 0.70000,0.08000 > key pos 0.70000,0.07000 > key pos 0.70000,0.06000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > surface dust #2 size 16.9 > select subtract #2 Nothing selected > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).png"" width 1243 height 913 > supersample 3 > volume #2 step 2 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > volume #2 step 1 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > hide #!2 models > show #!1 models > select add #1 2 models selected Surface Color: surface has no bounding box > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > ui mousemode right ""rotate selected models"" > hide #4 models > show #4 models > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.1 > volume #1 level 0.08 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png"" width 1243 height 913 > supersample 3 > volume #1 step 2 > volume #1 level 0.07 > volume #1 level 0.06 > volume #1 level 0.05 > volume #1 level 0.06 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png"" width 1243 height 913 > supersample 3 > surface undust #2 > select add #1 2 models selected > surface undust #1 > volume #1 level 0.2 > volume #1 step 1 > select subtract #1 Nothing selected > volume #1 level 0.1 > hide #!1 models > show #!2 models > volume #2 step 1 > volume #2 level 0.2 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > surface dust #2 size 16.9 > key #0cf0fa:200 blue:235 #9141ac:270 showTool true > ui mousemode right ""color key"" > key fontSize 17 > key fontSize 16 Could not find palette custom at COLOURlovers.com using keyword search > ui mousemode right ""rotate selected models"" > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).tif"" width 1243 height 913 > supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step1).tif"" width 1243 height 913 supersample 3 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step2).tif"" width 1243 height 913 supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"" ——— End of log from Mon Apr 14 19:17:23 2025 ——— opened ChimeraX session > close #1 > close #3 > ui tool show ""Surface Color"" > color radial #2.1 palette 210,#0cf0fa:240,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette > 160,#ff0000:180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff > center 304.1,346.73,364.43 > color radial #2.1 palette 120,#00ffff:160,#00ff00:200,#ffff00:240,#ff0000 > center 304.1,346.73,364.43 > color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff > center 304.1,346.73,364.43 > volume #2 step 1 > volume #2 level 0.2 > color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff > center 304.1,346.73,364.43 > color radial #2.1 palette 150,#ff0000:200,#f4f735:250,#0000ff center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 150,#ff0000:200,#ffff00:250,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ffff00:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ff7f7f:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ffffff center 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ffffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#ff0000:160,#ffffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#0000ff:160,#ffffff:240,#ff0000 center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#ff0000:220,#ffffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center > 304.1,346.73,364.43 [Repeated 1 time(s)] > key red:200 #f4f735:220 blue:240 showTool true > ui mousemode right ""color key"" > ui mousemode right translate > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/f-fold.tif"" width 1243 height 913 supersample 3 > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/3-fold.tif"" width 1243 height 913 supersample 3 > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > view matrix models > #2,0.93097,-0.36237,0.044589,38.647,0.36152,0.932,0.026031,-224.51,-0.05099,-0.0081145,0.99867,-42.311 > view matrix models > #2,0.83884,-0.53188,-0.11599,221.43,0.49449,0.83358,-0.24622,-121.6,0.22765,0.14919,0.96225,-215.26 > select subtract #2 Nothing selected > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/Assymmetric unit.tif"" width 1243 height 913 supersample 3 > hide #!2 models > show #!2 models > color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center > 304.1,346.73,364.43 > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/Assymmetric unit.tif"" width 1243 height 913 supersample 3 > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"" ——— End of log from Mon Apr 14 19:50:11 2025 ——— opened ChimeraX session > open ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"" format > session Error opening map ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- Fabs/DV2_N15_Fab13/J123 DV2_Fab13 chimerax session.cxs"": File J123 DV2_Fab13 chimerax session.cxs, format mrc MRC header value nsymbt (912209460) is invalid restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Redust"" returned None Unable to restore session, resetting. Traceback (most recent call last): File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/core/session.py"", line 873, in restore obj = sm.restore_snapshot(self, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/apps/chimerax/1.9-noble/usr/lib/ucsf-chimerax/lib/python3.11/site- packages/chimerax/surface/colorgeom.py"", line 236, in restore_snapshot % '.'.join('%d' % i for i in id)) ^^^^^^^^^^^^^^^^^^^^^^ TypeError: 'builtin_function_or_method' object is not iterable Log from Mon Apr 14 19:50:11 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"" Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.1, step 1, values float32 Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.17, step 2, values float32 Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at level 0.0843, step 1, values float32 Log from Mon Apr 14 19:17:23 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/kuhn/vnegi/Downloads/current_fittingE7kv8_DENV2Fab13_20250330.pdb > format pdb current_fittingE7kv8_DENV2Fab13_20250330.pdb title: Chimeric flavivirus between binjari virus and dengue virus serotype-2 [more info...] Chain information for current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- Chain | Description A B C | envelope protein E a b c | matrix protein M Non-standard residues in current_fittingE7kv8_DENV2Fab13_20250330.pdb #1 --- 1Q0 — (2S,3R,4Z)-3-hydroxy-2-[(9E)-octadec-9-enoylamino]octadec-4-en-1-yl dihydrogen phosphate 6OU — [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy- propan-2-yl] (~{Z})-octadec-9-enoate NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 13/cryosparc_P108_J123_011_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J123_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.269, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" format mrc Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > close session > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 23/cryosparc_P108_J246_011_volume_map_sharp.mrc"" Opened cryosparc_P108_J246_011_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 1.33, shown at level 0.355, step 2, values float32 > volume #1 level 0.17 > volume #1 level 0.13 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.15 > volume #1 level 0.16 > volume #1 level 0.17 > open ""/home/kuhn/vnegi/shared-scratch/DENV2-Fab maps_seq/DENV2-Fab > 26/cryosparc_P108_J282_009_volume_map_sharp.mrc"" Opened cryosparc_P108_J282_009_volume_map_sharp.mrc as #2, grid size 512,512,512, pixel 1.69, shown at level 0.326, step 2, values float32 > hide #!2 models > volume #1 > ui tool show ""Surface Color"" > color radial #1.1 palette #ff0000:#ffffff:#0000ff:#808080 center > 340.99,340.99,340.99 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 [Repeated 1 time(s)] > volume #1 level 0.13 > volume #1 level 0.12 > volume #1 level 0.11 > volume #1 level 0.1 > volume #1 level 0.0843 > volume #1 step 1 > select add #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-19.039,0,1,0,13.198,0,0,1,-39.45 > view matrix models #2,1,0,0,-31.094,0,1,0,21.512,0,0,1,-71.653 > view matrix models #2,1,0,0,-290.51,0,1,0,205.24,0,0,1,43.468 > ui mousemode right ""translate selected models"" > select subtract #2 Nothing selected > ui mousemode right ""translate selected models"" [Repeated 1 time(s)] > select add #2 2 models selected > view matrix models #2,1,0,0,-227.45,0,1,0,160.61,0,0,1,19.383 > view matrix models #2,1,0,0,-104.47,0,1,0,73.431,0,0,1,-47.477 > view matrix models #2,1,0,0,-117.28,0,1,0,-82.828,0,0,1,-107.62 > view matrix models #2,1,0,0,-137.63,0,1,0,-23.697,0,0,1,-145.41 > view matrix models #2,1,0,0,-16.762,0,1,0,-174.63,0,0,1,-26.901 > view matrix models #2,1,0,0,-96.496,0,1,0,-71.663,0,0,1,-92.853 > view matrix models #2,1,0,0,-95.804,0,1,0,-86.337,0,0,1,-96.068 > select add #1 4 models selected > fitmap #1 inMap #2 Fit map cryosparc_P108_J246_011_volume_map_sharp.mrc in map cryosparc_P108_J282_009_volume_map_sharp.mrc using 11003486 points correlation = 0.9133, correlation about mean = 0.8324, overlap = 7.888e+05 steps = 56, shift = 7.96, angle = 0.00238 degrees Position of cryosparc_P108_J246_011_volume_map_sharp.mrc (#1) relative to cryosparc_P108_J282_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00003026 0.00002609 91.91389849 0.00003026 1.00000000 -0.00001109 91.89891079 -0.00002609 0.00001109 1.00000000 91.91922251 Axis 0.26746273 0.62926682 0.72971704 Axis point 71695.94102549 1716204.69448452 0.00000000 Rotation angle (degrees) 0.00237592 Shift along axis 149.48750038 > select subtract #2 2 models selected > select subtract #1 Nothing selected > hide #!1 models > volume #2 step 1 > show #!1 models > color #2 #f5c211ff models > color #1 white models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > volume #2 level 0.17 > select add #2 2 models selected > surface dust #2 size 16.9 > volume #2 level 0.0843 > select subtract #2 Nothing selected > volume flip #1 Opened cryosparc_P108_J246_011_volume_map_sharp.mrc z flip as #3, grid size 512,512,512, pixel 1.33, shown at step 1, values float32 > surface dust #2 size 16.9 > surface dust #3 size 13.3 > hide #!2 models > show #!2 models > surface dust #2 size 16.9 > surface dust #3 size 13.3 > show #!1 models > hide #!3 models > surface undust #2 > volume #2 level 0.1844 > volume #2 level 0.2 > volume #2 level 0.25 > volume #2 level 0.27 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.3 > volume #2 level 0.35 > view > view orient > show #!1 models > surface undust #1 > volume #1 level 0.2 > color radial #1.1 palette > 250,#c061cb:150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 340.99,340.99,340.99 > hide #!1 models > color radial #2.1 palette > 150,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] Surface Color: surface has no bounding box [Repeated 2 time(s)] > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 0,#ffff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette > 0,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > color radial #1.1 palette > 180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 [Repeated 2 time(s)] > color radial #1.1 palette 200,#00ff00:220,#00ffff:240,#0000ff:250,#c061cb > center 337.1,346.56,336.84 > color radial #1.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.84 > hide #!1 models > show #!2 models > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:220,#0000ff:240,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:235,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 220,#00ffff:240,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 220,#00ffff:240,#0000ff:245,#c061cb center > 337.1,346.56,336.83 [Repeated 2 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:245,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:247,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:250,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 205,#00ffff:225,#0000ff:255,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:260,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 205,#00ffff:225,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 230,#00ffff:250,#0000ff:270,#c061cb center > 337.1,346.56,336.83 [Repeated 1 time(s)] > color radial #2.1 palette 170,#00ffff:220,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 190,#00ffff:230,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 337.1,346.56,336.83 > select add #2 2 models selected > select add #1 4 models selected > show #!1 models > hide #!1 models > view matrix models > #1,1,-3.026e-05,2.6094e-05,-40.413,3.026e-05,1,-1.1091e-05,4.5348,-2.6094e-05,1.1091e-05,1,17.421,#2,1,0,0,-132.33,0,1,0,-87.364,0,0,1,-74.498 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-34.956,3.026e-05,1,-1.1091e-05,5.6859,-2.6094e-05,1.1091e-05,1,26.716,#2,1,0,0,-126.87,0,1,0,-86.213,0,0,1,-65.203 > view matrix models > #1,1,-3.026e-05,2.6094e-05,-36.889,3.026e-05,1,-1.1091e-05,5.7265,-2.6094e-05,1.1091e-05,1,23.445,#2,1,0,0,-128.8,0,1,0,-86.172,0,0,1,-68.474 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98855,0.11479,-0.097936,-38.733,-0.10736,0.99116,0.078001,18.761,0.10602,-0.066593,0.99213,12.678,#2,0.98854,0.11482,-0.09796,-131.14,-0.10739,0.99115,0.078014,-69.625,0.10605,-0.066601,0.99213,-82.144 > view matrix models > #1,0.9973,-0.053362,-0.050463,-0.56575,0.054596,0.99823,0.023393,-20.258,0.049126,-0.026085,0.99845,16.111,#2,0.9973,-0.053332,-0.05049,-82.689,0.054567,0.99824,0.023403,-119.16,0.049153,-0.026095,0.99845,-77.785 > select subtract #1 2 models selected > select subtract #2 Nothing selected > ui mousemode right ""rotate selected models"" > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > show #!1 models > hide #!2 models Surface Color: surface has no bounding box > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > volume #1 level 0.17 > volume #1 level 0.13 > volume #1 level 0.1 > volume #1 level 0.09 > volume #1 level 0.08 > volume #1 level 0.09 > hide #!1 models > show #!2 models > set bgColor white > set bgColor #ffffff00 > surface dust #2 size 16.9 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #1.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > surface undust #1 > volume #2 level 0.3 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > color radial #2.1 palette 150,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > volume #2 level 0.2 > surface dust #2 size 16.9 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 19 > key fontSize 18 > key fontSize 17 > key fontSize 16 > key size 0.24000,0.05000 > key size 0.24000,0.04000 > key size 0.24000,0.03000 > key size 0.23000,0.03000 > key size 0.22000,0.03000 > key size 0.21000,0.03000 > key size 0.20000,0.03000 > key pos 0.671038,0.107382 > key pos 0,0.10738 > key pos 0.7000,0.10738 > key pos 0.70000,0.10738 > key pos 0.70000,0.10 > key pos 0.70000,0.10000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > key pos 0.70000,0.11000 > key pos 0.70000,0.10000 > key pos 0.70000,0.09000 > key pos 0.70000,0.08000 > key pos 0.70000,0.07000 > key pos 0.70000,0.06000 > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > surface dust #2 size 16.9 > select subtract #2 Nothing selected > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).png"" width 1243 height 913 > supersample 3 > volume #2 step 2 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > volume #2 step 1 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step2).png"" width 1243 height 913 > supersample 3 > hide #!2 models > show #!1 models > select add #1 2 models selected Surface Color: surface has no bounding box > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > key cyan:200 blue:235 #c061cb:270 showTool true > ui mousemode right ""color key"" > ui mousemode right ""rotate selected models"" > hide #4 models > show #4 models > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.1 > volume #1 level 0.08 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step1).png"" width 1243 height 913 > supersample 3 > volume #1 step 2 > volume #1 level 0.07 > volume #1 level 0.06 > volume #1 level 0.05 > volume #1 level 0.06 > select add #1 2 models selected > surface dust #1 size 13.3 > select subtract #1 Nothing selected > volume #1 level 0.05 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 map (step2).png"" width 1243 height 913 > supersample 3 > surface undust #2 > select add #1 2 models selected > surface undust #1 > volume #1 level 0.2 > volume #1 step 1 > select subtract #1 Nothing selected > volume #1 level 0.1 > hide #!1 models > show #!2 models > volume #2 step 1 > volume #2 level 0.2 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 206,#00ffff:238,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 210,#00ffff:240,#0000ff:270,#c061cb center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0c0a67:270,#c061cb center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#7562e8:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#3ee8de:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#00ffff:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#8df4f0:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#a5f7f8:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#4240bf:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#2ff5f5:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 200,#0cf0fa:235,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > surface dust #2 size 16.9 > key #0cf0fa:200 blue:235 #9141ac:270 showTool true > ui mousemode right ""color key"" > key fontSize 17 > key fontSize 16 Could not find palette custom at COLOURlovers.com using keyword search > ui mousemode right ""rotate selected models"" > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J282 control map (step1).tif"" width 1243 height 913 > supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step1).tif"" width 1243 height 913 supersample 3 > volume #2 step 2 > volume #2 level 0.17 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No > Fab ctrl)/J282 control map (step2).tif"" width 1243 height 913 supersample 3 > save ""/net/kuhn/home/vnegi/Desktop/Model Fitting DENV- > Fabs/DV2_N15_Fab23/J246 DV2_Fab23 chimerax session.cxs"" ——— End of log from Mon Apr 14 19:17:23 2025 ——— opened ChimeraX session > close #1 > close #3 > ui tool show ""Surface Color"" > color radial #2.1 palette 210,#0cf0fa:240,#0000ff:270,#9141ac center > 304.1,346.73,364.43 > color radial #2.1 palette > 160,#ff0000:180,#ffff00:200,#00ff00:220,#00ffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff > center 304.1,346.73,364.43 > color radial #2.1 palette 120,#00ffff:160,#00ff00:200,#ffff00:240,#ff0000 > center 304.1,346.73,364.43 > color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff > center 304.1,346.73,364.43 > volume #2 step 1 > volume #2 level 0.2 > color radial #2.1 palette 120,#ffff00:160,#00ff00:200,#00ffff:240,#0000ff > center 304.1,346.73,364.43 > color radial #2.1 palette 150,#ff0000:200,#f4f735:250,#0000ff center > 304.1,346.73,364.43 [Repeated 1 time(s)] > color radial #2.1 palette 150,#ff0000:200,#ffff00:250,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ffff00:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ff7f7f:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ffffff center 304.1,346.73,364.43 > color radial #2.1 palette 160,#ff0000:200,#ffffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#ff0000:160,#ffffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#0000ff:160,#ffffff:240,#ff0000 center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#ff0000:220,#ffffff:240,#0000ff center > 304.1,346.73,364.43 > color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center > 304.1,346.73,364.43 [Repeated 1 time(s)] > key red:200 #f4f735:220 blue:240 showTool true > ui mousemode right ""color key"" > ui mousemode right translate > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/f-fold.tif"" width 1243 height 913 supersample 3 > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/3-fold.tif"" width 1243 height 913 supersample 3 > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > view matrix models > #2,0.93097,-0.36237,0.044589,38.647,0.36152,0.932,0.026031,-224.51,-0.05099,-0.0081145,0.99867,-42.311 > view matrix models > #2,0.83884,-0.53188,-0.11599,221.43,0.49449,0.83358,-0.24622,-121.6,0.22765,0.14919,0.96225,-215.26 > select subtract #2 Nothing selected > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/Assymmetric unit.tif"" width 1243 height 913 supersample 3 > hide #!2 models > show #!2 models > color radial #2.1 palette 200,#ff0000:220,#f4f735:240,#0000ff center > 304.1,346.73,364.43 > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/Assymmetric unit.tif"" width 1243 height 913 supersample 3 > save ""/home/kuhn/vnegi/Desktop/Model Fitting DENV-Fabs/DV2_N15_Fab26 (No Fab > ctrl)/J282 DV2_N15 ctrl (Fab26 not bound) chimerax session.cxs"" ——— End of log from Mon Apr 14 19:50:11 2025 ——— opened ChimeraX session OpenGL version: 3.3.0 NVIDIA 535.183.01 OpenGL renderer: NVIDIA GeForce GTX 750 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: Supermicro Model: Super Server OS: Ubuntu 24.04 Architecture: 64bit ELF Virtual Machine: none CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz Cache Size: 15360 KB Memory: total used free shared buff/cache available Mem: 62Gi 19Gi 16Gi 414Mi 28Gi 43Gi Swap: 8.0Gi 171Mi 7.8Gi Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM107 [GeForce GTX 750 Ti] [10de:1380] (rev a2) Subsystem: eVga.com. Corp. GM107 [GeForce GTX 750 Ti] [3842:3751] Kernel driver in use: nvidia Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2024.8.30 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 distro: 1.9.0 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Sessions fixed all ChimeraX