id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1718 self._positions is None chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-18.2.0-x86_64-i386-64bit ChimeraX Version: 0.8 (2018-12-17) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.8 (2018-12-17) How to cite UCSF ChimeraX Updating list of available bundles failed: 'list' object has no attribute 'split' > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc Opened postprocess_masked.mrc, grid size 480,480,480, pixel 1.08, shown at level 0.0347, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc Opened kre33_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -2.76e-05, step 2, values float32 > color #3 light gray > volume #3 transparency 0.75 > volume #3 step 1 level 0.04 > volume #4 step 1 level 0.01 > surface dust #1-8 size 5 > set bgColor white > lighting soft > color #1 #2 light gray > color #2/R forest green > color #2/S cyan > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z tomato > hide #1 #2 target a > show #2/R /S /W /Z /Y target r > windowsize 600 800 > set silhouettes true > color zone #4 near #2 #1 distance 6 > view matrix camera 0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position.png supersample 3 > hide #1 #2 target r > show #2/R:790 target a > style #2/R:786 :797 :885 : 889 :890 :802 :794 stick Changed 63 atom styles > color #2/R@N* blue > color #2/R@O* red > windowsize 600 600 Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/graphics.py"", line 80, in resizeEvent v.draw(check_for_changes = False) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/view.py"", line 159, in draw self._draw_scene(camera, drawings) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/view.py"", line 213, in _draw_scene draw_depth(r, opaque_drawings) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 1379, in draw_depth draw_opaque(r, drawings) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 1360, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 1371, in _draw_multiple d.draw(renderer, draw_pass) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 684, in draw if not self.display: File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 311, in get_display return self._any_displayed_positions and len(self._positions) > 0 TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 311, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. > set silhouettes true > close > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb Summary of feedback from opening /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_utp.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 3723 messages similar to the above omitted Chain information for c5_utp.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E I | No description available F | No description available G | No description available H | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available X | No description available Y | No description available Z | No description available > open /Users/lijuanyin/project/kre33_90S/figures/figure1/c5_ribo.pdb Chain information for c5_ribo.pdb #2 --- Chain | Description 1 | No description available 2 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N d | No description available O | No description available P | No description available Q | No description available R S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available e g | No description available f | No description available h | No description available i | No description available j m | No description available k | No description available l | No description available n | No description available o | No description available p | No description available > open /Users/lijuanyin/project/kre33_90S/job028_class3d_job026_8c/c5_and_c146ofc2/second_refine/post_2/postprocess_masked.mrc Opened postprocess_masked.mrc, grid size 480,480,480, pixel 1.08, shown at level 0.0347, step 2, values float32 > open /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_map.mrc Opened kre33_map.mrc, grid size 480,480,480, pixel 1.08, shown at level -2.76e-05, step 2, values float32 > color #3 light gray > volume #3 transparency 0.75 > volume #3 step 1 level 0.04 > volume #4 step 1 level 0.01 > surface dust #1-8 size 5 > set bgColor white > lighting soft > color #1 #2 light gray > color #2/R forest green > color #2/S cyan > color #2/W cornflower blue > color #2/Y hot pink > color #2/Z tomato > hide #1 #2 target a > show #2/R /S /W /Z /Y target r > windowsize 600 800 > set silhouettes true > color zone #4 near #2 #1 distance 6 > view matrix camera 0.88647,-0.27586,-0.37157,21.602,-0.30963,0.24319,-0.91923,-306,0.34394,0.92993,0.13017,328.02 > save /Users/lijuanyin/project/kre33_90S/figures/for_ed/kre33_position.png supersample 3 > hide #1 #2 target r > show #2/R:790 target a > style #2/R:786 :797 :885 : 889 :890 :802 :794 stick Changed 63 atom styles > color #2/R@N* blue > color #2/R@O* red > windowsize 600 600 Traceback (most recent call last): File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/ui/graphics.py"", line 80, in resizeEvent v.draw(check_for_changes = False) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/view.py"", line 159, in draw self._draw_scene(camera, drawings) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/view.py"", line 213, in _draw_scene draw_depth(r, opaque_drawings) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 1379, in draw_depth draw_opaque(r, drawings) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 1360, in draw_opaque _draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 1371, in _draw_multiple d.draw(renderer, draw_pass) File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 684, in draw if not self.display: File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 311, in get_display return self._any_displayed_positions and len(self._positions) > 0 TypeError: object of type 'NoneType' has no len() TypeError: object of type 'NoneType' has no len() File ""/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site- packages/chimerax/core/graphics/drawing.py"", line 311, in get_display return self._any_displayed_positions and len(self._positions) > 0 See log for complete Python traceback. OpenGL version: 4.1 ATI-2.4.9 OpenGL renderer: AMD Radeon Pro 455 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " defect closed normal Graphics 0.8 duplicate all ChimeraX