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Opened 6 years ago
Last modified 6 years ago
#2817 assigned defect
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/gp17/Figure4-20200115.cxs opened ChimeraX session > open /data/disk3/modeling/gp17/Figure4-20191209.cxs Summary of feedback from opening /data/disk3/modeling/gp17/Figure4-20191209.cxs --- notes | 2 headers opened ChimeraX session > hide #!1 models > show #!11 models > show #!12 models > hide #!12 models > show #!13 models > show #!12 models > hide #!14 models > hide #!13 models > hide #!12 models > hide #!11 models > show #!8 models > show #!9 models > hide #!9 models > hide #!8 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!23 models > show #!26 models > show #!27 models > hide #!27 models > open /data/disk3/modeling/gp17/Figure4-20191123.cxs opened ChimeraX session > toolshed show "Model Panel" > hide #!26 models > show #!26 models > hide #!21 models > show #!11 models > hide #!11 models > hide #!22 models > show #!22 models > show #!3 models > hide #!3 models > hide #!4 models > show #!4 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > hide #!22 models > show #!22 models > hide #!26 models > show #!26 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > hide #!22 models > show #!22 models > hide #!22 models > show #!3 models > hide #!3 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > show #!58 models > hide #!58 models > show #!58 models > surface dust #38 size 50 No surfaces specified > surface dust #58 size 50 > hide #!58 models > show #!58 models > hide #!4 models > show #!6 models > hide #!6 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!4 models > hide #!4 models > show #!21 models > hide #!21 models > show #!27 models > surface dust #27 size 50 > hide #!58 models > show #!58 models > hide #!27 models > show #!22 models > hide #!22 models > select clear > open /data/disk3/modeling/gp12/6R21-gp12.pdb Chain information for 6R21-gp12.pdb #7 --- Chain | Description b | No description available > close #7 > open /data/disk3/modeling/gp12/gp12-6R21-c12.pdb Chain information for gp12-6R21-c12.pdb #7 --- Chain | Description a b c d e f | No description available > hide #!7 models > show #!7 models > select #7 37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected > hide selAtoms surfaces > show selAtoms ribbons > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > hide #!7 models > show #!7 models > fitmap #7 inMap #23 Fit molecule gp12-6R21-c12.pdb (#7) to map gp12-new.mrc (#23) using 37512 atoms average map value = 0.01737, steps = 112 shifted from previous position = 7.74 rotated from previous position = 10.7 degrees atoms outside contour = 13687, contour level = 0.014 Position of gp12-6R21-c12.pdb (#7) relative to gp12-new.mrc (#23) coordinates: Matrix rotation and translation -0.48622701 0.87383251 0.00002508 -81.40733112 -0.87383251 -0.48622701 0.00007151 285.60438351 0.00007468 0.00001285 0.99999998 -210.24309224 Axis -0.00003356 -0.00002838 -1.00000000 Axis point 43.26267838 166.73496710 0.00000000 Rotation angle (degrees) 119.09289534 Shift along axis 210.23771910 > ui mousemode rightMode "rotate selected models" > hide selAtoms > show selAtoms ribbons > hide #!58 models > show #!58 models > select clear > hide #!7 models > show #!7 models #7 Unknown command: sequence #7 > sequence chain #7 Alignment identifier is 1 2 headers > hide #!17 models > show #!17 models > hide #!23 models > select #7 37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected > show selAtoms > style selAtoms stick Changed 37512 atom styles > style selAtoms ball Changed 37512 atom styles > show selAtoms > style selAtoms sphere Changed 37512 atom styles > hide selAtoms > color #7/a-f:5 red > show selAtoms > style selAtoms stick Changed 36 atom styles > style selAtoms stick Changed 36 atom styles > show selAtoms surfaces > style selAtoms stick Changed 36 atom styles > style selAtoms sphere Changed 36 atom styles > hide selAtoms surfaces > style selAtoms sphere Changed 36 atom styles > style selAtoms ball Changed 36 atom styles > style selAtoms sphere Changed 36 atom styles > hide #!26 models > hide #!17 models > hide #!7 models > show #!7 models > hide #!58 models > color #7/a-f:76 red > style selAtoms sphere Changed 36 atom styles > show selAtoms > style selAtoms sphere Changed 36 atom styles > show selAtoms > style selAtoms ball Changed 36 atom styles > style selAtoms sphere Changed 36 atom styles > show selAtoms > style selAtoms sphere Changed 54 atom styles > show selAtoms > style selAtoms sphere Changed 42 atom styles > color #7/a-f:119 red > show selAtoms > color #7/a-f:121 red > style selAtoms sphere Changed 42 atom styles > color #7/a-f:151 red > show selAtoms > style selAtoms sphere Changed 48 atom styles > show selAtoms > style selAtoms sphere Changed 54 atom styles > color #7/a-f:186 red > style selAtoms sphere Changed 54 atom styles > show selAtoms > style selAtoms sphere Changed 48 atom styles > color #7/a-f:170 red > show selAtoms > style selAtoms sphere Changed 36 atom styles > color #7/a-f:183 red > show selAtoms > style selAtoms sphere Changed 54 atom styles > color #7/a-f:184 red > show selAtoms > style selAtoms sphere Changed 66 atom styles > style selAtoms sphere Changed 66 atom styles > color #7/a-f:254 red > show selAtoms > style selAtoms sphere Changed 48 atom styles > color #7/a-f:272 red > show selAtoms > style selAtoms sphere Changed 48 atom styles > color #7/a-f:384 red > show selAtoms > style selAtoms sphere Changed 36 atom styles > color #7/a-f:462red > show selAtoms > style selAtoms sphere Changed 42 atom styles > color #7/a-f:462 red > color #7/a-f:476 red > color #7/a-f:487 red > show selAtoms > style selAtoms sphere Changed 48 atom styles > show selAtoms > style selAtoms sphere Changed 54 atom styles > color #7/a-f:509red > color #7/a-f:509 red > color #7/a-f:510 red > show selAtoms > style selAtoms sphere Changed 48 atom styles > select #7/c:272@CA 1 atom, 1 model selected > show #!26 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!26 models > show #!26 models > surface dust #23 size 50 > surface dust #26 size 50 > open /data/disk3/modeling/gp11/gp11-6R21-c12.pdb Chain information for gp11-6R21-c12.pdb #8 --- Chain | Description M O Q S U W | No description available N P R T V X | No description available > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > select #8 18192 atoms, 18516 bonds, 1 model selected > hide selAtoms ribbons > show selAtoms ribbons > hide selAtoms > ~select #8 Nothing selected > select #8 18192 atoms, 18516 bonds, 1 model selected > ui mousemode rightMode "rotate selected models" > fitmap #7 inMap #26 Fit molecule gp12-6R21-c12.pdb (#7) to map gp11-c6-clean.mrc (#26) using 37512 atoms average map value = 0.001414, steps = 260 shifted from previous position = 36.7 rotated from previous position = 5.66 degrees atoms outside contour = 34469, contour level = 0.008 Position of gp12-6R21-c12.pdb (#7) relative to gp11-c6-clean.mrc (#26) coordinates: Matrix rotation and translation 0.51614175 -0.85469214 0.05566883 61.53083023 0.85637987 0.51387351 -0.05047280 -283.58903733 0.01453197 0.07372479 0.99717273 -186.44574290 Axis 0.07237341 0.02397160 0.99708949 Axis point 284.39966438 -73.07209393 0.00000000 Rotation angle (degrees) 59.09647754 Shift along axis -188.24797675 > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > fitmap #8 inMap #26 Fit molecule gp11-6R21-c12.pdb (#8) to map gp11-c6-clean.mrc (#26) using 18192 atoms average map value = 0.01542, steps = 80 shifted from previous position = 5.29 rotated from previous position = 4.58 degrees atoms outside contour = 4470, contour level = 0.008 Position of gp11-6R21-c12.pdb (#8) relative to gp11-c6-clean.mrc (#26) coordinates: Matrix rotation and translation -0.99998113 -0.00613688 -0.00002710 211.28975995 0.00613689 -0.99998113 -0.00004598 208.72016130 -0.00002682 -0.00004615 0.99999995 -210.11428321 Axis -0.00001314 -0.00002309 1.00000000 Axis point 105.32328065 104.68181934 0.00000000 Rotation angle (degrees) 179.64837996 Shift along axis -210.12187883 > select #7 37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected > fitmap #7 inMap #23 Fit molecule gp12-6R21-c12.pdb (#7) to map gp12-new.mrc (#23) using 37512 atoms average map value = 0.005269, steps = 168 shifted from previous position = 18 rotated from previous position = 9.49 degrees atoms outside contour = 31814, contour level = 0.014 Position of gp12-6R21-c12.pdb (#7) relative to gp12-new.mrc (#23) coordinates: Matrix rotation and translation -0.65901090 0.75213337 -0.00004699 -19.54685623 -0.75213337 -0.65901090 0.00002094 296.33826354 -0.00001522 0.00004914 0.99999998 -191.28154662 Axis 0.00001875 -0.00002112 -1.00000000 Axis point 57.40002612 152.60287091 0.00000000 Rotation angle (degrees) 131.22448305 Shift along axis 191.27492072 > ui mousemode rightMode "translate selected models" > fitmap #7 inMap #23 Fit molecule gp12-6R21-c12.pdb (#7) to map gp12-new.mrc (#23) using 37512 atoms average map value = 0.00808, steps = 128 shifted from previous position = 4.06 rotated from previous position = 11.8 degrees atoms outside contour = 28750, contour level = 0.014 Position of gp12-6R21-c12.pdb (#7) relative to gp12-new.mrc (#23) coordinates: Matrix rotation and translation -0.49086288 0.87123682 0.00009101 -79.89572937 -0.87123682 -0.49086288 0.00000501 286.04065698 0.00004904 -0.00007683 0.99999998 -204.94636812 Axis -0.00004697 0.00002409 -1.00000000 Axis point 43.63433684 166.35995119 0.00000000 Rotation angle (degrees) 119.39731298 Shift along axis 204.95701084 > sequence chain #8 Chains must have same sequence > hide #!8 models > show #!8 models > select #8 18192 atoms, 18516 bonds, 1 model selected > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > sequence chain #8 Chains must have same sequence > hide #!8 models > show #!8 models > hide #!23 models > hide #!26 models > show #!26 models > show #!23 models > select #7 37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected > ui mousemode rightMode "translate selected models" > fitmap #8 inMap #26 Fit molecule gp11-6R21-c12.pdb (#8) to map gp11-c6-clean.mrc (#26) using 18192 atoms average map value = 0.01542, steps = 24 shifted from previous position = 2.5e-05 rotated from previous position = 4.46e-05 degrees atoms outside contour = 4470, contour level = 0.008 Position of gp11-6R21-c12.pdb (#8) relative to gp11-c6-clean.mrc (#26) coordinates: Matrix rotation and translation -0.99998112 -0.00613762 -0.00002734 211.28994848 0.00613763 -0.99998113 -0.00004597 208.71998266 -0.00002706 -0.00004614 0.99999995 -210.11423878 Axis -0.00001326 -0.00002308 1.00000000 Axis point 105.32332392 104.68176980 0.00000000 Rotation angle (degrees) 179.64833758 Shift along axis -210.12185897 > fitmap #8 inMap #23 Fit molecule gp11-6R21-c12.pdb (#8) to map gp12-new.mrc (#23) using 18192 atoms average map value = 0.001196, steps = 72 shifted from previous position = 7.47 rotated from previous position = 0.92 degrees atoms outside contour = 17530, contour level = 0.014 Position of gp11-6R21-c12.pdb (#8) relative to gp12-new.mrc (#23) coordinates: Matrix rotation and translation 0.99979930 0.02003163 -0.00000198 -214.16050955 -0.02003164 0.99979930 0.00012023 -205.77355029 0.00000439 -0.00012016 0.99999994 -222.97270954 Axis -0.00600004 -0.00015919 -0.99998199 Axis point -10376.02688085 10519.99902557 0.00000000 Rotation angle (degrees) 1.14782567 Shift along axis 224.28642265 > fitmap #8 inMap #26 Fit molecule gp11-6R21-c12.pdb (#8) to map gp11-c6-clean.mrc (#26) using 18192 atoms average map value = 0.005572, steps = 68 shifted from previous position = 2.26 rotated from previous position = 2.63 degrees atoms outside contour = 12720, contour level = 0.008 Position of gp11-6R21-c12.pdb (#8) relative to gp11-c6-clean.mrc (#26) coordinates: Matrix rotation and translation -0.99935156 -0.03600509 -0.00004928 217.43270741 0.03600510 -0.99935157 -0.00004846 202.31489705 -0.00004750 -0.00005020 0.99999995 -215.31484781 Axis -0.00002415 -0.00002468 1.00000000 Axis point 106.89211949 103.11255074 0.00000000 Rotation angle (degrees) 177.93661387 Shift along axis -215.32509141 > select #8 18192 atoms, 18516 bonds, 1 model selected > ui mousemode rightMode "translate selected models" > fitmap #8 inMap #26 Fit molecule gp11-6R21-c12.pdb (#8) to map gp11-c6-clean.mrc (#26) using 18192 atoms average map value = 0.01542, steps = 60 shifted from previous position = 2.91 rotated from previous position = 1.73 degrees atoms outside contour = 4460, contour level = 0.008 Position of gp11-6R21-c12.pdb (#8) relative to gp11-c6-clean.mrc (#26) coordinates: Matrix rotation and translation -0.99998277 -0.00586365 -0.00002700 211.23274090 0.00586366 -0.99998277 -0.00004591 208.77792616 -0.00002673 -0.00004607 0.99999995 -210.11630144 Axis -0.00001308 -0.00002305 1.00000000 Axis point 105.30895002 104.69618892 0.00000000 Rotation angle (degrees) 179.66403531 Shift along axis -210.12387760 > hide #!8 models > show #!8 models > split #8 Chain information for gp11-6R21-c12.pdb M #8.1 --- Chain | Description M | No description available Chain information for gp11-6R21-c12.pdb N #8.2 --- Chain | Description N | No description available Chain information for gp11-6R21-c12.pdb O #8.3 --- Chain | Description O | No description available Chain information for gp11-6R21-c12.pdb P #8.4 --- Chain | Description P | No description available Chain information for gp11-6R21-c12.pdb Q #8.5 --- Chain | Description Q | No description available Chain information for gp11-6R21-c12.pdb R #8.6 --- Chain | Description R | No description available Chain information for gp11-6R21-c12.pdb S #8.7 --- Chain | Description S | No description available Chain information for gp11-6R21-c12.pdb T #8.8 --- Chain | Description T | No description available Chain information for gp11-6R21-c12.pdb U #8.9 --- Chain | Description U | No description available Chain information for gp11-6R21-c12.pdb V #8.10 --- Chain | Description V | No description available Chain information for gp11-6R21-c12.pdb W #8.11 --- Chain | Description W | No description available Chain information for gp11-6R21-c12.pdb X #8.12 --- Chain | Description X | No description available Split gp11-6R21-c12.pdb (#8) into 12 models > hide #!11 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!26 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > sequence chain #8.1 Alignment identifier is 8.1.M 2 headers > show selAtoms > hide selAtoms > select clear > show selAtoms > style selAtoms sphere Changed 7 atom styles > color #8.1:139 red > save session /data/disk3/modeling/gp7.3-mapping.cxs > select clear > show #!26 models > select clear > hide #!26 models > show #!26 models > hide #!8 models > show #!8 models > hide #!23 models > show #!23 models > show #!11 models > hide #!11 models > show #!11 models > surface dust #11 size 50 > hide #!11 models > show #!11 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!10 models > hide #!10 models > show #!10 models > hide selAtoms > hide #!11 models > show #!11 models > show #!21 models > hide #!21 models > show #!21 models > hide #!21 models > hide #!11 models > show #!11 models > show #!27 models > hide #!11 models > show #!21 models > hide #!21 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!21 models > hide #!21 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!23 models > show #!23 models > hide #!27 models > show #!27 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!27 models > surface dust #23 size 50 > surface dust #26 size 50 > surface dust #26 size 80 > surface dust #23 size 80 > lighting soft > select clear > lighting soft > hide #!23 models > hide #!26 models > show #!26 models > hide #!26 models > hide #!8 models > show #!8 models > hide #!8 models > show #!3 models > hide #!3 models > show #!23 models > hide #!23 models > show #!23 models > save image /data/disk3/Paper-use/Figure5-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!23 models > select #7 37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected > show selAtoms > show selAtoms ribbons > show selAtoms surfaces > hide selAtoms surfaces > hide selAtoms > hide #!7 models > show #!7 models > ~select #7 6 models selected > select #7 37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected > style selAtoms sphere Changed 36 atom styles > show selAtoms > style selAtoms sphere Changed 36 atom styles > style selAtoms sphere Changed 888 atom styles > show selAtoms > select clear > select clear > select #7/b:375 11 atoms, 11 bonds, 1 model selected > hide selAtoms > select #7/c:466 6 atoms, 5 bonds, 1 model selected > hide selAtoms > select clear > save image /data/disk3/Paper-use/Figure5-20200205-2.tif pixelSize 0.1 supersample 10 transparentBackground true internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > toolshed show "Side View" > show selAtoms > hide selAtoms > select clear > view cofr false > view orient cofr false > save image /data/disk3/Paper-use/Figure5-20200205-3.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-4.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-4.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-5.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-6.tif pixelSize 0.1 supersample 10 transparentBackground true > save session /data/disk3/modeling/gp7.3-mapping-20200206.cxs > color selAtoms byhetero > color selAtoms byhetero > select #7/b:510@CB 1 atom, 1 model selected > select #7/b:511 11 atoms, 11 bonds, 1 model selected > select #7/c:462@CA 1 atom, 1 model selected > select #7/b:254@CE1 1 atom, 1 model selected > select #7/b:511 11 atoms, 11 bonds, 1 model selected > select #7/b:509@CA 1 atom, 1 model selected > select #7/c:509 9 atoms, 8 bonds, 1 model selected > select #7/c:508 7 atoms, 6 bonds, 1 model selected > lighting flat > select #7/e:463 7 atoms, 7 bonds, 1 model selected > select #7/e:463 7 atoms, 7 bonds, 1 model selected > select clear > select #7/f:559 6 atoms, 5 bonds, 1 model selected > select #7/e:463 7 atoms, 7 bonds, 1 model selected > select #7/f:121@CA 1 atom, 1 model selected > select clear > style selAtoms stick Changed 36 atom styles > select #7/f:508 7 atoms, 6 bonds, 1 model selected > style selAtoms stick Changed 54 atom styles > style selAtoms sphere Changed 60 atom styles > color selAtoms byhetero > select clear > view orient cofr false > view cofr false > select #7/c:271 4 atoms, 3 bonds, 1 model selected > select #7/d:254@CD1 1 atom, 1 model selected > select #7/d:253 6 atoms, 5 bonds, 1 model selected > select #7/d:255 6 atoms, 5 bonds, 1 model selected > select #7/b:273 5 atoms, 4 bonds, 1 model selected > select #7/d:255 6 atoms, 5 bonds, 1 model selected > select clear > select clear > select clear > select #7/b:273 5 atoms, 4 bonds, 1 model selected > select #7/b:273 5 atoms, 4 bonds, 1 model selected > select #7/b:271 4 atoms, 3 bonds, 1 model selected > select #7/b:271 4 atoms, 3 bonds, 1 model selected > select #7/b:273 5 atoms, 4 bonds, 1 model selected > select #7/b:271 4 atoms, 3 bonds, 1 model selected > select #7/d:254@CA 1 atom, 1 model selected > select #7/d:253 6 atoms, 5 bonds, 1 model selected > show selAtoms > style selAtoms stick Changed 834 atom styles > show selAtoms > style selAtoms ball Changed 834 atom styles > style selAtoms sphere Changed 834 atom styles > show selAtoms ribbons > show selAtoms > hide selAtoms > hide selAtoms > select clear > select clear > select up Nothing selected > select up Nothing selected > color #7/a-f:5 green > color #7/a-f:5 magenta > color #7/a-f:76 magenta > color #7/a-f:119 magenta > color #7/a-f:121 magenta > color #7/a-f:151 magenta > color #7/a-f:186 magenta > color #7/a-f:170 magenta > color #7/a-f:183 magenta > color #7/a-f:184 magenta > color #7/a-f:186 magenta > color #7/a-f:254magenta > color #7/a-f:254 magenta > color #7/a-f:272 magenta > color #7/a-f:384 magenta > color #7/a-f:462 magenta > color #7/a-f:476 magenta > color #7/a-f:487 magenta > color #7/a-f:509 magenta > color #7/a-f:510 magenta > select #7/e:346 6 atoms, 5 bonds, 1 model selected > select clear > select #7/c:377 11 atoms, 11 bonds, 1 model selected > hide selAtoms > select clear > lighting soft > select clear > color selAtoms byhetero > select clear > view cofr false > view orient cofr false > view orient cofr false > view orient cofr false > view orient cofr false > select #7/d:171 4 atoms, 3 bonds, 1 model selected > select #7/d:171 4 atoms, 3 bonds, 1 model selected > select #7/a:383 5 atoms, 4 bonds, 1 model selected > select #7/a:383 5 atoms, 4 bonds, 1 model selected > select #7/f:511 11 atoms, 11 bonds, 1 model selected > select #7/a:76@CA 1 atom, 1 model selected > select #7/c:383 5 atoms, 4 bonds, 1 model selected > select #7/b:384@CA 1 atom, 1 model selected > select #7/b:384@CA 1 atom, 1 model selected > select #7/c:385 8 atoms, 7 bonds, 1 model selected > select #7/e:171 4 atoms, 3 bonds, 1 model selected > select #7/d:185 7 atoms, 7 bonds, 1 model selected internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > select #7/b:385 8 atoms, 7 bonds, 1 model selected > color #7/a-f:76 green > color #7/a-f:170 green > color #7/a-f:184 green > color #7/a-f:384 green > color selAtoms byhetero > select clear > show selAtoms > color #7/a-f:151 cyan > color #7/a-f:186 cyan > color #7/a-f:272 cyan > color #7/a-f:487 cyan > color #7/a-f:509 cyan > color selAtoms byhetero > select clear > select clear > color #7/a-f:119 pink > color #7/a-f:121 pink > color #7/a-f:476 pink > select clear > color selAtoms byhetero > color selAtoms byhetero > color selAtoms byhetero > select clear internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > color #7/a-f:254 black > color selAtoms byhetero > select clear > select #7/b:271 4 atoms, 3 bonds, 1 model selected > select #7/b:272@CA 1 atom, 1 model selected > select #7/b:271 4 atoms, 3 bonds, 1 model selected > select clear > view cofr false > view orient cofr false > save image /data/disk3/Paper-use/Figure5-20200205-1.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-2.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-3.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-4.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-5.tif pixelSize 0.1 supersample 10 transparentBackground true > view orient cofr false > select #7/d:278 8 atoms, 7 bonds, 1 model selected > select #7/b:272@CA 1 atom, 1 model selected > select #7/b:271 4 atoms, 3 bonds, 1 model selected > select #7/d:255 6 atoms, 5 bonds, 1 model selected > show selAtoms > show selAtoms > select #7/d:272@OD1 1 atom, 1 model selected > toolshed show Distances > distance #7/d:256@NZ #7/d:272@OD1 Distance between gp12-6R21-c12.pdb #7/d LYS 256 NZ and ASP 272 OD1: 5.966Å > view orient cofr false > view cofr false > lighting shadows true intensity 0.5 > lighting flat > select #7/c:187 10 atoms, 10 bonds, 1 model selected > select #7/c:186@CB 1 atom, 1 model selected > select clear > select #7/b:152 4 atoms, 3 bonds, 1 model selected > select #7/a:271 4 atoms, 3 bonds, 1 model selected > view cofr false > select #7/f:580 9 atoms, 8 bonds, 1 model selected > select #7/f:580 9 atoms, 8 bonds, 1 model selected > select #7/e:488 8 atoms, 7 bonds, 1 model selected > view cofr false > select #7/d:477 9 atoms, 8 bonds, 1 model selected > select #7/d:266 8 atoms, 7 bonds, 1 model selected > select #7/d:477 9 atoms, 8 bonds, 1 model selected > select clear > select #7/d:477 9 atoms, 8 bonds, 1 model selected > select clear > select #7/f:318 4 atoms, 3 bonds, 1 model selected > select #7/f:119@CA 1 atom, 1 model selected > select clear > select clear > select #7/e:487@CA 1 atom, 1 model selected > select #7/f:476@CA 1 atom, 1 model selected > select #7/f:476@CA 1 atom, 1 model selected > select #7/f:476@CA 1 atom, 1 model selected > select #7/e:488 8 atoms, 7 bonds, 1 model selected > select #7/e:508 7 atoms, 6 bonds, 1 model selected > select #7/f:384@CA 1 atom, 1 model selected > select #7/d:275 9 atoms, 8 bonds, 1 model selected > select #7/d:383 5 atoms, 4 bonds, 1 model selected > select #7/d:477 9 atoms, 8 bonds, 1 model selected > lighting soft > view cofr false > hide #!7.1 models > hide #!7.2 models > hide #!7.3 models > hide #!7.4 models > hide #!7.5 models > hide #!7 models > show #!7 models > ~select #7.2 80 atoms, 90 bonds, 7 models selected > ~select #7.3 64 atoms, 90 bonds, 6 models selected > ~select #7.4 48 atoms, 90 bonds, 6 models selected > ~select #7.5 32 atoms, 90 bonds, 4 models selected > ~select #7.6 16 atoms, 90 bonds, 3 models selected > select #7.6 6252 atoms, 1 model selected > hide #7.1-5 target m > hide selAtoms ribbons > select #7.7 6252 atoms, 1 model selected > show selAtoms ribbons > hide selAtoms ribbons > select #7.3 6252 atoms, 1 model selected > hide selAtoms ribbons > select #7.4 6252 atoms, 1 model selected > hide selAtoms ribbons > select #7.5 6252 atoms, 1 model selected > show #!7.5 models > select #7.6 6252 atoms, 1 model selected > show selAtoms ribbons > select clear > select #7.7 6252 atoms, 1 model selected > hide selAtoms ribbons > ~select #7.7 1 model selected > select #7.7 6252 atoms, 1 model selected > select #7.6 6252 atoms, 1 model selected > ~select #7.6 1 model selected > select #7.7 6252 atoms, 1 model selected > hide #!7.7 models > hide selAtoms ribbons > ~select #7.7 1 model selected > select #7.6 6252 atoms, 1 model selected > select #7.5 6252 atoms, 1 model selected > hide #!7 models > show #!7 models > select #7.7 6252 atoms, 1 model selected > show #!7.7 models > hide #!7.7 models > ~select #7.7 1 model selected > select #7.7 6252 atoms, 1 model selected > select #7.1 6 pseudobonds, 1 model selected > show #!7.1 models > hide selAtoms > hide selAtoms ribbons > show #!7.2 models > select #7.2 6252 atoms, 1 model selected > hide selAtoms ribbons > hide selAtoms > show #!7.3 models > select #7.3 6252 atoms, 1 model selected > hide selAtoms > hide selAtoms ribbons > show #!7.4 models > select #7.4 6252 atoms, 1 model selected > hide selAtoms > hide selAtoms ribbons > hide selAtoms ribbons > select #7.7 6252 atoms, 1 model selected > show #!7.7 models > hide selAtoms ribbons > hide selAtoms > select clear > select #7/d:364 9 atoms, 8 bonds, 1 model selected > show selAtoms > select clear > select #7/e:123 8 atoms, 7 bonds, 1 model selected > show selAtoms > hide selAtoms > select #7/e:122 5 atoms, 4 bonds, 1 model selected > show selAtoms > hide selAtoms > select #7/d:364 9 atoms, 8 bonds, 1 model selected > select #7/e:123 8 atoms, 7 bonds, 1 model selected > show selAtoms > hide selAtoms > select #7/d:363 4 atoms, 3 bonds, 1 model selected > hide selAtoms > select clear > select clear > select #7/e:152 4 atoms, 3 bonds, 1 model selected > select clear > select #7/e:223 7 atoms, 6 bonds, 1 model selected > select #7/e:265 12 atoms, 12 bonds, 1 model selected > select #7/e:223 7 atoms, 6 bonds, 1 model selected > select #7/e:221 10 atoms, 10 bonds, 1 model selected > select #7/e:226 6 atoms, 5 bonds, 1 model selected > select #7/e:225 7 atoms, 7 bonds, 1 model selected > select #7/e:223 7 atoms, 6 bonds, 1 model selected > show selAtoms > hide selAtoms > select #7/d:465 6 atoms, 5 bonds, 1 model selected > select #7/d:466 6 atoms, 5 bonds, 1 model selected > show selAtoms > select #7/d:466@CA 1 atom, 1 model selected > hide selAtoms > hide selAtoms > select #7/d:464 11 atoms, 10 bonds, 1 model selected > show selAtoms > select #7/e:509 9 atoms, 8 bonds, 1 model selected > select #7/e:508 7 atoms, 6 bonds, 1 model selected > select #7/d:257 8 atoms, 7 bonds, 1 model selected > hide selAtoms > view orient cofr false > view cofr false > select clear > select #7/d:256 9 atoms, 8 bonds, 1 model selected > hide selAtoms > select clear > select #7/d:270 7 atoms, 6 bonds, 1 model selected > select clear > view cofr false > select #7/e:511 11 atoms, 11 bonds, 1 model selected > select #7/e:511 11 atoms, 11 bonds, 1 model selected > select #7/d:487 8 atoms, 7 bonds, 1 model selected > select #7/e:511 11 atoms, 11 bonds, 1 model selected > color #7/a-f:510 green > color selAtoms byhetero > select clear > select #7/e:510@ND2 1 atom, 1 model selected > distance #7/d:487@OD2 #7/e:510@ND2 Distance between gp12-6R21-c12.pdb #7/d ASP 487 OD2 and /e ASN 510 ND2: 6.490Å > ~distance #7/d:487@OD2 #7/e:510@ND2 > ~distance #7/d:256@NZ #7/d:272@OD1 > distance #7/d:487@OD2 #7/e:510@ND2 Distance between gp12-6R21-c12.pdb #7/d ASP 487 OD2 and /e ASN 510 ND2: 6.490Å Must select one or more distances in the table > ~distance #7/d:487@OD2 #7/e:510@ND2 > select #7.1 6 pseudobonds, 1 model selected > ~select #7.1 Nothing selected > select #7 37512 atoms, 38472 bonds, 6 pseudobonds, 2 models selected > show selAtoms ribbons > select clear > color #7/a-f:476 pink > style selAtoms sphere Changed 804 atom styles > show selAtoms > select clear > view orient cofr false > select #7/c:510@ND2 1 atom, 1 model selected > distance #7/a:487@OD2 #7/c:510@ND2 Distance between gp12-6R21-c12.pdb #7/a ASP 487 OD2 and /c ASN 510 ND2: 6.488Å > select clear > hide #!9 models > select clear > save image /data/disk3/Paper-use/Figure5-20200205-6.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-6.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-5.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-4.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-3.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Figure5-20200205-2.tif pixelSize 0.1 supersample 10 transparentBackground true > view orient cofr false > select #7/d:791 6 atoms, 5 bonds, 1 model selected > show selAtoms > select #7/d:790 11 atoms, 10 bonds, 1 model selected > show selAtoms > select #7/d:695 7 atoms, 6 bonds, 1 model selected > select #7/d:792 6 atoms, 5 bonds, 1 model selected > lighting flat 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 → Graphics |
| 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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