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Opened 6 years ago
Last modified 6 years ago
#2794 assigned defect
SideVIew self.view.render is None
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-4.4.0-173-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-06-29) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-06-29) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /data/disk3/20200202-Figure6new-SPA-ET.cxs format session opened ChimeraX session > show #!18 models > show #!19 models > show #!20 models > hide #!20 models > hide #!19 models > hide #!18 models > show #!32 models > hide #!32 models > show #!34 models > hide #!34 models > show #!34 models > hide #!51 models > show #!51 models > hide #!51 models > show #!51 models > hide #!65 models > show #!65 models > hide #!62 models > hide #!65 models > show #!65 models > show #!46 models > hide #!34 models > show #!34 models > hide #!34 models > hide #!51 models > show #!51 models > hide #!49 models > show #!49 models > hide #!46 models > show #!46 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!7 models > hide #!7 models > hide #!46 models > show #!46 models > hide #!46 models > show #!46 models > hide #!51 models > show #!51 models > hide #!51 models > hide #!50 models > show #!50 models > show #!51 models > show #!48 models > hide #!48 models > show #!48 models > hide #!48 models > show #!38 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > show #!39 models > show #!35 models > hide #!35 models > show #!35 models > hide #!35 models > show #!30 models > hide #!30 models > show #!29 models > hide #!29 models > show #!29 models > hide #!29 models > hide #!46 models > show #!46 models > select #46 2 models selected > ui mousemode rightMode "translate selected models" > select clear > select clear > open /data/disk3/modeling/gp12/genome-inside-channel.mrc Opened genome-inside-channel.mrc, grid size 400,400,400, pixel 1.05, shown at level -7.94e-18, step 2, values float32 > select #67 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > hide #!51 models > show #!44 models > show #!43 models > hide #!43 models > hide #!44 models > show #!42 models > show #!43 models > show #!44 models > hide #!44 models > hide #!43 models > show #!44 models > show #!43 models > hide #!43 models > hide #!44 models > hide #!65 models > ui mousemode rightMode "translate selected models" > select #42 12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected > ~select #42 2 models selected > select #67 2 models selected > open /data/disk3/modeling/gp12/dsDNA-model.pdb Chain information for dsDNA-model.pdb --- Chain | Description 68.1/A 68.1/B 68.1/C 68.1/D 68.1/E 68.1/F 68.1/G 68.1/H 68.1/I 68.1/J 68.1/K 68.1/L | No description available 68.2/A 68.2/B 68.2/C 68.2/D 68.2/E 68.2/F 68.2/G 68.2/H 68.2/I 68.2/J 68.2/K 68.2/L | No description available 68.3/A 68.3/B 68.3/C 68.3/D 68.3/E 68.3/F | No description available 68.4/A 68.4/B 68.4/C 68.4/D 68.4/E 68.4/F 68.4/G 68.4/H 68.4/I 68.4/J 68.4/K 68.4/L 68.4/M 68.4/N 68.4/O 68.4/P 68.4/Q 68.4/R | No description available 68.5/A 68.5/B 68.5/C 68.5/D 68.5/E 68.5/F 68.5/G 68.5/H 68.5/I 68.5/J 68.5/K 68.5/L | No description available 68.8/A 68.8/B 68.8/C 68.8/D 68.8/F 68.8/G 68.8/H 68.8/I 68.8/J 68.8/K 68.8/L 68.8/M | No description available 68.13/A 68.14/A 68.13/G 68.14/G | No description available 68.17/A 68.19/A 68.21/A 68.23/A 68.18/B 68.20/B 68.22/B 68.24/B | No description available 68.8/E 68.8/N 68.8/O 68.8/P 68.8/Q 68.8/R 68.8/S 68.8/T 68.8/U 68.8/V 68.8/W 68.8/X | No description available 68.6/M 68.9/M 68.6/O 68.9/O 68.6/Q 68.9/Q 68.6/S 68.9/S 68.6/U 68.9/U 68.6/W 68.9/W | No description available 68.6/N 68.9/N 68.6/P 68.9/P 68.11/P 68.15/P 68.6/R 68.9/R 68.6/T 68.9/T 68.6/V 68.9/V 68.11/V 68.15/V 68.6/X 68.9/X | No description available 68.7/a 68.10/a 68.7/b 68.10/b 68.7/c 68.10/c 68.12/c 68.16/c 68.7/d 68.10/d 68.7/e 68.10/e 68.12/e 68.16/e 68.7/f 68.10/f | No description available > select clear > hide #!68 models > show #!68 models > hide #!68.24 models > hide #!68.23 models > hide #!68.22 models > hide #!68.21 models > hide #!68.20 models > hide #!68.19 models > hide #!68.18 models > hide #!68.17 models > hide #!68.16 models > hide #!68.15 models > hide #!68.14 models > hide #!68.13 models > hide #!68.12 models > hide #!68.11 models > hide #!68.10 models > hide #!68.9 models > hide #!68.8 models > hide #!68.7 models > hide #!68.6 models > hide #!68.5 models > hide #!68.4 models > hide #!68.3 models > hide #!68.2 models > hide #!68.1 models > hide #!68 models > show #!68 models > hide #!68 models > show #!68.1 models > hide #!68.1 models > show #!68.2 models > hide #!68.2 models > show #!68.3 models > hide #!68.3 models > show #!68.4 models > hide #!68.4 models > show #!68.5 models > hide #!68.5 models > show #!68.7 models > hide #!68.7 models > show #!68.8 models > hide #!68.8 models > show #!68.11 models > show #!68.12 models > hide #!68.12 models > hide #!68.11 models > show #!68.13 models > hide #!68.13 models > show #!68.14 models > hide #!68.14 models > show #!68.16 models > hide #!68.16 models > show #!68.17 models > show #!68.18 models > show #!68.19 models > show #!68.20 models > show #!68.21 models > show #!68.22 models > show #!68.23 models > show #!68.24 models > close #68.1,2,4-6,9,11,13-15,3,7,8,10,12,16 > hide #!67 models > select #68 2264 atoms, 2176 bonds, 9 models selected > show #!67 models > ui mousemode rightMode "translate selected models" > fitmap #68 inMap #67 Fit molecules dsDNA-model.pdb (#68.17), dsDNA-model.pdb (#68.18), dsDNA- model.pdb (#68.19), dsDNA-model.pdb (#68.20), dsDNA-model.pdb (#68.21), dsDNA- model.pdb (#68.22), dsDNA-model.pdb (#68.23), dsDNA-model.pdb (#68.24) to map genome-inside-channel.mrc (#67) using 2264 atoms average map value = 0.003365, steps = 56 shifted from previous position = 2.29 rotated from previous position = 0.692 degrees atoms outside contour = 591, contour level = 0.00051136 Position of dsDNA-model.pdb (#68.17) relative to genome-inside-channel.mrc (#67) coordinates: Matrix rotation and translation 0.99916891 0.00742705 -0.04007909 -207.12204246 -0.00500496 0.99817390 0.06019817 -221.11499424 0.04045299 -0.05994754 0.99738150 -283.15010974 Axis -0.82760837 -0.55473491 -0.08563627 Axis point 0.00000000 -4295.18513571 609.42187588 Rotation angle (degrees) 4.16253735 Shift along axis 318.32405956 Position of dsDNA-model.pdb (#68.18) relative to genome-inside-channel.mrc (#67) coordinates: Matrix rotation and translation 0.99916891 0.00742705 -0.04007909 -207.12204246 -0.00500496 0.99817390 0.06019817 -221.11499424 0.04045299 -0.05994754 0.99738150 -283.15010974 Axis -0.82760837 -0.55473491 -0.08563627 Axis point 0.00000000 -4295.18513571 609.42187588 Rotation angle (degrees) 4.16253735 Shift along axis 318.32405956 Position of dsDNA-model.pdb (#68.19) relative to genome-inside-channel.mrc (#67) coordinates: Matrix rotation and translation 0.99916891 0.00742705 -0.04007909 -207.12204246 -0.00500496 0.99817390 0.06019817 -221.11499424 0.04045299 -0.05994754 0.99738150 -283.15010974 Axis -0.82760837 -0.55473491 -0.08563627 Axis point 0.00000000 -4295.18513571 609.42187588 Rotation angle (degrees) 4.16253735 Shift along axis 318.32405956 Position of dsDNA-model.pdb (#68.20) relative to genome-inside-channel.mrc (#67) coordinates: Matrix rotation and translation 0.99916891 0.00742705 -0.04007909 -207.12204246 -0.00500496 0.99817390 0.06019817 -221.11499424 0.04045299 -0.05994754 0.99738150 -283.15010974 Axis -0.82760837 -0.55473491 -0.08563627 Axis point 0.00000000 -4295.18513571 609.42187588 Rotation angle (degrees) 4.16253735 Shift along axis 318.32405956 Position of dsDNA-model.pdb (#68.21) relative to genome-inside-channel.mrc (#67) coordinates: Matrix rotation and translation 0.99916891 0.00742705 -0.04007909 -207.12204246 -0.00500496 0.99817390 0.06019817 -221.11499424 0.04045299 -0.05994754 0.99738150 -283.15010974 Axis -0.82760837 -0.55473491 -0.08563627 Axis point 0.00000000 -4295.18513571 609.42187588 Rotation angle (degrees) 4.16253735 Shift along axis 318.32405956 Position of dsDNA-model.pdb (#68.22) relative to genome-inside-channel.mrc (#67) coordinates: Matrix rotation and translation 0.99916891 0.00742705 -0.04007909 -207.12204246 -0.00500496 0.99817390 0.06019817 -221.11499424 0.04045299 -0.05994754 0.99738150 -283.15010974 Axis -0.82760837 -0.55473491 -0.08563627 Axis point 0.00000000 -4295.18513571 609.42187588 Rotation angle (degrees) 4.16253735 Shift along axis 318.32405956 Position of dsDNA-model.pdb (#68.23) relative to genome-inside-channel.mrc (#67) coordinates: Matrix rotation and translation 0.99916891 0.00742705 -0.04007909 -207.12204246 -0.00500496 0.99817390 0.06019817 -221.11499424 0.04045299 -0.05994754 0.99738150 -283.15010974 Axis -0.82760837 -0.55473491 -0.08563627 Axis point 0.00000000 -4295.18513571 609.42187588 Rotation angle (degrees) 4.16253735 Shift along axis 318.32405956 Position of dsDNA-model.pdb (#68.24) relative to genome-inside-channel.mrc (#67) coordinates: Matrix rotation and translation 0.99916891 0.00742705 -0.04007909 -207.12204246 -0.00500496 0.99817390 0.06019817 -221.11499424 0.04045299 -0.05994754 0.99738150 -283.15010974 Axis -0.82760837 -0.55473491 -0.08563627 Axis point 0.00000000 -4295.18513571 609.42187588 Rotation angle (degrees) 4.16253735 Shift along axis 318.32405956 > select clear > hide #!67 models > hide #!68.18 models > show #!68.18 models > select clear > show #!67 models > transparency #67 70 > transparency #67 80 > transparency #67 50 > transparency #67 0 > hide #!67 models > show #!67 models > hide #!68 models > show #!68 models > select #68 2264 atoms, 2176 bonds, 9 models selected > ui mousemode rightMode "translate selected models" > select clear > show #!56 models > select clear > hide #!56 models > show #!56 models > hide #!56 models > hide #!67 models > show #!67 models > select #67 2 models selected > open /data/disk3/modeling/gp12/genome-inside-channel.mrc Opened genome-inside-channel.mrc, grid size 400,400,400, pixel 1.05, shown at level -7.94e-18, step 2, values float32 > select #69 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select #67 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #68 2264 atoms, 2176 bonds, 9 models selected > ~select #68 Nothing selected > select #69 2 models selected > select #67 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #68 2264 atoms, 2176 bonds, 9 models selected > hide #!68 models > show #!68 models > hide #!67 models > hide #!69 models > hide #!68 models > show #!68 models > open /data/disk3/modeling/gp12/dsDNA-model1.pdb Chain information for dsDNA-model1.pdb --- Chain | Description 70.3/A 70.19/A 70.19/D 70.19/E 70.19/F 70.19/G 70.19/H | No description available 70.4/A 70.22/B 70.23/B | No description available 70.5/A 70.8/A 70.9/A 70.10/A 70.11/A 70.12/A 70.13/A 70.14/A 70.15/A 70.16/A 70.17/A 70.18/A | No description available 70.24/A 70.25/A 70.25/B 70.3/C 70.19/C 70.24/C 70.25/C 70.19/N 70.19/O 70.19/P 70.19/Q 70.19/R | No description available 70.26/A 70.28/A 70.30/A 70.32/A 70.27/B 70.29/B 70.31/B 70.33/B | No description available 70.3/B 70.19/B 70.19/I 70.19/J 70.19/K 70.19/L 70.19/M | No description available 70.6/B 70.8/B 70.9/B 70.10/B 70.11/B 70.12/B 70.13/B 70.14/B 70.15/B 70.16/B 70.17/B 70.18/B 70.7/C 70.8/C 70.9/C 70.10/C 70.11/C 70.12/C 70.13/C 70.14/C 70.15/C 70.16/C 70.17/C 70.18/C | No description available 70.24/B | No description available 70.24/D | No description available 70.1/T | No description available 70.1/U | No description available 70.2/a 70.20/a 70.20/b 70.21/b 70.20/c 70.20/d 70.20/e 70.20/f 70.21/f | No description available > hide #!70 models > hide #!70.33 models > hide #!70.32 models > show #!70.32 models > show #!70.33 models > hide #!70 models > hide #!70.1 models > hide #!70.2 models > hide #!70.3 models > hide #!70.4 models > hide #!70.5 models > hide #!70.6 models > hide #!70.7 models > hide #!70.9 models > hide #!70.8 models > hide #!70.10 models > hide #!70.11 models > hide #!70.12 models > hide #!70.13 models > hide #!70.14 models > hide #!70.15 models > hide #!70.16 models > hide #!70.17 models > hide #!70.18 models > hide #!70.19 models > hide #!70.20 models > hide #!70.21 models > hide #!70.22 models > hide #!70.23 models > hide #!70.24 models > hide #!70.25 models > hide #!70.26 models > hide #!70.27 models > hide #!70.28 models > hide #!70.29 models > hide #!70.30 models > hide #!70.31 models > hide #!70.32 models > hide #!70.33 models > show #!70 models > show #!70.1 models > hide #!70.1 models > show #!70.2 models > hide #!70.2 models > show #!70.2 models > hide #!70.2 models > show #!70.3 models > hide #!70.3 models > show #!70.4 models > hide #!70.4 models > show #!70.4 models > hide #!70.4 models > show #!70.5 models > show #!70.6 models > hide #!70.6 models > hide #!70.5 models > show #!70.7 models > hide #!70.7 models > show #!70.8 models > hide #!70.8 models > show #!70.9 models > hide #!70.9 models > show #!70.10 models > hide #!70.10 models > show #!70.11 models > hide #!70.11 models > show #!70.12 models > hide #!70.12 models > show #!70.13 models > hide #!70.13 models > show #!70.14 models > hide #!70.14 models > show #!70.14 models > show #!70.13 models > hide #!70.13 models > hide #!70.14 models > show #!70.15 models > hide #!70.15 models > show #!70.16 models > hide #!70.16 models > show #!70.17 models > hide #!70.17 models > show #!70.18 models > hide #!70.18 models > show #!70.19 models > hide #!70.19 models > show #!70.19 models > hide #!70.19 models > show #!70.20 models > hide #!70.20 models > show #!70.20 models > hide #!70.20 models > show #!70.21 models > hide #!70.21 models > show #!70.22 models > hide #!70.22 models > show #!70.23 models > hide #!70.23 models > show #!70.24 models > hide #!70.24 models > show #!70.25 models > hide #!70.25 models > show #!70.25 models > hide #!70.25 models > show #!70.27 models > show #!70.26 models > hide #!70.26 models > hide #!70.27 models > show #!70.28 models > hide #!70.28 models > show #!70.29 models > hide #!70.29 models > show #!70.30 models > hide #!70.30 models > show #!70.30 models > hide #!70.30 models > show #!70.30 models > select #70.30 280 atoms, 272 bonds, 1 model selected > undo > undo > show #!70.26 models > show #!70.27 models > show #!70.28 models > show #!70.29 models > show #!70.30 models > show #!70.31 models > show #!70.32 models > show #!70.33 models > hide #!70.27 models > show #!70.27 models > show #!70.25 models > hide #!70.25 models > hide #!70 models > show #!70 models > hide #!70 models > show #!70 models > hide #!68 models > undo > undo > close #70.0-1,3,5-19,25,2,4,20,21,22,23,24 > show #!70 models > hide #!70 models > hide #!68 models > show #!70 models > select #70.27 286 atoms, 272 bonds, 1 model selected > hide #!70.27 models > show #!70.27 models > ~select #70.27 Nothing selected > hide #!70.30 models > show #!70.30 models > select #70.30 280 atoms, 272 bonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > show #!68 models > hide #!70 models > show #!69 models > show #!67 models > ~select #70.30 Nothing selected > select #70.30 280 atoms, 272 bonds, 1 model selected > hide #!67 models > hide #!69 models > show #!69 models > hide #!68 models > show #!68 models > show #!65 models > hide #!65 models > show #!65 models > hide #!65 models > hide #!42 models > show #!43 models > show #!44 models > show #!53 models > hide #!39 models > show #!39 models > hide #!39 models > hide #!49 models > show #!49 models > hide #!50 models > hide #!49 models > show #!49 models > hide #!38 models > show #!35 models > hide #!35 models > show #!33 models > hide #!33 models > show #!33 models > hide #!33 models > show #!33 models > show #!22 models > hide #!22 models > show #!23 models > hide #!23 models > hide #!33 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!21 models > hide #!21 models > show #!35 models > hide #!35 models > show #!36 models > hide #!36 models > show #!38 models > show #!40 models > hide #!69 models > show #!69 models > hide #!70.26 models > show #!70.26 models > hide #!68 models > show #!68 models > hide #!70 models > hide #!70.30 models > hide #!68 models > hide #!38 models > show #!38 models > hide #!53 models > show #!53 models > hide #!53 models > hide #!43 models > show #!43 models > select clear > hide #!69 models > show #!69 models > select #69 2 models selected > ui mousemode rightMode "translate selected models" > select clear > show #!70 models > hide #!70 models > show #!68 models > select #68 2264 atoms, 2176 bonds, 9 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > hide #!68 models > select clear > hide #!46 models > show #!46 models > select #46 2 models selected > show #!48 models > hide #!49 models > hide #!48 models > show #!48 models > hide #!46 models > show #!46 models > hide #!46 models > hide #!48 models > show #!48 models > hide #!38 models > show #!46 models > hide #!46 models > show #!46 models > select clear > lighting soft > lighting simple > lighting shadows true > lighting full > select clear > lighting soft > lighting simple > lighting full > select clear > save image /data/disk3/Paper-use/channel-20200202.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!43 models > show #!43 models > hide #!46 models > show #!46 models Expected a keyword > surface dust #46 size 50 > save image /data/disk3/Paper-use/channel-20200202.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!69 models > show #!70 models > hide #!70 models > show #!68 models > hide #!43 models > hide #!44 models > show #!43 models > select #43 6289 atoms, 6447 bonds, 1 pseudobond, 2 models selected > hide selAtoms surfaces > select #44 6289 atoms, 6447 bonds, 1 pseudobond, 2 models selected > show #!44 models > hide selAtoms surfaces > select clear > hide #!46 models > show #!46 models > hide #!40 models > show #!40 models > select #40 2 models selected > transparency #40 80 > select clear > transparency #48 0 > transparency #48 80 > select clear > show #!69 models > hide #!68 models > select #69 2 models selected > select clear > select #44 6289 atoms, 6447 bonds, 1 pseudobond, 2 models selected > select #43 6289 atoms, 6447 bonds, 1 pseudobond, 2 models selected > show selAtoms surfaces > select #44 6289 atoms, 6447 bonds, 1 pseudobond, 2 models selected > show selAtoms surfaces > select clear > show #!70 models > hide #!70 models > close #70 > open /data/disk3/modeling/gp12/dsDNA-model1.pdb Chain information for dsDNA-model1.pdb --- Chain | Description 70.3/A 70.19/A 70.19/D 70.19/E 70.19/F 70.19/G 70.19/H | No description available 70.4/A 70.22/B 70.23/B | No description available 70.5/A 70.8/A 70.9/A 70.10/A 70.11/A 70.12/A 70.13/A 70.14/A 70.15/A 70.16/A 70.17/A 70.18/A | No description available 70.24/A 70.25/A 70.25/B 70.3/C 70.19/C 70.24/C 70.25/C 70.19/N 70.19/O 70.19/P 70.19/Q 70.19/R | No description available 70.26/A 70.28/A 70.30/A 70.32/A 70.27/B 70.29/B 70.31/B 70.33/B | No description available 70.3/B 70.19/B 70.19/I 70.19/J 70.19/K 70.19/L 70.19/M | No description available 70.6/B 70.8/B 70.9/B 70.10/B 70.11/B 70.12/B 70.13/B 70.14/B 70.15/B 70.16/B 70.17/B 70.18/B 70.7/C 70.8/C 70.9/C 70.10/C 70.11/C 70.12/C 70.13/C 70.14/C 70.15/C 70.16/C 70.17/C 70.18/C | No description available 70.24/B | No description available 70.24/D | No description available 70.1/T | No description available 70.1/U | No description available 70.2/a 70.20/a 70.20/b 70.21/b 70.20/c 70.20/d 70.20/e 70.20/f 70.21/f | No description available > hide #!69 models > hide #!70 models > show #!69 models > show #!68 models > hide #!68 models > show #!67 models > hide #!67 models > hide #!70.3 models > show #!70.3 models > hide #!70 models > show #!70 models > hide #!70.1 models > hide #!70.2 models > hide #!70.3 models > hide #!70.4 models > hide #70.4,5-19,25-33,20,21,22,23,24 target m > show #!70.33 models > show #!70.32 models > show #!70.31 models > show #!70.29 models > show #!70.30 models > show #!70.28 models > show #!70.27 models > show #!70.26 models > show #!70.25 models > show #!70.24 models > show #!70.23 models > show #!70.22 models > show #!70.21 models > show #!70.20 models > hide #!70.20 models > show #!70.20 models > select #70.20 37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected > close #70.21 > show #!70.19 models > close #70.20 > hide #!70.19 models > show #!70.19 models > select #70.19 16878 atoms, 17130 bonds, 1 model selected > close #70.19 > show #!70.18 models > hide #!70.18 models > show #!70.17 models > hide #!70.17 models > show #!70.16 models > hide #!70.16 models > show #!70.15 models > hide #!70.15 models > show #!70.14 models > hide #!70.14 models > show #!70.13 models > hide #!70.13 models > show #!70.12 models > hide #!70.12 models > show #!70.11 models > hide #!70.11 models > show #!70.10 models > hide #!70.10 models > show #!70.9 models > hide #!70.9 models > show #!70.8 models > hide #!70.8 models > show #!70.8 models > hide #!70.8 models > show #!70.7 models > hide #!70.7 models > show #!70.6 models > hide #!70.6 models > show #!70.5 models > show #!70.4 models > show #!70.3 models > show #!70.1 models > show #!70.2 models > hide #!70.1 models > hide #!70.2 models > hide #!70.3 models > hide #!70.4 models > hide #!70.5 models > hide #!70.22 models > hide #!70.23 models > hide #!70.24 models > hide #!70.25 models > close #70.1,3,5-18,25,2,4,22,23,24 > hide #!70 models > show #!1 models > hide #!1 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > show #!22 models > hide #!22 models > open /data/disk3/modeling/gp11/gp11-6R21-c2.pdb Chain information for gp11-6R21-c2.pdb #71 --- Chain | Description T | No description available U | No description available > select #71 3032 atoms, 3086 bonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > show #!56 models > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > hide #!56 models > show #!56 models > hide #!56 models > show #!56 models > fitmap #71 inMap #56 Fit molecule gp11-6R21-c2.pdb (#71) to map gp11-c6-clean-lp.mrc (#56) using 3032 atoms average map value = 0.007648, steps = 216 shifted from previous position = 13.3 rotated from previous position = 44.9 degrees atoms outside contour = 256, contour level = 0.0026326 Position of gp11-6R21-c2.pdb (#71) relative to gp11-c6-clean-lp.mrc (#56) coordinates: Matrix rotation and translation -0.86390503 -0.50365397 -0.00088417 0.10034065 0.50365471 -0.86390425 -0.00117846 -0.05799866 -0.00017030 -0.00146339 0.99999891 -0.13149974 Axis -0.00028287 -0.00070869 0.99999971 Axis point 0.05800037 -0.01549419 0.00000000 Rotation angle (degrees) 149.75792509 Shift along axis -0.13148698 > open /data/disk3/modeling/gp11/gp11-6R21-c2.pdb Chain information for gp11-6R21-c2.pdb #72 --- Chain | Description T | No description available U | No description available > select #72 3032 atoms, 3086 bonds, 1 model selected > view cofr false > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > fitmap #72 inMap #56 Fit molecule gp11-6R21-c2.pdb (#72) to map gp11-c6-clean-lp.mrc (#56) using 3032 atoms average map value = 0.007648, steps = 208 shifted from previous position = 15.1 rotated from previous position = 27.9 degrees atoms outside contour = 258, contour level = 0.0026326 Position of gp11-6R21-c2.pdb (#72) relative to gp11-c6-clean-lp.mrc (#56) coordinates: Matrix rotation and translation 0.86393131 0.50360854 0.00103514 -0.09924487 -0.50360939 0.86393102 0.00085142 0.05416421 -0.00046551 -0.00125687 0.99999908 -0.12807866 Axis -0.00209317 0.00148990 -0.99999670 Axis point 0.05039254 0.21014936 0.00000000 Rotation angle (degrees) 30.23916731 Shift along axis 0.12836667 > hide #!56 models > select #71 3032 atoms, 3086 bonds, 1 model selected > show selAtoms surfaces > select #16 5115 atoms, 4473 bonds, 1 model selected > ~select #16 Nothing selected > select #72 3032 atoms, 3086 bonds, 1 model selected > show selAtoms surfaces > select #43/B:353@CB 1 atom, 1 model selected > select clear > select clear > open /data/disk3/modeling/gp8/gp8_wcy-C2.pdb Chain information for gp8_wcy-C2.pdb #73 --- Chain | Description A B | No description available C E | No description available > open /data/disk3/modeling/gp8/gp8_wcy-C2.pdb Chain information for gp8_wcy-C2.pdb #74 --- Chain | Description A B | No description available C E | No description available > select #73 8052 atoms, 8166 bonds, 2 pseudobonds, 2 models selected > hide #!74 models > show #!74 models > select #74 8052 atoms, 8166 bonds, 2 pseudobonds, 2 models selected > select #73 8052 atoms, 8166 bonds, 2 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > hide #!73 models > show #!73 models > hide #!74 models > hide #!73 models > show #!73 models > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > show #!37 models > ui mousemode rightMode "translate selected models" > hide #!37 models > show #!37 models > fitmap #73 inMap #37 Fit molecule gp8_wcy-C2.pdb (#73) to map tail-c6-flip-lp15.mrc (#37) using 8052 atoms average map value = 0.003822, steps = 144 shifted from previous position = 13.5 rotated from previous position = 7.07 degrees atoms outside contour = 4495, contour level = 0.004095 Position of gp8_wcy-C2.pdb (#73) relative to tail-c6-flip-lp15.mrc (#37) coordinates: Matrix rotation and translation -0.01087583 0.99994088 -0.00003024 -0.00341220 -0.99994086 -0.01087583 0.00003753 0.00307899 0.00003719 0.00003064 1.00000004 1.34473537 Axis -0.00000344 -0.00003372 -1.00000000 Axis point -0.00020800 0.00320676 0.00000000 Rotation angle (degrees) 90.62315055 Shift along axis -1.34473546 > hide #!37 models > select clear > select #73 8052 atoms, 8166 bonds, 2 pseudobonds, 2 models selected > show selAtoms surfaces > hide #!69 models > show #!69 models > hide #!48 models > show #!48 models > hide #!40 models > show #!40 models > fitmap #69 inMap #40 Fit map genome-inside-channel.mrc in map nochan-tail-new-lp15.mrc using 3895 points correlation = 0.7926, correlation about mean = 0.2696, overlap = 100.4 steps = 64, shift = 7.75, angle = 1.65 degrees Position of genome-inside-channel.mrc (#69) relative to nochan-tail-new- lp15.mrc (#40) coordinates: Matrix rotation and translation -0.23947465 -0.97090259 0.00018076 0.62053743 -0.97090257 0.23947469 0.00024413 0.38159203 -0.00028032 -0.00011703 -0.99999995 292.46793545 Axis -0.61663707 0.78724756 0.00003537 Axis point 0.48691422 0.00000000 146.23390557 Rotation angle (degrees) 179.98322129 Shift along axis -0.07189487 > save session /data/disk3/modeling/gp12/Figure6new-20200202.cxs > select clear > select clear > select clear > view name new1 > view name new1 > save image /data/disk3/Paper-use/channel-20200202.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!73 models > show #!73 models > open /data/disk3/modeling/gp8/gp8-6R21-C2.pdb Chain information for gp8-6R21-C2.pdb #75 --- Chain | Description F L | No description available > show #!74 models > close #74 > matchmaker #75 to #73 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker gp8_wcy-C2.pdb, chain A (#73) with gp8-6R21-C2.pdb, chain F (#75), sequence alignment score = 2049.3 RMSD between 365 pruned atom pairs is 0.685 angstroms; (across all 454 pairs: 2.481) > hide #!73 models > select #75 7560 atoms, 7680 bonds, 1 model selected > show selAtoms surfaces > select clear > hide #!75 models > show #!75 models > show #!73 models > hide #!73 models > show #!73 models > hide #!73 models > show #!73 models > hide #!73 models > show #!73 models > hide #!75 models > save image /data/disk3/Paper-use/channel-20200202.tif pixelSize 0.1 supersample 10 transparentBackground true > save session /data/disk3/modeling/gp12/Figure6new-20200202.cxs > save image /data/disk3/Paper-use/channel-20200202.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting soft > lighting simple > lighting shadows true > lighting full > lighting soft > lighting simple > lighting full > lighting soft > lighting simple > lighting full > lighting simple > save image /data/disk3/Paper-use/channel-20200202.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!65 models > hide #!65 models > hide #!73 models > show #!75 models > show #!42 models > hide #!43 models > hide #!44 models > hide #!46 models > show #!46 models > hide #!40 models > show #!45 models > hide #!45 models > show #!45 models > show #!57 models > hide #!57 models > show #!59 models > hide #!59 models > show #!60 models > hide #!60 models > show #!61 models > hide #!61 models > hide #!72 models > show #!72 models > hide #!75 models > show #!75 models > hide #!45 models > show #!45 models > hide #!48 models > show #!48 models > hide #!48 models > show #!35 models > hide #!35 models > show #!36 models > hide #!36 models > show #!38 models > transparency #45 80 > select clear > show #!67 models > select #67 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > hide #!69 models > show #!69 models > select #69 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > select clear > select #46 2 models selected > select clear > select clear > view name new2 > save image /data/disk3/Paper-use/channel-20200202-1.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!67 models > hide #!69 models > show #!69 models > hide #!69 models > show #!69 models > show #!67 models > select #71 3032 atoms, 3086 bonds, 1 model selected > select #72 3032 atoms, 3086 bonds, 1 model selected > hide selAtoms surfaces > hide selAtoms surfaces > select #71.2 1512 atoms, 1 model selected > hide selAtoms surfaces > select clear > select #71.1 1520 atoms, 1 model selected > hide selAtoms ribbons > show selAtoms ribbons > show selAtoms surfaces > hide selAtoms surfaces > select clear > hide #!46 models > hide #!45 models > show #!45 models > show #!46 models > hide #!38 models > hide #!45 models > show #!45 models > hide #!67 models > show #!67 models > hide #!67 models > show #!67 models > show #!35 models > hide #!35 models > hide #!42 models > show #!42 models > show #!5 models > select #5 2813 atoms, 2855 bonds, 1 model selected > ui mousemode rightMode "rotate selected models" > select clear > ui mousemode rightMode "translate selected models" > select #5 2813 atoms, 2855 bonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > hide #!45 models > show #!45 models > fitmap #5 inMap #45 Fit molecule gp16-abc-wcy.pdb (#5) to map chan-tail-c6-new-lp15-noOM.mrc (#45) using 2813 atoms average map value = 11.73, steps = 60 shifted from previous position = 8.6 rotated from previous position = 15.8 degrees atoms outside contour = 75, contour level = 1.7738 Position of gp16-abc-wcy.pdb (#5) relative to chan-tail-c6-new-lp15-noOM.mrc (#45) coordinates: Matrix rotation and translation -0.42642203 0.24360215 0.87110404 -61.90581632 0.60770990 -0.63615810 0.47538567 -81.24382016 0.66996486 0.73209348 0.12323239 -117.90553612 Axis 0.52517427 0.41149166 0.74489368 Axis point 12.10732142 -6.48542353 0.00000000 Rotation angle (degrees) 165.85347411 Shift along axis -153.76958553 > select #46 2 models selected > show #!35 models > hide #!35 models > show #!36 models > hide #!36 models > show #!27 models > fitmap #5 inMap #27 Fit molecule gp16-abc-wcy.pdb (#5) to map fiber-6-fromtail-clean.mrc (#27) using 2813 atoms average map value = 0.007622, steps = 140 shifted from previous position = 3.82 rotated from previous position = 19.2 degrees atoms outside contour = 1990, contour level = 0.0115 Position of gp16-abc-wcy.pdb (#5) relative to fiber-6-fromtail-clean.mrc (#27) coordinates: Matrix rotation and translation -0.70341364 0.70932252 0.04550671 232.32209150 -0.13218433 -0.19345257 0.97216430 136.17810152 0.69838141 0.67781834 0.22983849 -215.67001276 Axis -0.26637712 -0.59083836 -0.76154662 Axis point 183.38167225 104.63443495 0.00000000 Rotation angle (degrees) 146.46140557 Shift along axis 21.89823377 > hide #!27 models > show #!27 models > hide #!27 models > show #!27 models > hide #!27 models > show #!27 models > select #27 2 models selected > hide #!45 models > show #!45 models > hide #!42 models > show #!42 models > hide #!27 models > show #!27 models > hide #!45 models > show #!45 models > hide #!46 models > show #!46 models > hide #!45 models > show #!45 models > hide #!27 models > hide #!46 models > show #!46 models > hide #!46 models > show #!46 models > hide #!71 models > show #!71 models > show #!56 models > show #!52 models > hide #!52 models > show #!52 models > hide #!52 models > show #!54 models > hide #!54 models > show #!54 models > hide #!46 models > show #!46 models > hide #!69 models > show #!69 models > hide #!71 models > show #!71 models > fitmap #71 inMap #56 Fit molecule gp11-6R21-c2.pdb (#71) to map gp11-c6-clean-lp.mrc (#56) using 3032 atoms average map value = 0.007648, steps = 24 shifted from previous position = 0.00673 rotated from previous position = 0.02 degrees atoms outside contour = 255, contour level = 0.0026326 Position of gp11-6R21-c2.pdb (#71) relative to gp11-c6-clean-lp.mrc (#56) coordinates: Matrix rotation and translation -0.86393736 -0.50359818 -0.00105370 0.10677872 0.50359906 -0.86393705 -0.00088059 -0.05842639 -0.00046687 -0.00129141 0.99999905 -0.12732971 Axis -0.00040789 -0.00058264 0.99999975 Axis point 0.06126624 -0.01483256 0.00000000 Rotation angle (degrees) 149.76162190 Shift along axis -0.12733919 > hide #!67 models > show #!67 models > hide #!46 models > show #!46 models > hide #!42 models > show #!42 models > hide #!46 models > show #!46 models > hide #!54 models > show #!54 models > hide #!54 models > show #!54 models > show #!27 models > hide #!27 models > show #!27 models > hide #!27 models > show #!27 models > hide #!27 models > show #!27 models > hide #!54 models > show #!54 models > fitmap #27 inMap #54 Fit map fiber-6-fromtail-clean.mrc in map tail-c6-flip-lp15-fiber.mrc using 184947 points correlation = 0.7977, correlation about mean = 0.3355, overlap = 14.93 steps = 60, shift = 2.66, angle = 0.841 degrees Position of fiber-6-fromtail-clean.mrc (#27) relative to tail-c6-flip- lp15-fiber.mrc (#54) coordinates: Matrix rotation and translation -0.99995695 -0.00927726 -0.00001072 212.02554674 0.00927720 -0.99995579 0.00152509 207.94465553 -0.00002487 0.00152493 0.99999883 -209.65754963 Axis -0.00000869 0.00076250 0.99999971 Axis point 105.52919415 104.54401915 0.00000000 Rotation angle (degrees) 179.46844619 Shift along axis -209.50077168 > select #46 2 models selected > hide #!54 models > hide #!56 models > show #!56 models > hide #!56 models > show #!56 models > show #!54 models > hide #!54 models > show #!54 models > hide #!54 models > show #!54 models > show #!37 models > hide #!56 models > show #!56 models > hide #!46 models > show #!46 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!37 models > show #!37 models > fitmap #56 inMap #37 Fit map gp11-c6-clean-lp.mrc in map tail-c6-flip-lp15.mrc using 276499 points correlation = 0.9381, correlation about mean = 0.5631, overlap = 11.32 steps = 64, shift = 4.99, angle = 1.28 degrees Position of gp11-c6-clean-lp.mrc (#56) relative to tail-c6-flip-lp15.mrc (#37) coordinates: Matrix rotation and translation -0.49179875 -0.87070891 -0.00001159 0.01343927 0.87070891 -0.49179875 0.00001269 -0.00156811 -0.00001675 -0.00000385 1.00000001 0.21751413 Axis -0.00000950 0.00000296 1.00000000 Axis point 0.00717848 0.00313823 0.00000000 Rotation angle (degrees) 119.45887651 Shift along axis 0.21751400 > hide #!54 models > show #!54 models > fitmap #54 inMap #37 Fit map tail-c6-flip-lp15-fiber.mrc in map tail-c6-flip-lp15.mrc using 496902 points correlation = 0.9915, correlation about mean = 0.877, overlap = 20.77 steps = 68, shift = 3.59, angle = 0.912 degrees Position of tail-c6-flip-lp15-fiber.mrc (#54) relative to tail-c6-flip- lp15.mrc (#37) coordinates: Matrix rotation and translation 0.50091901 0.86549392 -0.00064492 -0.06321585 -0.86549417 0.50091895 -0.00029671 -0.00509573 0.00006625 0.00070681 0.99999975 0.26296629 Axis 0.00057974 -0.00041085 -0.99999975 Axis point -0.03604384 0.05207961 0.00000000 Rotation angle (degrees) 59.93919079 Shift along axis -0.26300078 > hide #!37 models > hide #!27 models > select #46 2 models selected > hide #!75 models > select clear > hide #!67 models > show #!67 models > hide #!56 models > show #!56 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > show #!37 models > hide #!45 models > hide #!5 models > show #!5 models > hide #!42 models > show #!42 models > hide #!46 models > show #!46 models > hide #!54 models > show #!54 models > hide #!54 models > show #!54 models > hide #!46 models > show #!46 models > hide #!54 models > show #!54 models > hide #!56 models > show #!56 models > hide #!67 models > show #!67 models > hide #!69 models > show #!69 models > show #!60 models > hide #!60 models > show #!53 models > hide #!54 models > show #!54 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!67 models > show #!67 models > hide #!71 models > show #!71 models > hide #!54 models > show #!54 models > hide #!53 models > hide #!46 models > show #!46 models > hide #!46 models > show #!46 models > hide #!56 models > show #!56 models > hide #!69 models > show #!69 models > hide #!54 models > show #!54 models > hide #!56 models > show #!56 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!35 models > hide #!35 models > show #!37 models > hide #!42 models > show #!43 models > show #!44 models > hide #!46 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > show #!48 models > hide #!48 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!48 models > hide #!48 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > show #!38 models > hide #!38 models > show #!48 models > hide #!48 models > show #!65 models > hide #!65 models > show #!66 models > hide #!66 models > show #!45 models > hide #!45 models > show #!45 models > show #!42 models > hide #!42 models > show #!42 models > hide #!42 models > show #!42 models > hide #!42 models > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > hide #!43 models > show #!43 models > hide #!43 models > hide #!47 models > show #!47 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!44 models > show #!44 models > hide #!56 models > show #!56 models > show #!60 models > hide #!60 models > hide #!47 models > show #!47 models > hide #!47 models > hide #!56 models > show #!56 models > hide #!56 models > show #!56 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > show #!47 models > hide #!47 models > show #!47 models > hide #!45 models > hide #!67 models > hide #!69 models > show #!69 models > show #!62 models > show #!63 models > hide #!37 models > hide #!44 models > hide #!5 models > show #!37 models > hide #!47 models > hide #!54 models > hide #!37 models > show #!40 models > hide #!63 models > show #!63 models > hide #!40 models > show #!40 models > fitmap #63 inMap #40 Fit map nochan-tail-new-gp12-re.mrc in map nochan-tail-new-lp15.mrc using 695 points correlation = 0.9933, correlation about mean = 0.9268, overlap = 1.78e+05 steps = 80, shift = 1.02, angle = 7.11 degrees Position of nochan-tail-new-gp12-re.mrc (#63) relative to nochan-tail-new- lp15.mrc (#40) coordinates: Matrix rotation and translation 0.56408451 -0.82530261 -0.02615958 130.55458102 0.82396929 0.56466818 -0.04716458 -573.87860589 0.05369653 0.00505013 0.99854455 -455.40307386 Axis 0.03160641 -0.04833819 0.99833083 Axis point 635.94667462 -161.51892970 0.00000000 Rotation angle (degrees) 55.69149950 Shift along axis -422.77631816 > lighting soft > hide #!62 models > show #!62 models > show #!54 models > hide #!54 models > show #!55 models > hide #!55 models > show #!48 models > hide #!48 models > show #!54 models > hide #!54 models > show #!54 models > hide #!69 models > hide #!56 models > hide #!71 models > hide #!71.1 models > hide #!71.2 models > hide #!72 models > show #!56 models > hide #!63 models > show #!63 models > show #!64 models > hide #!54 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!64 models > show #!64 models > hide #!56 models > show #!56 models > show #!51 models > hide #!56 models > hide #!62 models > show #!62 models > hide #!40 models > show #!47 models > hide #!47 models > show #!49 models > show #!50 models > hide #!50 models > hide #!49 models > show #!52 models > hide #!52 models > show #!53 models > show #!47 models > hide #!47 models > show #!40 models > hide #!40 models > show #!60 models > hide #!60 models > show #!40 models > hide #!40 models > show #!40 models > hide #!40 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > hide #!53 models > show #!53 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > show #!60.1 models > hide #!64 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!62 models > show #!62 models > select clear > hide #!63 models > show #!63 models > select clear > save image /data/disk3/Paper-use/channel-20200203.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!60 models > save image /data/disk3/Paper-use/channel-20200203-1.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!63 models > show #!63 models > hide #!60.1 models > show #!60.1 models > hide #!60.1 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > show #!48 models > hide #!48 models > show #!38 models > hide #!38 models > show #!48 models > hide #!48 models > show #!37 models > hide #!37 models > show #!32 models > hide #!32 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!37 models > hide #!37 models > show #!33 models > hide #!33 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!48 models > hide #!48 models > show #!64 models > hide #!62 models > save image /data/disk3/Paper-use/channel-20200203-2.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!64 models > show #!64 models > show #!62 models > save image /data/disk3/Paper-use/channel-20200203-3.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!65 models > hide #!60 models > show #!60 models > hide #!60 models > hide #!65 models > show #!65 models > hide #!63 models > hide #!65 models > show #!65 models > show #!54 models > hide #!54 models > show #!45 models > hide #!45 models > show #!50 models > hide #!53 models > show #!53 models > hide #!53 models > show #!53 models > hide #!53 models > hide #!50 models > show #!50 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!64 models > show #!66 models > hide #!66 models > show #!66 models > hide #!66 models > show #!66 models > hide #!50 models > show #!50 models > hide #!51 models > show #!51 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > show #!27 models > hide #!27 models > show #!49 models > hide #!49 models > hide #!65 models > show #!65 models > hide #!65 models > show #!65 models > show #!64 models > hide #!64 models > show #!72 models > hide #!72 models > open /data/disk3/chan-tail-c6-new-fiber-re.mrc Opened chan-tail-c6-new-fiber-re.mrc, grid size 160,160,160, pixel 5.4, shown at level 0, step 1, values float32 > view cofr false > hide #!50 models > show #!50 models > show #!64 models > hide #!64 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!50 models > show #!50 models > hide #!49 models > show #!49 models > show #!60 models > hide #!60 models > show #!60 models > show #!60.1 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!50 models > show #!50 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!65 models > show #!65 models > hide #!50 models > show #!50 models > hide #!45 models > show #!45 models > fitmap #65 inMap #45 Fit map chan-tail-c6-new-gp12-re.mrc in map chan-tail-c6-new-lp15-noOM.mrc using 944 points correlation = 0.9865, correlation about mean = 0.8933, overlap = 1.364e+05 steps = 60, shift = 3.21, angle = 1.79 degrees Position of chan-tail-c6-new-gp12-re.mrc (#65) relative to chan-tail-c6-new- lp15-noOM.mrc (#45) coordinates: Matrix rotation and translation 0.44264908 0.89595137 0.03651101 -602.89848046 -0.89669493 0.44229625 0.01767328 188.29405352 -0.00031427 -0.04056229 0.99917702 -411.02859836 Axis -0.03246184 0.02052726 -0.99926216 Axis point -150.47247767 563.57841843 0.00000000 Rotation angle (degrees) 63.76453570 Shift along axis 434.16168223 > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > show #!37 models > hide #!45 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!65 models > hide #!51 models > hide #!50 models > hide #!47 models > hide #!37 models > show #!60 models > show #!65 models > show #!64 models > show #!63 models > hide #!63 models > show #!67 models > hide #!67 models > show #!59 models > hide #!62 models > show #!58 models > hide #!58 models > show #!57 models > hide #!57 models > show #!55 models > show #!54 models > hide #!54 models > show #!62 models > hide #!62 models > show #!49 models > show #!48 models > hide #!48 models > show #!50 models > hide #!50 models > show #!50 models > hide #!55 models > show #!55 models > hide #!55 models > hide #!64 models > show #!64 models > hide #!64 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!49 models > show #!49 models > select clear > show #!47 models > hide #!47 models > show #!51 models > select clear > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > show #!38 models > hide #!38 models > show #!64 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > hide #!64 models > hide #!60 models > show #!60 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > show #!63 models > hide #!63 models > hide #!60 models > show #!60 models > hide #!60 models > hide #!62 models > show #!62 models > lighting soft > hide #!62 models > show #!62 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > hide #!50 models > show #!50 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > show #!49 models > hide #!50 models > show #!50 models > hide #!50 models > show #!50 models > hide #!50 models > show #!50 models > hide #!50 models > show #!50 models > hide #!50 models > show #!50 models > hide #!59 models > show #!59 models > hide #!59 models > show #!59 models > hide #!59 models > hide #!65 models > show #!46 models > hide #!50 models > show #!50 models > hide #!46 models > show #!46 models > hide #!62 models > show #!62 models > hide #!62 models > lighting soft > lighting simple > lighting soft > lighting full > save image /data/disk3/Paper-use/channel-20200203-3.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!50 models > show #!50 models > lighting soft > lighting simple > lighting soft > lighting full > lighting shadows false > save image /data/disk3/Paper-use/channel-20200203-3.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!50 models > show #!50 models > hide #!50 models > show #!50 models > hide #!50 models > show #!50 models > hide #!50 models > show #!63 models > hide #!63 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!63 models > hide #!63 models > show #!60 models > hide #!49 models > show #!47 models > hide #!47 models > show #!40 models > hide #!40 models > show #!62 models > hide #!62 models > show #!40 models > hide #!40 models > show #!47 models > hide #!47 models > show #!53 models > hide #!46 models > show #!46 models > select #46 2 models selected > ui mousemode rightMode "translate selected models" > select clear > select #46 2 models selected > select clear > save image /data/disk3/Paper-use/channel-20200203-3.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!60 models > show #!60 models > hide #!47 models > show #!47 models > fitmap #60 inMap #47 Fit map nochan-tail-new-fiber.mrc in map nochan-tail-new-lp15-noOM.mrc using 3385 points correlation = 0.9797, correlation about mean = 0.8943, overlap = 5.221e+05 steps = 28, shift = 0.01, angle = 0.0709 degrees Position of nochan-tail-new-fiber.mrc (#60) relative to nochan-tail-new- lp15-noOM.mrc (#47) coordinates: Matrix rotation and translation -0.50305437 -0.86425450 -0.00069448 591.11964354 0.86425477 -0.50305434 -0.00022501 -155.90532441 -0.00015489 -0.00071340 0.99999974 -431.22236487 Axis -0.00028255 -0.00031217 0.99999991 Axis point 340.36031415 91.89158507 0.00000000 Rotation angle (degrees) 120.20228929 Shift along axis -431.34067732 > hide #!47 models > hide #!60 models > show #!63 models > hide #!63 models > show #!40 models > hide #!40 models > show #!40 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!46 models > show #!46 models > hide #!46 models > show #!46 models > hide #!40 models > show #!40 models > fitmap #62 inMap #40 Fit map nochan-tail-new-gp17-re.mrc in map nochan-tail-new-lp15.mrc using 578 points correlation = 0.986, correlation about mean = 0.8817, overlap = 1.178e+05 steps = 68, shift = 5.38, angle = 8.49 degrees Position of nochan-tail-new-gp17-re.mrc (#62) relative to nochan-tail-new- lp15.mrc (#40) coordinates: Matrix rotation and translation 0.99601495 0.08894291 -0.00658876 -464.21228740 -0.08882907 0.99591960 0.01592336 -410.20598812 0.00797813 -0.01527461 0.99985151 -427.87870820 Axis -0.17229249 -0.08044645 -0.98175540 Axis point -4318.60277104 3993.13969016 0.00000000 Rotation angle (degrees) 5.19454807 Shift along axis 533.05213864 > select clear > hide #!62 models > show #!62 models > select #62 2 models selected > fitmap #62 inMap #40 Fit map nochan-tail-new-gp17-re.mrc in map nochan-tail-new-lp15.mrc using 649 points correlation = 0.9816, correlation about mean = 0.8849, overlap = 1.195e+05 steps = 48, shift = 1.2, angle = 0.598 degrees Position of nochan-tail-new-gp17-re.mrc (#62) relative to nochan-tail-new- lp15.mrc (#40) coordinates: Matrix rotation and translation 0.99523200 0.09697376 -0.01045890 -464.63852450 -0.09673463 0.99508107 0.02135618 -410.84548274 0.01247843 -0.02024259 0.99971722 -427.09054910 Axis -0.20856946 -0.11500402 -0.97122235 Axis point -3755.73563322 3404.52410773 0.00000000 Rotation angle (degrees) 5.72327835 Shift along axis 558.95817362 > select clear > hide #!40 models > save image /data/disk3/Paper-use/channel-20200203-5.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!53 models > show #!53 models > show #!60 models > hide #!60 models > show #!60 models > hide #!60 models > show #!60 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!60 models > show #!60 models > select #60 2 models selected > close #60 > open /data/disk3/nochan-tail-new-gp17-re-sym.mrc Opened nochan-tail-new-gp17-re-sym.mrc, grid size 160,160,160, pixel 5.4, shown at level 0, step 1, values float32 > select #60 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > hide #!60 models > show #!60 models > show #!63 models > hide #!63 models > hide #!62 models > show #!62 models > show #!40 models > hide #!40 models > show #!40 models > fitmap #61 inMap #40 Fit molecule gp17-refined-good-nochan-coot-recombine.pdb (#61) to map nochan- tail-new-lp15.mrc (#40) using 2796 atoms average map value = 13.2, steps = 68 shifted from previous position = 4.27 rotated from previous position = 18 degrees atoms outside contour = 96, contour level = 2.2097 Position of gp17-refined-good-nochan-coot-recombine.pdb (#61) relative to nochan-tail-new-lp15.mrc (#40) coordinates: Matrix rotation and translation -0.59647413 0.80263088 -0.00151112 -82.02750447 -0.80211630 -0.59615711 -0.03472961 622.11350229 -0.02877593 -0.01950323 0.99939560 -408.78819055 Axis 0.00948654 0.01698688 -0.99981071 Axis point 111.63937139 329.20113275 0.00000000 Rotation angle (degrees) 126.62804888 Shift along axis 418.50041789 > ui mousemode rightMode "translate selected models" > fitmap #60 inMap #40 Fit map nochan-tail-new-gp17-re-sym.mrc in map nochan-tail-new-lp15.mrc using 4415 points correlation = 0.988, correlation about mean = 0.9442, overlap = 1.166e+05 steps = 52, shift = 6.98, angle = 3.54 degrees Position of nochan-tail-new-gp17-re-sym.mrc (#60) relative to nochan-tail-new- lp15.mrc (#40) coordinates: Matrix rotation and translation -0.50008119 0.86597846 -0.00025396 0.05322822 -0.86597840 -0.50008126 -0.00030576 0.05710564 -0.00039179 0.00006701 0.99999990 0.13007121 Axis 0.00021523 0.00007958 -0.99999997 Axis point 0.04311428 0.01318592 0.00000000 Rotation angle (degrees) 120.00537786 Shift along axis -0.13005520 > select clear > hide #!40 models > select clear > hide #!62 models > show #!62 models > hide #!60 models > show #!60 models > hide #!62 models > save image /data/disk3/Paper-use/new-channel-20200203.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!60 models > show #!64 models > hide #!64 models > show #!48 models > hide #!48 models > show #!37 models > hide #!37 models > show #!38 models > hide #!38 models > show #!9 models > hide #!9 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!37 models > show #!48 models > hide #!48 models > show #!54 models > hide #!37 models > hide #!54 models > show #!54 models > save image /data/disk3/Paper-use/new-channel-20200203-1.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/new-channel-20200203.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!54 models > show #!54 models > show #!37 models > hide #!37 models > show #!37 models > hide #!54 models > show #!54 models > fitmap #54 inMap #36 Fit map tail-c6-flip-lp15-fiber.mrc in map fiber-c6-flip-add.mrc using 385473 points correlation = 0.8612, correlation about mean = 0.1998, overlap = 18.23 steps = 60, shift = 1.36, angle = 1.06 degrees Position of tail-c6-flip-lp15-fiber.mrc (#54) relative to fiber-c6-flip- add.mrc (#36) coordinates: Matrix rotation and translation -0.88920567 -0.45739230 -0.01027521 356.95126224 0.45749213 -0.88913645 -0.01171986 357.18747781 -0.00377549 -0.01512219 0.99987852 239.96390028 Axis -0.00371874 -0.00710419 0.99996785 Axis point 135.47283778 222.76975985 0.00000000 Rotation angle (degrees) 152.77687163 Shift along axis 236.09124893 > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > hide #!54 models > show #!54 models > show #!64 models > close #54 > show #!9 models > hide #!9 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!38 models > hide #!38 models > show #!48 models > hide #!48 models > show #!49 models > hide #!49 models > show #!55 models > hide #!55 models > show #!55 models > select clear > hide #!64 models internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > show #!37 models > hide #!37 models > hide #!46 models > save image /data/disk3/Paper-use/new-channel-20200203.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!55 models > show #!64 models > show #!55 models > hide #!55 models > hide #!64 models > show #!64 models > hide #!53 models > show #!53 models > show #!63 models > save image /data/disk3/Paper-use/new-channel-20200203-1.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!64 models > show #!62 models > save image /data/disk3/Paper-use/new-channel-20200203-2.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!63 models > hide #!62 models > hide #!53 models > show #!53 models > show #!62 models > hide #!62 models > show #!60 models > save image /data/disk3/Paper-use/new-channel-20200203-3.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!46 models > save image /data/disk3/Paper-use/new-channel-20200203-3.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!53 models > show #!50 models > show #!49 models > hide #!60 models > show #!60 models > hide #!60 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > save image /data/disk3/Paper-use/new-channel-20200203-4.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!50 models > show #!50 models > show #!65 models > hide #!49 models > show #!49 models > hide #!49 models > show #!7 models > hide #!7 models > show #!49 models > hide #!49 models > show #!49 models > hide #!65 models > show #!65 models > show #!52 models > hide #!52 models > hide #!49 models > show #!35 models > hide #!35 models > show #!33 models > hide #!33 models > show #!39 models > hide #!39 models > show #!39 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!45 models > hide #!45 models > show #!48 models > hide #!48 models > show #!49 models > hide #!49 models > hide #!50 models > show #!50 models > hide #!50 models > show #!50 models > hide #!39 models > hide #!65 models > show #!65 models > show #!63 models > hide #!63 models > hide #!65 models > show #!65 models > hide #!50 models > show #!50 models > fitmap #65 inMap #50 Fit map chan-tail-c6-new-gp12-re.mrc in map chan-tail-c6-new-gp12-re-sym.mrc using 944 points correlation = 0.9944, correlation about mean = 0.9585, overlap = 2.504e+04 steps = 44, shift = 1.97, angle = 1.49 degrees Position of chan-tail-c6-new-gp12-re.mrc (#65) relative to chan-tail-c6-new- gp12-re-sym.mrc (#50) coordinates: Matrix rotation and translation 0.47130585 0.88174675 0.01983817 -597.25234524 -0.88196955 0.47120574 0.00974267 172.97679140 -0.00075729 -0.02208844 0.99975576 -421.45645084 Axis -0.01804358 0.01167461 -0.99976904 Axis point -154.76906564 575.66773915 0.00000000 Rotation angle (degrees) 61.89209010 Shift along axis 434.15511853 > show #!49 models > hide #!49 models > show #!49 models > hide #!49 models > open /data/disk3/chan-tail-c6-new-fiber-re.mrc Opened chan-tail-c6-new-fiber-re.mrc, grid size 160,160,160, pixel 5.4, shown at level 0, step 1, values float32 > hide #!54 models > show #!54 models > show #!49 models > view name test > view cofr false > hide #!65 models > show #!65 models > hide #!54 models > show #!54 models > hide #!54 models > show #!54 models > hide #!54 models > show #!54 models > hide #!65 models > show #!65 models > hide #!54 models > close #54 > open /data/disk3/chan-tail-c6-new-fiber-re.mrc Opened chan-tail-c6-new-fiber-re.mrc, grid size 160,160,160, pixel 5.4, shown at level 0, step 1, values float32 > select #54 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > close #54 > view test > open /data/disk3/chan-tail-c6-new-fiber-re.mrc Opened chan-tail-c6-new-fiber-re.mrc, grid size 160,160,160, pixel 5.4, shown at level 0, step 1, values float32 > select #54 2 models selected > view cofr false > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > hide #!49 models > show #!49 models > fitmap #54 inMap #49 Fit map chan-tail-c6-new-fiber-re.mrc in map chan-tail-c6-new-fiber-re-sym.mrc using 514 points correlation = 0.9964, correlation about mean = 0.9684, overlap = 3.82e+04 steps = 64, shift = 10.7, angle = 17.1 degrees Position of chan-tail-c6-new-fiber-re.mrc (#54) relative to chan-tail-c6-new- fiber-re-sym.mrc (#49) coordinates: Matrix rotation and translation -0.50539515 -0.86286648 -0.00608026 595.44288863 0.86288794 -0.50538322 -0.00346759 -152.46806942 -0.00008079 -0.00699909 0.99997541 -429.19601068 Axis -0.00204634 -0.00347640 0.99999186 Axis point 341.40770961 93.42079179 0.00000000 Rotation angle (degrees) 120.35800926 Shift along axis -429.88095365 > hide #!49 models > select #46 2 models selected > select clear > view name test1 > view test > save image /data/disk3/Paper-use/new-channel-20200203-5.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!65 models > hide #!46 models > show #!46 models > hide #!50 models > show #!53 models > show #!63 models > save image /data/disk3/Paper-use/new-channel-20200203-6.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!54 models > show #!60 models > hide #!60 models > show #!40 models > hide #!40 models > show #!40 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!47 models > hide #!47 models > show #!56 models > hide #!56 models > show #!62 models > hide #!62 models > show #!62 models > hide #!51 models > show #!51 models > hide #!53 models > show #!53 models > hide #!46 models > show #!46 models > hide #!40 models > save image /data/disk3/Paper-use/new-channel-20200203-6.tif pixelSize 0.1 supersample 10 transparentBackground true > save session /data/disk3/modeling/gp12/Figure6new-20200202.cxs > open /data/disk3/modeling/gp17/gp17-main-body.pdb /data/disk3/modeling/gp17/gp17-small-body.pdb Chain information for gp17-main-body.pdb #66.1 --- Chain | Description A C | No description available B | No description available Chain information for gp17-small-body.pdb #66.2 --- Chain | Description D | No description available > show #!4 models > hide #!4 models > show #!5 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!8 models > show #!9 models > hide #!8 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!66 models > show #!66 models > hide #!66 models > hide #!66.2 models > show #!66.2 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > hide #!62 models > show #!62 models > show #!50 models > hide #!50 models > hide #!46 models > show #!46 models > show #!57 models > hide #!57 models > show #!57 models > show #!58 models > hide #!58 models > hide #!57 models > show #!57 models > hide #!57 models > hide #!62 models > hide #!66.1 models > show #!66.1 models > hide #!66 models > show #!66 models > select #66 2796 atoms, 2836 bonds, 1 pseudobond, 4 models selected > view cofr false > view test > show #!5 models > hide #!5 models > show #!5 models Invalid "to" argument: invalid atoms specifier Invalid "to" argument: invalid atoms specifier > matchmaker #66 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker gp16-abc-wcy.pdb, chain C (#5) with gp17-main-body.pdb, chain A (#66.1), sequence alignment score = 509.2 RMSD between 113 pruned atom pairs is 0.562 angstroms; (across all 116 pairs: 0.763) Matchmaker gp16-abc-wcy.pdb, chain A (#5) with gp17-small-body.pdb, chain D (#66.2), sequence alignment score = 311.8 RMSD between 75 pruned atom pairs is 0.599 angstroms; (across all 75 pairs: 0.599) > select clear > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!66.1 models > show #!66.1 models > hide #!66.1 models > show #!66.1 models > select #66.1 2187 atoms, 2216 bonds, 1 pseudobond, 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > hide #!53 models > show #!53 models > hide #!46 models > show #!46 models > hide #!46 models > show #!46 models > hide #!51 models > show #!51 models > hide #!53 models > show #!53 models > fitmap #66.1 inMap #9 Fit molecule gp17-main-body.pdb (#66.1) to map tail-c6-flip-lp15-fiber-re- trim-masked-sym.mrc (#9) using 2187 atoms average map value = 0.0013, steps = 96 shifted from previous position = 4.8 rotated from previous position = 18.4 degrees atoms outside contour = 60, contour level = 0.00072623 Position of gp17-main-body.pdb (#66.1) relative to tail-c6-flip-lp15-fiber-re- trim-masked-sym.mrc (#9) coordinates: Matrix rotation and translation -0.17942355 0.32769115 -0.92759138 1047.06385122 0.48535085 -0.79066777 -0.37320119 -154.77222704 -0.85571129 -0.51716832 -0.01718076 -611.57122921 Axis -0.63906632 -0.31907381 0.69984723 Axis point 264.04557385 -201.56288230 0.00000000 Rotation angle (degrees) 173.53255540 Shift along axis -1047.76591056 > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > show #!2 models > hide #!2 models > show #!20 models > hide #!20 models > ui mousemode rightMode "translate selected models" > select #66.2 609 atoms, 620 bonds, 1 model selected > ~select #66.2 Nothing selected > ui mousemode rightMode "rotate selected models" > select #66.2 609 atoms, 620 bonds, 1 model selected > matchmaker #66.2 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker gp16-abc-wcy.pdb, chain A (#5) with gp17-small-body.pdb, chain D (#66.2), sequence alignment score = 311.8 RMSD between 75 pruned atom pairs is 0.599 angstroms; (across all 75 pairs: 0.599) > matchmaker #66.1 to #5 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker gp16-abc-wcy.pdb, chain C (#5) with gp17-main-body.pdb, chain A (#66.1), sequence alignment score = 509.2 RMSD between 113 pruned atom pairs is 0.562 angstroms; (across all 116 pairs: 0.763) > undo > ui mousemode rightMode "rotate selected models" > select #66.1 2187 atoms, 2216 bonds, 1 pseudobond, 2 models selected > ui mousemode rightMode "translate selected models" > select clear > select #66.2 609 atoms, 620 bonds, 1 model selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > select #46 2 models selected > hide #!53 models > hide #!51 models > show #!51 models > hide #!51 models > hide #!63 models > hide #!66 models > show #!66 models > hide #!46 models > hide #!9 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!38 models > hide #!38 models > show #!39 models > hide #!39 models > show #!39 models > hide #!39 models > show #!40 models > hide #!40 models > show #!48 models > hide #!48 models > show #!38 models > hide #!38 models > show #!8 models > hide #!8 models > show #!64 models > select #66.2 609 atoms, 620 bonds, 1 model selected > select #66.1 2187 atoms, 2216 bonds, 1 pseudobond, 2 models selected > ui mousemode rightMode "translate selected models" > select clear > select #66.1 2187 atoms, 2216 bonds, 1 pseudobond, 2 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > select clear > view cofr false > toolshed show "Side View" Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 116, in exposeEvent self.render() File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) AttributeError: 'NoneType' object has no attribute 'use_shared_context' AttributeError: 'NoneType' object has no attribute 'use_shared_context' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 116, in exposeEvent self.render() File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) AttributeError: 'NoneType' object has no attribute 'use_shared_context' AttributeError: 'NoneType' object has no attribute 'use_shared_context' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/sideview/tool.py", line 139, in render mvwin = self.view.render.use_shared_context(self, width, height) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 384.130 OpenGL renderer: Quadro K2200/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (1)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → General Controls |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SideVIew self.view.render is None |
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