Side View: self.view.render is None

[chimerax-bug-report@…]

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/disk3/20200129-Figure6new-SPA-ET.cxs format session

opened ChimeraX session  

> show #!47 models

> hide #!52 models

> hide #!47 models

> hide #!56 models

> show #!56 models

> show #!57 models

> hide #!57 models

> hide #!58 models

> show #!58 models

> hide #!58 models

> hide #!59 models

> show #!59 models

> hide #!60 models

> show #!60 models

> hide #!60 models

> show #!8 models

> show #!7 models

> hide #!8 models

> hide #!7 models

> show #!8 models

> show #!9 models

> show #!10 models

> show #!11 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> show #!10 models

> hide #!10 models

> show #!10 models

> show #!4 models

> hide #!4 models

> show #!3 models

> hide #!3 models

> show #!9 models

> hide #!9 models

> close #9

> show #!11 models

> hide #!11 models

> show #!12 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!5 models

> show #!5 models

> select #10

3 models selected  

> hide #!10 models

> show #!10 models

> vop gaussian #10 sdev 3.15

> surface dust #10 size 50

> surface dust #10 size 30

> surface dust #10 size 80

> surface dust #10 size 100

> surface dust #9 size 100

> hide #!8 models

> show #!10 models

> hide #!10 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!9 models

> show #!9 models

> fitmap #8 inMap #9

Fit map tail-fiber-c6-refined-trimmed-up.mrc in map fiber-c6-flip-trim.mrc
gaussian using 696084 points  
correlation = 0.8168, correlation about mean = 0.09116, overlap = 27.32  
steps = 88, shift = 2.72, angle = 1.51 degrees  
  
Position of tail-fiber-c6-refined-trimmed-up.mrc (#8) relative to
fiber-c6-flip-trim.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
-0.99998814 -0.00102200 0.00475798 713.81108099  
0.00105181 -0.99997979 0.00626689 713.64077310  
0.00475148 0.00627182 0.99996903 -3.67623596  
Axis 0.00237758 0.00313406 0.99999226  
Axis point 356.72491365 357.01118873 0.00000000  
Rotation angle (degrees) 179.94058924  
Shift along axis 0.25753176  
  

> transparency #9 70

> transparency #9 70

> select clear

> select #12

16878 atoms, 17130 bonds, 1 model selected  

> hide selAtoms surfaces

> show selAtoms ribbons

> select clear

> show #!3 models

> hide #!3 models

> show #!2 models

> hide #!56 models

> hide #!59 models

> show #!41 models

> hide #!41 models

> show #!42 models

> hide #!42 models

> show #!43 models

> hide #!43 models

> show #!34 models

> show #!56 models

> hide #!56 models

> show #!26 models

> surface dust #26 size 50

> select clear

> show #!27 models

> surface dust #27 size 50

> select clear

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> show #!10 models

> hide #!10 models

> hide #!9 models

> show #!9 models

> show #!7 models

> hide #!7 models

> select clear

> hide #!8 models

> show #!22 models

> hide #!22 models

> show #!21 models

> hide #!21 models

> show #!35 models

> select clear

> hide #!35 models

> show #!35 models

> hide #!9 models

> show #!9 models

> fitmap #35 inMap #9

Fit map fiber-arm-leg-flip-trim.mrc in map fiber-c6-flip-trim.mrc gaussian
using 151811 points  
correlation = 0.889, correlation about mean = 0.329, overlap = 6.426  
steps = 52, shift = 1.37, angle = 0.45 degrees  
  
Position of fiber-arm-leg-flip-trim.mrc (#35) relative to fiber-c6-flip-
trim.mrc gaussian (#9) coordinates:  
Matrix rotation and translation  
0.21210524 -0.70286852 -0.67896040 680.17374542  
0.30605783 0.70759371 -0.63689853 389.10081846  
0.92808404 -0.07271165 0.36520275 64.55108251  
Axis 0.28499990 -0.81180106 0.50966076  
Axis point 330.20717289 0.00000000 656.01105675  
Rotation angle (degrees) 81.81030872  
Shift along axis -89.12385358  
  

> hide #!9 models

> show #!9 models

> select clear

> select clear

> select clear

> save session /data/disk3/modeling/gp12/Figure6new-20200218.cxs

Expected a keyword  

> save image /data/disk3/Paper-use/20200218-Figure6-1.tif pixelSize 0.1
supersample 10 transparentBackground true

> hide #!9 models

> show #!9 models

> lighting soft

> lighting soft

> lighting full

> lighting simple

> lighting full

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting full

> hide #!9 models

> show #!9 models

> transparency #9 90

> transparency #9 80

> save image /data/disk3/Paper-use/20200218-Figure6-1.tif pixelSize 0.1
supersample 10 transparentBackground true

> lighting soft

> save image /data/disk3/Paper-use/20200218-Figure6-1.tif pixelSize 0.1
supersample 10 transparentBackground true

> show #!8 models

> hide #!8 models

> hide #!9 models

> hide #!12 models

> hide #!26 models

> hide #!35 models

> show #!35 models

> hide #!34 models

> hide #!2 models

> hide #!27 models

> hide #!5 models

> show #!53 models

> hide #!53 models

> show #!8 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> show #!9 models

> hide #!9 models

> show #!9 models

> show #!32 models

> hide #!32 models

> show #!27 models

> hide #!27 models

> show #!37 models

> hide #!37 models

> show #!37 models

> show #!38 models

> hide #!38 models

> show #!38 models

> hide #!38 models

> show #!49 models

> hide #!49 models

> show #!48 models

> hide #!48 models

> show #!48 models

> show #!52 models

> hide #!52 models

> show #!52 models

> show #!53 models

> hide #!53 models

> show #!53 models

> show #!51 models

> hide #!48 models

> hide #!37 models

> show #!36 models

> hide #!36 models

> hide #!35 models

> show #!35 models

> hide #!52 models

> hide #!53 models

> hide #!51 models

> show #!59 models

> show #!56 models

> show #!58 models

> hide #!58 models

> show #!57 models

> hide #!57 models

> show #!57 models

> hide #!57 models

> show #!57 models

> hide #!57 models

> show #!52 models

> hide #!52 models

> show #!49 models

> hide #!49 models

> show #!49 models

> hide #!49 models

> show #!43 models

> hide #!43 models

> show #!39 models

> hide #!39 models

> show #!38 models

> hide #!38 models

> show #!36 models

> hide #!36 models

> show #!34 models

> hide #!56 models

> hide #!59 models

> show #!26 models

> show #!21 models

> hide #!21 models

> show #!33 models

> show #!38 models

> hide #!38 models

> lighting soft

> lighting simple

> lighting full

> lighting shadows false

> save image /data/disk3/Paper-use/20200218-Figure6-2.tif pixelSize 0.1
supersample 10 transparentBackground true

> surface dust #35 size 50

> surface dust #33 size 50

> save image /data/disk3/Paper-use/20200218-Figure6-2.tif pixelSize 0.1
supersample 10 transparentBackground true

> save image /data/disk3/Paper-use/20200218-Figure6-3.tif pixelSize 0.1
supersample 10 transparentBackground true

> show #!38 models

> show #!46 models

> hide #!38 models

> show #!38 models

> hide #!38 models

> show #!38 models

> hide #!35 models

> show #!35 models

> show #!8 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> show #!10 models

> hide #!10 models

> show #!13 models

> hide #!13 models

> show #!21 models

> hide #!21 models

> hide #!38 models

> show #!38 models

> hide #!35 models

> show #!35 models

> hide #!33 models

> show #!33 models

> show #!48 models

> hide #!38 models

> select clear

> save image /data/disk3/Paper-use/20200218-Figure6-4.tif pixelSize 0.1
supersample 10 transparentBackground true

> show #!42 models

> hide #!42 models

> hide #!9 models

> hide #!35 models

> show #!51 models

> hide #!51 models

> show #!50 models

> hide #!50 models

> show #!53 models

> transparency #53 90

> show #!57 models

> hide #!57 models

> show #!55 models

> hide #!55 models

> show #!54 models

> hide #!54 models

> show #!49 models

> hide #!49 models

> show #!47 models

> hide #!47 models

> show #!60 models

> transparency #60 90

> show #!56 models

> transparency #56 90

> select clear

> select clear

> save image /data/disk3/Paper-use/20200218-Figure6-5.tif pixelSize 0.1
supersample 10 transparentBackground true

> hide #!56 models

> show #!56 models

> hide #!60 models

> show #!60 models

> show #!45 models

> hide #!45 models

> show #!49 models

> hide #!49 models

> show #!49 models

> hide #!49 models

> show #!49 models

> hide #!49 models

> show #!50 models

> show #!43 models

> show #!44 models

> hide #!43 models

> hide #!44 models

> hide #!34 models

> open /data/disk3/modeling/gp12/gp12_phre.pdb

Chain information for gp12_phre.pdb #62  
---  
Chain | Description  
| No description available  
  

> close #62

> show #!42 models

> show #!43 models

> show #!44 models

> hide #!44 models

> hide #!43 models

> open /data/disk3/modeling/gp12/gp12-dim-chan.pdb

Chain information for gp12-dim-chan.pdb #62  
---  
Chain | Description  
b f | No description available  
  

> open /data/disk3/modeling/gp12/gp12-dim-chan.pdb

Chain information for gp12-dim-chan.pdb #63  
---  
Chain | Description  
b f | No description available  
  

> view name fiber

> select #62

12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected  

> select #63

12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected  

> select #62

12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected  

> ui mousemode rightMode "rotate selected models"

> lighting flat

> matchmaker #62 to #42

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 gp12-dim-chan.pdb, chain b (#42) with gp12-dim-chan.pdb, chain b
(#62), sequence alignment score = 3980.2  
RMSD between 784 pruned atom pairs is 0.000 angstroms; (across all 784 pairs:
0.000)  
  

> matchmaker #61 to #42

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 gp12-dim-chan.pdb, chain b (#42) with gp17-refined-good-nochan-
coot-recombine.pdb, chain C (#61), sequence alignment score = 84.5  
RMSD between 5 pruned atom pairs is 0.957 angstroms; (across all 112 pairs:
37.149)  
  

> show #!61 models

> hide #!61 models

> show #!61 models

> close #61

> matchmaker #63 to #42

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 gp12-dim-chan.pdb, chain b (#42) with gp12-dim-chan.pdb, chain b
(#63), sequence alignment score = 3980.2  
RMSD between 784 pruned atom pairs is 0.000 angstroms; (across all 784 pairs:
0.000)  
  

> ui mousemode rightMode "rotate selected models"

> select #63

12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected  

> ui mousemode rightMode "rotate selected models"

> hide #!50 models

> show #!50 models

> hide #!50 models

> show #!50 models

> hide #!53 models

> hide #!50 models

> show #!50 models

> fitmap #42 inMap #50

Fit molecule gp12-dim-chan.pdb (#42) to map chan-tail-c6-new-gp12-re-sym.mrc
(#50) using 12504 atoms  
average map value = 1.767, steps = 52  
shifted from previous position = 6.09  
rotated from previous position = 0.68 degrees  
atoms outside contour = 1469, contour level = 0.22421  
  
Position of gp12-dim-chan.pdb (#42) relative to chan-tail-c6-new-gp12-re-
sym.mrc (#50) coordinates:  
Matrix rotation and translation  
-0.37251725 -0.92695373 -0.04458331 243.84842380  
0.92799349 -0.37247171 -0.00963447 -93.32122449  
-0.00767531 -0.04496202 0.99895917 74.11616203  
Axis -0.01903783 -0.01988952 0.99962091  
Axis point 153.69386142 36.95802311 0.00000000  
Rotation angle (degrees) 111.90167453  
Shift along axis 71.30183591  
  

> fitmap #62 inMap #50

Fit molecule gp12-dim-chan.pdb (#62) to map chan-tail-c6-new-gp12-re-sym.mrc
(#50) using 12504 atoms  
average map value = 1.82, steps = 84  
shifted from previous position = 7.23  
rotated from previous position = 14.5 degrees  
atoms outside contour = 1643, contour level = 0.22421  
  
Position of gp12-dim-chan.pdb (#62) relative to chan-tail-c6-new-gp12-re-
sym.mrc (#50) coordinates:  
Matrix rotation and translation  
-0.99000303 -0.14024811 -0.01498007 202.77345845  
0.14078079 -0.98906184 -0.04401502 164.72384749  
-0.00864319 -0.04568391 0.99891849 74.48344578  
Axis -0.00593689 -0.02254274 0.99972825  
Axis point 95.73396492 90.37884076 0.00000000  
Rotation angle (degrees) 171.92017320  
Shift along axis 69.54603584  
  

> fitmap #63 inMap #50

Fit molecule gp12-dim-chan.pdb (#63) to map chan-tail-c6-new-gp12-re-sym.mrc
(#50) using 12504 atoms  
average map value = 1.768, steps = 80  
shifted from previous position = 6.39  
rotated from previous position = 16.2 degrees  
atoms outside contour = 1474, contour level = 0.22421  
  
Position of gp12-dim-chan.pdb (#63) relative to chan-tail-c6-new-gp12-re-
sym.mrc (#50) coordinates:  
Matrix rotation and translation  
-0.61708422 0.78628109 0.03113008 -41.19097887  
-0.78686022 -0.61618940 -0.03408137 257.82141266  
-0.00761551 -0.04552610 0.99893408 74.18847238  
Axis -0.00727268 0.02462132 -0.99967039  
Axis point 42.28105512 139.96779885 0.00000000  
Rotation angle (degrees) 128.10975018  
Shift along axis -67.51654670  
  

> select #62

12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected  

> show selAtoms surfaces

> select #63

12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected  

> show selAtoms surfaces

> select #62

12504 atoms, 12824 bonds, 2 pseudobonds, 2 models selected  

> select clear

> lighting soft

> view name test

> view fiber

> view test

> hide #!50 models

> show #!50 models

> hide #!33 models

> show #!33 models

> hide #!48 models

> show #!48 models

> show #!57 models

> hide #!57 models

> show #!52 models

> hide #!52 models

> show #!38 models

> hide #!48 models

> select #46

2 models selected  

> ui mousemode rightMode "translate selected models"

> select clear

> save image /data/disk3/Paper-use/20200218-Figure6-6.tif pixelSize 0.1
supersample 10 transparentBackground true

> lighting soft

> lighting soft

> lighting simple

> lighting shadows true

> lighting flat

> lighting full

> lighting simple

> select clear

> save image /data/disk3/Paper-use/20200218-Figure6-6.tif pixelSize 0.1
supersample 10 transparentBackground true

> hide #!46 models

> show #!46 models

> surface dust #46 size 50

> view test

> hide #!38 models

> show #!32 models

> hide #!32 models

> show #!8 models

> hide #!8 models

> hide #!42 models

> hide #!62 models

> hide #!63 models

> hide #!56 models

> show #!56 models

> hide #!50 models

> show #!42 models

> hide #!42 models

> show #!41 models

> hide #!41 models

> show #!40 models

> hide #!40 models

> show #!37 models

> hide #!37 models

> show #!36 models

> hide #!36 models

> show #!35 models

> hide #!35 models

> show #!35 models

> hide #!35 models

> show #!8 models

> hide #!8 models

> show #!7 models

> hide #!7 models

> show #!9 models

> show #!35 models

> hide #!35 models

> show #!35 models

> hide #!35 models

> show #!35 models

> show #!48 models

> show #!59 models

> hide #!59 models

> show #!34 models

> lighting soft

> lighting simple

> lighting full

> lighting full

> lighting shadows false

> lighting full

> lighting full

> show #!6 models

> hide #!6 models

> show #!13 models

> hide #!13 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!35 models

> show #!35 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> lighting simple

> lighting soft

> lighting flat

> lighting shadows true intensity 0.5

> lighting full

> lighting simple

internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on
mapped window  

> view cofr false

> toolshed show "Side View"

> save image /data/disk3/Paper-use/20200218-Figure6-1.tif pixelSize 0.1
supersample 10 transparentBackground true

> save session /data/disk3/modeling/gp12/Figure6new-20200218.cxs

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!8 models

> hide #!8 models

> show #!8 models

> open /data/disk3/modeling/gp17/tail-fiber-c6-refined-trimmed-up-five.mrc

Opened tail-fiber-c6-refined-trimmed-up-five.mrc, grid size 680,680,680, pixel
1.05, shown at step 1, values float32  

> view cofr false

> hide #!8 models

> show #!8 models

> hide #!48 models

> show #!48 models

> hide #!61 models

> show #!61 models

> hide #!61 models

> show #!61 models

> hide #!8 models

> view cofr false

> hide #!61 models

> show #!61 models

> select #61

2 models selected  

> select #61

2 models selected  

> select #61

2 models 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"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> hide #!61 models

> show #!61 models

> hide #!46 models

> show #!46 models

> hide #!60 models

> show #!60 models

> hide #!48 models

> show #!48 models

> show #!10 models

> hide #!10 models

> show #!8 models

> fitmap #61 inMap #8

Fit map tail-fiber-c6-refined-trimmed-up-five.mrc in map tail-
fiber-c6-refined-trimmed-up.mrc using 933526 points  
correlation = 0.8628, correlation about mean = 0.4112, overlap = 102.2  
steps = 324, shift = 20.6, angle = 11.9 degrees  
  
Position of tail-fiber-c6-refined-trimmed-up-five.mrc (#61) relative to tail-
fiber-c6-refined-trimmed-up.mrc (#8) coordinates:  
Matrix rotation and translation  
0.49964794 0.86600257 -0.01978680 -126.79024063  
-0.86614771 0.49978308 0.00224961 487.36236408  
0.01183727 0.01601428 0.99980171 -11.38432790  
Axis 0.00794500 -0.01825349 -0.99980182  
Axis point 358.51902851 353.56445899 0.00000000  
Rotation angle (degrees) 60.02537877  
Shift along axis 1.47865676  
  

> hide #!8 models

> select clear

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