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Opened 6 years ago
Closed 6 years ago
#2816 closed defect (duplicate)
SideVIew self.view.render is None
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | 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/modeling/gp10/capsid-tail-20200204.cxs opened ChimeraX session > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!1 models > surface dust #7 size 50 > surface dust #31 size 50 > lighting soft > lighting soft > lighting simple > select clear > save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!7 models > show #!7 models > hide #!23 models > show #!23 models > surface dust #23 size 50 > surface dust #26 size 50 > hide #!7 models > show #!7 models > hide #!11.1 models > show #!11.1 models > hide #!11.1 models > hide #!11 models > show #!11 models > show #!11.1 models > hide #!11 models > show #!11 models > surface dust #11 size 50 > hide #!7 models > show #!7 models > hide #!11.1 models > hide #!11 models > lighting soft > lighting full > lighting shadows false > lighting flat > lighting full > lighting simple > lighting shadows true > lighting full > lighting soft > lighting flat > set silhouettes false > set silhouettes true > lighting shadows true intensity 0.5 > lighting simple > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting soft > lighting simple > save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting simple > surface dust #23 size 50 > surface dust #23 size 10 > surface dust #31 size 50 > surface dust #31 size 30 > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting soft > lighting simple > lighting flat > lighting full > lighting soft > lighting simple > save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > surface dust #31 size 100 > surface dust #31 size 50 > lighting flat > select clear > lighting simple > lighting soft > lighting full > lighting shadows false > lighting full > lighting soft > lighting flat > lighting simple > select clear internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > select up Nothing selected > save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!6 models > hide #!6 models > show #!11 models > show #!11.1 models > zoom 0.5 > save image /data/disk3/Paper-use/Figure1-20200205-2.tif pixelSize 0.1 supersample 10 transparentBackground true internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > save image /data/disk3/Paper-use/Figure1-20200205-2.tif pixelSize 0.1 supersample 10 transparentBackground true internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > save image /data/disk3/Paper-use/Figure1-20200205-3.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!23 models > show #!23 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > transparency #11 70 > transparency #11 40 > transparency #11 0 > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > transparency #23 70 > transparency #7 70 > lighting soft > toolshed show "Side View" > hide #!9 models > hide #!7 models > show #!7 models > hide #!15 models > hide #!16 models > hide #!17 models > hide #!19 models > ui mousemode rightMode "rotate selected models" > view cofr false > lighting simple > lighting soft > lighting flat > lighting full > lighting soft > lighting full > lighting soft > hide #!11 models > show #!11 models > hide #!23 models > hide #!7 models > show #!10 models > hide #!10 models > hide #!26 models > save image /data/disk3/Paper-use/Figure1-20200205-4.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!26 models > lighting soft > save image /data/disk3/Paper-use/Figure1-20200205-5.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting soft > lighting simple > save image /data/disk3/Paper-use/Figure1-20200205-5.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure1-20200205-5.tif pixelSize 0.1 supersample 10 transparentBackground true > view name portal > show #!23 models > view name gp8 > view name gp8 > save image /data/disk3/Paper-use/Figure1-20200205-4.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!7 models > select clear > save image /data/disk3/Paper-use/Figure1-20200205-6.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure1-20200205-6.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting flat > lighting soft > lighting soft > lighting flat > lighting simple > lighting soft > lighting simple Expected an objects specifier or a view name or a keyword > show #!13 models > hide #!13 models > show #!9 models > hide #!9 models > show #!4 models > hide #!4 models > show #!177 models > hide #!177 models > hide #!7 models > show #!7 models > save image /data/disk3/Paper-use/Figure1-20200205-7.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure1-20200205-7.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure1-20200205-7.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure1-20200205-7.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!31 models > show #!31 models > hide #!23 models > save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure2-20200205-2.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting full > lighting simple > lighting soft > lighting full > lighting soft > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > save image /data/disk3/Paper-use/Figure2-20200205-2.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!17 models > hide #!16 models > hide #!15 models > hide #!19 models > hide #!9 models > show #!23 models > show #!27 models > show #!7 models internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting soft > lighting soft > lighting soft > show #!9 models > hide #!9 models > save image /data/disk3/Paper-use/Figure2-20200205-3.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!5 models > hide #!31 models > show #!31 models > select #31 3 models selected > ~select #31 Nothing selected > hide #!31 models > select #5 49008 atoms, 49740 bonds, 1 model selected > show selAtoms ribbons > select clear > ui mousemode rightMode "translate selected models" > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting soft > show #!31 models > hide #!31 models > show #!31 models > transparency #31 70 > transparency #31 50 > select clear > select clear > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > show #!14 models > hide #!14 models > show #!3 models > hide #!3 models > show #!14 models > select #14 76410 atoms, 77460 bonds, 3 models selected > show selAtoms ribbons > select clear > hide #!11 models > show #!11 models > show #!13 models > hide #!13 models > show #!13 models > hide #!23 models > hide #!14 models > hide #!7 models > surface dust #13 size 50 > surface dust #13 size 100 > surface dust #13 size 150 > surface dust #13 size 100 > transparency #13 80 > transparency #13 40 > save image /data/disk3/Paper-use/Figure2-20200205-4.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!11 models > show #!11 models > surface dust #13 size 150 > surface dust #13 size 200 > surface dust #13 size 300 > surface dust #13 size 500 > surface dust #13 size 400 > surface dust #13 size 300 > hide #!5 models > save image /data/disk3/Paper-use/Figure2-20200205-4.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!11 models > show #!11 models > hide #!11 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!11.1 models > hide #!31 models > hide #!26 models > show #!26 models > hide #!26 models > hide #!27 models > show #!27 models > hide #!27 models > save image /data/disk3/Paper-use/Figure2-20200205-5.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!11 models > show #!11.1 models > select up Nothing selected > transparency #13 40 > lighting flat > show #!26 models > hide #!26 models > show #!31 models > lighting soft > show #!26 models > hide #!26 models > lighting flat > lighting full > lighting simple > lighting simple > lighting soft > save image /data/disk3/Paper-use/Figure2-20200205-6.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting flat > show #!29 models > hide #!13 models > hide #!29 models > lighting soft > open /data/disk3/modeling/gp8/gp8-C12-clean.mrc Opened gp8-C12-clean.mrc, grid size 400,400,400, pixel 1.05, shown at level -4.87e-06, step 2, values float32 > hide #!11 models > hide #!11.1 models > lighting flat > hide #!20 models > show #!20 models > select #20 2 models selected > ui mousemode rightMode "translate selected models" > hide #!20 models > show #!20 models > ui mousemode rightMode "translate selected models" > hide #!20 models > show #!20 models > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > hide #!20 models > show #!20 models > fitmap #20 inMap #31 Fit map gp8-C12-clean.mrc in map gp8-Res2.9-clean.mrc using 28724 points correlation = 0.9108, correlation about mean = 0.7448, overlap = 15.77 steps = 104, shift = 2.16, angle = 7.73 degrees Position of gp8-C12-clean.mrc (#20) relative to gp8-Res2.9-clean.mrc (#31) coordinates: Matrix rotation and translation -0.40431498 0.91461981 -0.00002575 102.83950342 0.91461981 0.40431498 0.00006074 -66.98431350 0.00006596 0.00000101 -1.00000000 420.15908783 Axis -0.54577749 -0.83793015 -0.00001475 Axis point 73.22767612 0.00000000 210.08181233 Rotation angle (degrees) 179.99686465 Shift along axis -0.00550679 > show #!30 models > hide #!30 models > show #!26 models > show #!11 models > show #!11.1 models > hide #!31 models > select clear > lighting flat > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!11 models > show #!11 models > hide #!11 models > lighting soft > show #!1 models > surface dust #1 size 400 > surface dust #1 size 40 > hide #!20 models > show #!20 models > hide #!26 models > show #!26 models > hide #!1 models > hide #!26 models > show #!26 models > lighting flat > zoom 0.5 > lighting flat > lighting soft > hide #!20 models > show #!20 models > hide #!26 models > show #!26 models > surface dust #26 size 40 > surface dust #26 size 80 > surface dust #26 size 60 > surface dust #26 size 70 > hide #!26 models > show #!26 models > hide #!20 models > show #!20 models > surface dust #20 size 70 > show #!11 models > hide #!11 models > show #!11 models > show #!23 models > show #!7 models > hide #!11 models > select clear > lighting flat > lighting flat > lighting soft > lighting simple > lighting shadows true > lighting flat > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > select clear > lighting flat > lighting soft > lighting simple > save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!11 models > save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting soft > lighting soft > lighting soft > lighting simple > lighting soft > lighting soft > save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting flat > lighting soft > lighting flat > lighting soft > lighting shadows true intensity 0.5 > lighting full > lighting soft > view name 1 > save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true 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. > show #!14 models > close #14 > show #!5 models > hide #!5 models > show #!5 models > show #!10 models > select #10 18336 atoms, 18660 bonds, 1 model selected > select clear > hide #!5 models > show #!5 models > hide #!20 models > hide selAtoms ribbons > hide selAtoms ribbons > show #!20 models > open /data/disk3/modeling/gp10/3j7w-C5-C6-pentamer-V.pdb Chain information for 3j7w-C5-C6-pentamer-V.pdb #14 --- Chain | Description B D L M N O T U V W | No description available F b c e | No description available d | No description available > hide #!5 models > show #!5 models > hide #!14 models > show #!14 models > select #14 37263 atoms, 37783 bonds, 1 model selected > close #14 > open /data/disk3/modeling/gp10/3j7w-C5-C6-pentamer-1.pdb /data/disk3/modeling/gp10/3j7w-C5-C6-pentamer-2.pdb Chain information for 3j7w-C5-C6-pentamer-1.pdb #14.1 --- Chain | Description A C E H I J K P Q R S X Y Z a | No description available Chain information for 3j7w-C5-C6-pentamer-2.pdb #14.2 --- Chain | Description B D F L M N O T U V W b c d e | No description available > select #14 76410 atoms, 77460 bonds, 3 models selected > ~select #14.1 38205 atoms, 38730 bonds, 2 models selected > ~select #14.2 1 model selected > select #14.1 38205 atoms, 38730 bonds, 1 model selected > select #14 76410 atoms, 77460 bonds, 3 models selected > hide selAtoms > show selAtoms ribbons > show selAtoms > show selAtoms ribbons > hide selAtoms > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > hide #!14 models > show #!14 models > fitmap #14.1 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.003277, steps = 184 shifted from previous position = 13 rotated from previous position = 8.82 degrees atoms outside contour = 33158, contour level = 0.014 Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.87077427 0.44074248 0.21794086 -255.17401789 0.44300176 -0.89557672 0.04113117 341.22465748 0.21331102 0.06073222 -0.97509487 421.71636726 Axis 0.96715335 0.22844510 0.11147749 Axis point 0.00000000 199.60859977 226.53103304 Rotation angle (degrees) 179.41939043 Shift along axis -121.82942344 > fitmap #14.2 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.00301, steps = 176 shifted from previous position = 8.24 rotated from previous position = 8.69 degrees atoms outside contour = 33669, contour level = 0.014 Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.88858723 0.39914992 0.22603554 -254.94469240 0.40067124 -0.91529584 0.04118342 356.75744205 0.22332776 0.05397088 -0.97324809 420.44709225 Axis 0.97174749 0.20577055 0.11560839 Axis point 0.00000000 204.63507213 226.03657012 Rotation angle (degrees) 179.62301282 Shift along axis -125.72447641 > lighting flat > view cofr false > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > fitmap #14.2 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.003896, steps = 124 shifted from previous position = 8.5 rotated from previous position = 4.92 degrees atoms outside contour = 32300, contour level = 0.014 Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.91098479 0.38597423 0.14536367 -230.26877151 0.38664508 -0.92189595 0.02476749 373.85349728 0.14356980 0.03364134 -0.98906823 460.38543728 Axis 0.97749291 0.19760269 0.07389709 Axis point 0.00000000 209.65694133 239.35760756 Rotation angle (degrees) 179.73992877 Shift along axis -117.19049440 > fitmap #14.1 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.003879, steps = 96 shifted from previous position = 5.46 rotated from previous position = 2.73 degrees atoms outside contour = 32342, contour level = 0.014 Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.88041990 0.43828982 0.18100501 -246.92143020 0.43340100 -0.89863979 0.06789759 333.77575063 0.19241714 0.01866936 -0.98113562 446.82207444 Axis -0.96963925 -0.22478250 -0.09629411 Axis point 0.00000000 198.51001869 233.30835046 Rotation angle (degrees) 178.54540104 Shift along axis 121.37142807 > 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" > fitmap #14.1 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.004629, steps = 160 shifted from previous position = 13 rotated from previous position = 5.29 degrees atoms outside contour = 31217, contour level = 0.014 Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.86597982 0.42442861 0.26446038 -258.59400689 0.41367029 -0.90513039 0.09806047 339.76900742 0.28099081 0.02448101 -0.95939817 410.82950911 Axis -0.96590142 -0.21700025 -0.14122794 Axis point 0.00000000 203.14840431 220.71640569 Rotation angle (degrees) 177.81716196 Shift along axis 118.02575589 > fitmap #14.2 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.01396, steps = 128 shifted from previous position = 6.68 rotated from previous position = 6.31 degrees atoms outside contour = 21091, contour level = 0.014 Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.87105169 0.43180772 0.23411755 -259.31100606 0.43088566 -0.90055103 0.05783932 345.21826870 0.23581028 0.05049685 -0.97048626 417.79531053 Axis -0.96722557 -0.22298304 -0.12146302 Axis point 0.00000000 202.92431247 224.81402889 Rotation angle (degrees) 179.78252577 Shift along axis 123.08773570 > select clear > hide #!11 models > hide #!5 models > show #!5 models > hide #!14 models > hide #!20 models > hide selAtoms ribbons > hide selAtoms ribbons > hide selAtoms ribbons > hide selAtoms ribbons > hide selAtoms ribbons > hide selAtoms ribbons > hide selAtoms > hide selAtoms ribbons > hide selAtoms ribbons > show #!11 models > show #!14 models > hide #!5 models > select #11 3 models selected > select #14.1 38205 atoms, 38730 bonds, 1 model selected > ui mousemode rightMode "translate selected models" > fitmap #14.1 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.01449, steps = 104 shifted from previous position = 11.5 rotated from previous position = 2.95 degrees atoms outside contour = 17054, contour level = 0.01 Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.87266983 0.43809630 0.21568259 -240.34437556 0.42481187 -0.89892619 0.10708207 343.62425563 0.24079500 -0.00182277 -0.97057428 446.57565351 Axis -0.96761791 -0.22312336 -0.11803200 Axis point 0.00000000 206.19802213 232.61159406 Rotation angle (degrees) 176.77399198 Shift along axis 103.18070608 > fitmap #14.1 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.01449, steps = 96 shifted from previous position = 9.67 rotated from previous position = 1.44 degrees atoms outside contour = 17069, contour level = 0.01 Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.87165040 0.44382963 0.20794429 -246.40304653 0.43574272 -0.89597161 0.08580871 351.05434471 0.22439664 0.01581501 -0.97436955 441.53038546 Axis -0.96736971 -0.22738480 -0.11176760 Axis point 0.00000000 208.72980426 231.48417700 Rotation angle (degrees) 177.92673932 Shift along axis 109.18962883 > select #14.2 38205 atoms, 38730 bonds, 1 model selected > fitmap #14.2 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.01396, steps = 92 shifted from previous position = 10.2 rotated from previous position = 1.68 degrees atoms outside contour = 17709, contour level = 0.01 Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.87154036 0.43231440 0.23134747 -247.82239723 0.42424380 -0.90143033 0.08625865 348.94881293 0.24583450 0.02296983 -0.96903962 435.65959681 Axis -0.96734324 -0.22142808 -0.12335580 Axis point 0.00000000 206.63567257 230.47650121 Rotation angle (degrees) 178.12536568 Shift along axis 108.72111917 > select #23 4 models selected > select clear > lighting soft > lighting soft > hide #!23 models > hide #!26 models > show #!26 models > hide #!10 models > hide #!11.1 models > show #!11.1 models > hide #!11 models > show #!11 models > hide #!26 models > select #14.1 38205 atoms, 38730 bonds, 1 model selected > fitmap #14.1 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.01449, steps = 52 shifted from previous position = 0.516 rotated from previous position = 0.722 degrees atoms outside contour = 17051, contour level = 0.01 Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.87141650 0.43979498 0.21728700 -248.28937285 0.43369597 -0.89770555 0.07766951 351.17649597 0.22921841 0.02655400 -0.97301274 435.34455599 Axis -0.96731431 -0.22579111 -0.11541833 Axis point 0.00000000 207.62667240 229.91596728 Rotation angle (degrees) 178.48599181 Shift along axis 110.63459153 > select #14.2 38205 atoms, 38730 bonds, 1 model selected > ui mousemode rightMode "translate selected models" > fitmap #14.2 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.01396, steps = 76 shifted from previous position = 3.04 rotated from previous position = 0.834 degrees atoms outside contour = 17716, contour level = 0.01 Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.87175271 0.43856635 0.21841873 -246.90795772 0.42950250 -0.89856792 0.09001831 346.42211180 0.23574307 0.01533768 -0.97169437 439.08637210 Axis -0.96739466 -0.22441532 -0.11741097 Axis point 0.00000000 206.35965402 230.82439841 Rotation angle (degrees) 177.78789990 Shift along axis 109.56145253 > ui mousemode rightMode "translate selected models" > fitmap #14.2 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.01396, steps = 52 shifted from previous position = 1.9 rotated from previous position = 0.417 degrees atoms outside contour = 17692, contour level = 0.01 Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.87147552 0.44032347 0.21597603 -246.54997704 0.43271422 -0.89761051 0.08398675 348.78865188 0.23084370 0.02026350 -0.97277982 437.67284585 Axis -0.96732636 -0.22569295 -0.11550933 Axis point 0.00000000 206.99054785 230.37700702 Rotation angle (degrees) 178.11246041 Shift along axis 109.21985671 > select #14 76410 atoms, 77460 bonds, 3 models selected > select clear > ui mousemode rightMode "translate selected models" > lighting soft > select clear > hide #!7 models > select #14.1 38205 atoms, 38730 bonds, 1 model selected > ~select #14.1 Nothing selected > select #14.2 38205 atoms, 38730 bonds, 1 model selected > ~select #14.2 Nothing selected > select #14.1 38205 atoms, 38730 bonds, 1 model selected > ui mousemode rightMode "translate selected models" > fitmap #14.1 inMap #11 Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail- vertex.mrc (#11) using 38205 atoms average map value = 0.01449, steps = 48 shifted from previous position = 1.35 rotated from previous position = 0.36 degrees atoms outside contour = 17052, contour level = 0.01 Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates: Matrix rotation and translation 0.87152575 0.43744295 0.22155475 -248.08390878 0.43059629 -0.89890364 0.08098810 349.84460221 0.23458405 0.02481743 -0.97177899 435.45368809 Axis -0.96734135 -0.22438373 -0.11790947 Axis point 0.00000000 207.06052433 230.03528537 Rotation angle (degrees) 178.33626741 Shift along axis 110.13827118 > select clear > hide #!14.2 models > show #!14.2 models > sequence chain #14.3 Chains must have same sequence > sequence chain #14.2 Alignment identifier is 1 2 headers > select clear > select clear > select clear > hide #!14 models > show #!14 models > hide #!14.1 models > show #!14.1 models > hide #!14.2 models > show #!14.2 models > color #14.2/B-W:2-28 red > color #14.2/b-e:2-28 red > select clear > color #14.2/W:2-28 red > color #14.2/B:2-28 red > color #14.2/D:2-28 red Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword > color #14.2/W:2-28 red > color #14.2/V:2-28 red > color #14.2/U:2-28 red > color #14.2/T:2-28 red > color #14.2/O:2-28 red > color #14.2/L:2-28 red > color #14.2/M:2-28 red > color #14.2/N:2-28 red > color #14.2/D:2-28 red > color #14.2/F:2-28 red > color #14.2/F,b-e:2-28 red > select clear > select clear > select clear > save session /data/disk3/modeling/gp10/capsid-tail-20200205.cxs > save image /data/disk3/Paper-use/Figure2-20200205-2.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!5 models > show #!20 models > show #!10 models > show #!26 models > toolshed show "Side View" > lighting flat > hide #!10 models > show #!10 models > sequence chain #10 Alignment identifier is 2 2 headers > hide #10/A-L:4-10 > hide selAtoms ribbons > select clear > lighting flat > view cofr false > lighting soft > save image /data/disk3/Paper-use/Figure2-20200205-3.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!10 models > hide #!26 models > save image /data/disk3/Paper-use/Figure2-20200205-3.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!20 models > show #!20 models > show #!10 models > show #!26 models > save image /data/disk3/Paper-use/Figure2-20200205-4.tif pixelSize 0.1 supersample 10 transparentBackground true 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. > hide selAtoms ribbons > select #14.1/X:2 5 atoms, 4 bonds, 1 model selected > show selAtoms > style selAtoms sphere Changed 120 atom styles > style selAtoms stick Changed 120 atom styles > style selAtoms ball Changed 120 atom styles > color selAtoms byhetero > style selAtoms ball Changed 120 atom styles > color selAtoms byhetero > style selAtoms sphere Changed 120 atom styles > color #14.2/b-e,F:29 red > color #14.2/b-e,F:29 magenta > select clear > save image /data/disk3/Paper-use/Figure2-20200205-8.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!23 models > show #!7 models > hide #!7 models > hide #!20 models > show #!20 models > hide #!23 models > save image /data/disk3/Paper-use/Figure2-20200205-9.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting flat > lighting soft > save image /data/disk3/Paper-use/Figure2-20200205-9.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!10 models > hide #!26 models > save image /data/disk3/Paper-use/Figure2-20200205-10.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!5 models > hide #!20 models > save image /data/disk3/Paper-use/Figure2-20200205-11.tif pixelSize 0.1 supersample 10 transparentBackground true > toolshed show "Side View" > show #!10 models > show #!26 models > show #!5 models > show #!20 models > show #!23 models > show #!7 models > save image /data/disk3/Paper-use/Figure2-20200205-12.tif pixelSize 0.1 supersample 10 transparentBackground true > view cofr false > hide #!23 models > hide #!7 models > save image /data/disk3/Paper-use/Figure2-20200205-13.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure2-20200205-14.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting flat > hide #!5 models > show #!5 models > sequence chain #5 Alignment identifier is 3 2 headers > select #5/K:351 11 atoms, 10 bonds, 1 model selected > select #5/K:352 8 atoms, 7 bonds, 1 model selected > select #5/K:370 7 atoms, 6 bonds, 1 model selected > hide selAtoms ribbons > hide selAtoms ribbons > select clear > hide selAtoms ribbons > show selAtoms ribbons > hide selAtoms > select clear > hide #!14 models > show #!14 models > hide #!11 models > show #!11 models > save image /data/disk3/Paper-use/Figure2-20200205-15.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure2-20200205-15.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!20 models > lighting soft > show #!13 models > hide #!13 models > show #!20 models > save image /data/disk3/Paper-use/Figure2-20200205-15.tif pixelSize 0.1 supersample 10 transparentBackground true > lighting flat > hide #!20 models > hide #!11 models > hide #!14 models > hide selAtoms ribbons > show #!14 models > view cofr false > show #!11 models > lighting soft > lighting flat > lighting simple > lighting flat > lighting flat > lighting soft > save image /data/disk3/Paper-use/Figure2-20200205-16.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!5 models > hide #!14 models > show #!14 models > select #14 76410 atoms, 77460 bonds, 3 models selected > hbonds selAtoms 4619 hydrogen bonds found > show selAtoms > style selAtoms stick Changed 76410 atom styles > style selAtoms ball Changed 76410 atom styles > style selAtoms ball Changed 76410 atom styles > show #!5 models > hide #!5 models > select clear > show #!5 models > select #14 76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected > color selAtoms byhetero > style selAtoms sphere Changed 76410 atom styles > style selAtoms ball Changed 76410 atom styles > style selAtoms sphere Changed 76410 atom styles > select clear > select #14 76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected > style selAtoms ball Changed 76410 atom styles > select clear > style selAtoms sphere Changed 257163 atom styles > select clear > select #14 76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected > style selAtoms stick Changed 76410 atom styles > style selAtoms ball Changed 76410 atom styles > hide #!11 models > select clear > select #14.2/N:295 11 atoms, 10 bonds, 1 model selected > select #14.2/N:295 11 atoms, 10 bonds, 1 model selected 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 (2)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SideVIew self.view.render is None |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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dup of #2813