id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2419 Model.positions is None wenfeili@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-4.4.0-154-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-07-18) Description i was going to save the session (.cxs) when this error came out. Log: UCSF ChimeraX version: 0.91 (2019-07-18) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 190716_NPN_tRNA_mRNA_NC_PF_figure.cxs opened ChimeraX session > select #5 5029 atoms, 5295 bonds, 2 pseudobonds, 2 models selected > show selAtoms > show #!1 models > hide #!1 models > select clear > hide selAtoms > hide selAtoms ribbons > hide selAtoms > select clear > hide selAtoms > select #5/A:1@K 1 atom, 1 model selected > hide selAtoms > hide selAtoms > hide selAtoms > hide selAtoms > hide selAtoms ribbons > select clear > hide selAtoms > select #5/k:1061@C5' 1 atom, 1 model selected > select #5/k 270 atoms, 300 bonds, 1 model selected > show selAtoms > nucleotides selAtoms atoms > style nucleic & selAtoms stick Changed 270 atom styles Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > select clear > hide selAtoms > hide selAtoms > hide selAtoms > hide selAtoms > color zone #6 near #5/v,k distance 2.1 > show #!6 models > surface zone #6 nearAtoms #5/v,k distance 2.1 > hide #!6 models Expected an objects specifier or a keyword > surface zone #6 nearAtoms sel distance 2.1 > show #!6 models Expected an objects specifier or a keyword > select #5/v:34-37 #5/k:1053-1055 159 atoms, 175 bonds, 1 model selected > select #5/v:34-37 #5/k:1053-1055 159 atoms, 175 bonds, 1 model selected > surface zone #6 nearAtoms sel distance 2.1 > select #6 2 models selected > hide #!5 models > show #!5 models > hide #!5 models > select #6 2 models selected > select clear > select #6 2 models selected > select #6 2 models selected > volume selMaps style mesh > select clear > show #!5 models > select #5/v:34-37 #5/k:1053-1055 159 atoms, 175 bonds, 1 model selected > select clear > select #5 5029 atoms, 5295 bonds, 2 pseudobonds, 2 models selected > hide selAtoms > select #5/v:34-37 #5/k:1053-1055 159 atoms, 175 bonds, 1 model selected > show selAtoms > view all > open /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_mRNA- tRNA_rs_eRF1-301-coot-17.pdb Summary of feedback from opening /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_mRNA- tRNA_rs_eRF1-301-coot-17.pdb --- warnings | Ignored bad PDB record found on line 20 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 21 BOND : 0.008 0.136 5389 Ignored bad PDB record found on line 22 ANGLE : 1.210 13.021 7691 Ignored bad PDB record found on line 23 CHIRALITY : 0.062 0.318 938 Ignored bad PDB record found on line 24 PLANARITY : 0.006 0.067 657 15 messages similar to the above omitted Start residue of secondary structure not found: SHEET 1 D 3 GLU j 341 LEU j 346 0 End residue of secondary structure not found: SHEET 2 D 3 MET j 329 CYS j 335 -1 N LEU j 333 O LYS j 342 Start residue of secondary structure not found: SHEET 3 D 3 HIS j 366 LEU j 368 -1 N GLU j 367 O HIS j 334 Chain information for 190915_mRNA-tRNA_rs_eRF1-301-coot-17.pdb #4 --- Chain | Description C | No description available j | No description available k | No description available v | No description available > select #4 5029 atoms, 5295 bonds, 2 pseudobonds, 2 models selected > hide selAtoms ribbons > nucleotides selAtoms atoms > style nucleic & selAtoms stick Changed 1891 atom styles > toolshed show ""Fit in Map"" Fit molecule 190513_mRNA-tRNA_rs_eRF1-301-coot-16.pdb (#5) to map mask_40S_refine.mrc (#6) using 5029 atoms average map value = 0.01485, steps = 48 shifted from previous position = 0.717 rotated from previous position = 0.19 degrees atoms outside contour = 2499, contour level = 0.013545 Position of 190513_mRNA-tRNA_rs_eRF1-301-coot-16.pdb (#5) relative to mask_40S_refine.mrc (#6) coordinates: Matrix rotation and translation 0.99999472 0.00052762 0.00320707 -0.72332226 -0.00052986 0.99999962 0.00069567 0.01380152 -0.00320670 -0.00069737 0.99999462 0.92624473 Axis -0.20954412 0.96477375 -0.15906876 Axis point 289.33929807 0.00000000 224.86991413 Rotation angle (degrees) 0.19045025 Shift along axis 0.01754667 > close #4 > volume #6 subdivideSurface true > lighting full > lighting soft > lighting simple > volume selMaps style surface > transparency #6 80 > transparency #6 70 > volume selMaps style mesh > volume selMaps style surface > volume selMaps style solid > volume selMaps style surface > lighting full > lighting soft > lighting simple > select #5/v 1622 atoms, 1808 bonds, 1 model selected > color sel orange > select clear > select up Nothing selected > select up Nothing selected > select #5/k 270 atoms, 300 bonds, 1 model selected > nucleotides selAtoms tube/slab shape ellipsoid > nucleotides selAtoms tube/slab shape muffler > nucleotides selAtoms ladder > nucleotides selAtoms stubs > nucleotides selAtoms tube/slab shape box > nucleotides selAtoms slab > style nucleic & selAtoms stick Changed 270 atom styles > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 270 atom styles > nucleotides selAtoms ladder > nucleotides selAtoms stubs > nucleotides selAtoms tube/slab shape muffler > nucleotides selAtoms slab > style nucleic & selAtoms stick Changed 270 atom styles > nucleotides selAtoms tube/slab shape box > nucleotides selAtoms slab > style nucleic & selAtoms stick Changed 270 atom styles > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 270 atom styles > select clear > select #5/v 1622 atoms, 1808 bonds, 1 model selected > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 1621 atom styles > select clear > open /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_mRNA- tRNA_rs_eRF1-301-coot-17.pdb Summary of feedback from opening /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_mRNA- tRNA_rs_eRF1-301-coot-17.pdb --- warnings | Ignored bad PDB record found on line 20 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 21 BOND : 0.008 0.136 5389 Ignored bad PDB record found on line 22 ANGLE : 1.210 13.021 7691 Ignored bad PDB record found on line 23 CHIRALITY : 0.062 0.318 938 Ignored bad PDB record found on line 24 PLANARITY : 0.006 0.067 657 15 messages similar to the above omitted Start residue of secondary structure not found: SHEET 1 D 3 GLU j 341 LEU j 346 0 End residue of secondary structure not found: SHEET 2 D 3 MET j 329 CYS j 335 -1 N LEU j 333 O LYS j 342 Start residue of secondary structure not found: SHEET 3 D 3 HIS j 366 LEU j 368 -1 N GLU j 367 O HIS j 334 Chain information for 190915_mRNA-tRNA_rs_eRF1-301-coot-17.pdb #4 --- Chain | Description C | No description available j | No description available k | No description available v | No description available > select #4 5029 atoms, 5295 bonds, 2 pseudobonds, 2 models selected > hide selAtoms ribbons > hide selAtoms > select #4/v, k 1892 atoms, 2108 bonds, 1 model selected > show selAtoms > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > color #4/v orange > color #4/k ""hot pink"" > surface zone #6 nearAtoms sel distance 2.1 > volume #6 subdivideSurface true > hide #!5 models > show #!5 models > hide #!5 models > select up 1891 atoms, 2108 bonds, 1 model selected > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 159 atom styles > nucleotides selAtoms tube/slab shape box > nucleotides selAtoms tube/slab shape muffler > select #4/v:34-37 95 atoms, 104 bonds, 1 model selected > nucleotides selAtoms tube/slab shape muffler > nucleotides selAtoms ladder > nucleotides selAtoms tube/slab shape muffler > nucleotides selAtoms stubs > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 95 atom styles > nucleotides selAtoms atoms > style nucleic & selAtoms stick Changed 95 atom styles > nucleotides selAtoms tube/slab shape box > nucleotides selAtoms tube/slab shape muffler > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 95 atom styles > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > nucleotides selAtoms tube/slab shape muffler > nucleotides selAtoms tube/slab shape box > nucleotides selAtoms slab > style nucleic & selAtoms stick Changed 159 atom styles > nucleotides selAtoms tube/slab shape box > select clear > select #4/v 1622 atoms, 1808 bonds, 1 model selected Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > nucleotides selAtoms tube/slab shape box > preset cartoons/nucleotides ribbons/slabs Changed 206827 atom styles Preset expands to these ChimeraX commands: surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > hide selAtoms ribbons > select #4/j 2928 atoms, 2974 bonds, 2 pseudobonds, 2 models selected > hide selAtoms ribbons > select #4/k 270 atoms, 300 bonds, 1 model selected > hide selAtoms ribbons > select #4/v #4/k 1892 atoms, 2108 bonds, 1 model selected > hide selAtoms > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > show selAtoms > select clear > select #4/k:1053-1055 64 atoms, 71 bonds, 1 model selected Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 64 atom styles > select clear > surface zone #6 nearAtoms sel distance 2.1 No atoms specified > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > surface zone #6 nearAtoms sel distance 2 > volume selMaps style mesh > color zone #6 near sel distance 2 > volume selMaps style surface > transparency #6 80 > surface dust #6 size 5 > surface zone #6 nearAtoms sel distance 2.1 > select #6 5 models selected > surface dust sel size 5 > surface dust sel size 50 > surface zone #6 nearAtoms sel distance 2.1 No atoms specified > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > surface zone #6 nearAtoms sel distance 2 > surface zone #6 nearAtoms sel distance 1.8 > select clear > surface zone #6 nearAtoms sel distance 1.5 No atoms specified > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > surface zone #6 nearAtoms sel distance 1.5 > select clear > hide #!6 models > show #!6 models > save session /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL.cxs > lighting full > lighting simple > lighting soft > lighting full > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL.tif width 842 height 726 > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > color zone #6 near sel distance 1.5 > transparency #6 80 > select clear > lighting simple > lighting full > lighting simple > transparency #6 70 > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_simple.tif width 842 height 726 > hide #!6 models > show #!6 models > lighting simple > lighting soft > lighting full > lighting simple > transparency #6 50 > volume selMaps style surface > volume selMaps style surface > transparency #6 30 > transparency #6 60 > volume selMaps style mesh > volume #6 subdivideSurface true > volume selMaps style surface > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_map.tif width 842 height 726 > volume selMaps style mesh > volume #6 subdivideSurface true > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_mesh.tif width 842 height 726 > select #4/v:36-37 #4/k:1053 74 atoms, 80 bonds, 1 model selected > surface zone #6 nearAtoms sel distance 1.5 > select up 42 atoms, 45 bonds, 1 model selected > select up 1891 atoms, 2108 bonds, 1 model selected > hide selAtoms > select #4/v:36-37 #4/k:1053 74 atoms, 80 bonds, 1 model selected > show selAtoms > select clear > view all > hide selAtoms ribbons > view all > volume #6 subdivideSurface true > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_37_mesh.tif width 842 height 726 > volume selMaps style surface > volume selMaps style mesh > view all > select #4 5029 atoms, 5295 bonds, 2 pseudobonds, 2 models selected > hide selAtoms > select #4/v:36-37 #4/k:1053 74 atoms, 80 bonds, 1 model selected > show selAtoms > select clear > hide #!6 models > show #!6 models > volume selMaps style surface > volume selMaps style mesh > volume selMaps style surface > volume selMaps style mesh > volume #6 subdivideSurface true > volume #6 style mesh level 0.8 > volume #6 style mesh level 0.2 > undo > undo > undo > surface zone #6 nearAtoms sel distance 1.5 > hide #!6 models > show #!6 models > volume selMaps style surface > surface zone #6 nearAtoms sel distance 1.5 > color zone #6 near sel distance 1.5 > volume selMaps style mesh > volume selMaps style surface > transparency #6 60 > select clear > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_37_side_map.tif width 842 height 726 > volume selMaps style mesh > volume #6 subdivideSurface true > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_37_side_mesh.tif width 842 height 726 Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > select up 20 atoms, 21 bonds, 1 model selected > hide selAtoms ribbons > hide selAtoms > select #4/v:37@O01 1 atom, 1 model selected > select up 3 atoms, 1 bond, 1 model selected > select up 54 atoms, 58 bonds, 1 model selected > surface zone #6 nearAtoms sel distance 1.5 > select clear > view all > select clear Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > select clear > select #4/k:1053@O3' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > hide selAtoms > select #4/v:37@C07 1 atom, 1 model selected > select up 32 atoms, 34 bonds, 1 model selected Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > surface zone #6 nearAtoms sel distance 1.5 > select clear > view all > volume #6 subdivideSurface true > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_37_only_mesh.tif width 842 height 726 > volume selMaps style surface > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_37_only_map.tif width 842 height 726 Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 855, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 595, in file_save_cb self.save_dialog.display(self, session) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 138, in display fmt.save(session, filename) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 55, in save fmt.export(session, self.add_missing_file_suffix(filename, fmt), fmt.name) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/seqalign/__init__.py"", line 59, in save_file alignments = list(session.alignments.alignments.values()) AttributeError: 'list' object has no attribute 'values' AttributeError: 'list' object has no attribute 'values' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/seqalign/__init__.py"", line 59, in save_file alignments = list(session.alignments.alignments.values()) See log for complete Python traceback. > volume selMaps style mesh > volume #6 subdivideSurface true > save session /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_37_only_map.cxs [Errno 2] No such file or directory: '/media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_37_only_map.cxs.tmp' [Errno 2] No such file or directory: '/media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190915_ASL_37_only_map.cxs.tmp' > select #5/v:34-37 #5/k:1053-1055 159 atoms, 175 bonds, 1 model selected > show selAtoms > hide #!6 models > show selAtoms > select #4/v:34-37 #5/k:1053-1055 159 atoms, 175 bonds, 2 models selected > show selAtoms > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > show selAtoms > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > select #4/v:37 32 atoms, 34 bonds, 1 model selected > select sel:< 3.5 236 atoms, 260 bonds, 2 models selected > show selAtoms > hide selAtoms > select clear > hide selAtoms > select #4/v:37 32 atoms, 34 bonds, 1 model selected > select sel:< 3.5 236 atoms, 260 bonds, 2 models selected > show selAtoms > style selAtoms stick Changed 236 atom styles > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 236 atom styles > select clear > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190917_ASL_37_distance_3p5.tif width 842 height 726 > select #4/v:37 32 atoms, 34 bonds, 1 model selected > select sel:< 3.5 236 atoms, 260 bonds, 2 models selected > surface zone #6 nearAtoms sel distance 1.5 Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > show #!6 models > select #4/v:37 32 atoms, 34 bonds, 1 model selected > select sel:< 3.5 236 atoms, 260 bonds, 2 models selected > color zone #6 near sel distance 1.5 > select clear > volume selMaps style surface > volume selMaps style mesh > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190917_ASL_37_distance_3p5_mesh.tif width 842 height 726 > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190917_ASL_37_distance_3p5_mesh_or1.tif width 842 height 726 > hide #!6 models > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190917_ASL_37_distance_3p5_or1.tif width 842 height 726 > show #!6 models > hide #!6 models > ui mousemode rightMode translate > ui mousemode rightMode rotate Unknown command: rotate 180 > view all > lighting simple > lighting soft > lighting full > lighting simple > show #!6 models > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190917_ASL_37_distance_3p5_mesh_or2.tif width 842 height 726 > hide #!6 models > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190917_ASL_37_distance_3p5_or2.tif width 842 height 726 > save session /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190917_ASL_37_distance_3p5.cxs > select #4/v:36-37 #4/k:1053 74 atoms, 80 bonds, 1 model selected > show selAtoms > style selAtoms stick Changed 74 atom styles > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > show selAtoms > select #4 5029 atoms, 5295 bonds, 2 pseudobonds, 2 models selected > ~select #4 Nothing selected > open /media/HDD5/Wenfei/190327_NPN/Model/Model2NPN/190915_mRNA- tRNA_rs_eRF1-301-coot-18.pdb Summary of feedback from opening /media/HDD5/Wenfei/190327_NPN/Model/Model2NPN/190915_mRNA- tRNA_rs_eRF1-301-coot-18.pdb --- warnings | Ignored bad PDB record found on line 20 DEVIATIONS FROM IDEAL VALUES. Ignored bad PDB record found on line 21 BOND : 0.008 0.136 5389 Ignored bad PDB record found on line 22 ANGLE : 1.210 13.021 7691 Ignored bad PDB record found on line 23 CHIRALITY : 0.062 0.318 938 Ignored bad PDB record found on line 24 PLANARITY : 0.006 0.067 657 15 messages similar to the above omitted Start residue of secondary structure not found: SHEET 1 D 3 GLU j 341 LEU j 346 0 End residue of secondary structure not found: SHEET 2 D 3 MET j 329 CYS j 335 -1 N LEU j 333 O LYS j 342 Start residue of secondary structure not found: SHEET 3 D 3 HIS j 366 LEU j 368 -1 N GLU j 367 O HIS j 334 Chain information for 190915_mRNA-tRNA_rs_eRF1-301-coot-18.pdb #7 --- Chain | Description C | No description available j | No description available k | No description available v | No description available Fit molecule 190915_mRNA-tRNA_rs_eRF1-301-coot-18.pdb (#7) to map mask_40S_refine.mrc (#6) using 5029 atoms average map value = 0.01486, steps = 64 shifted from previous position = 0.166 rotated from previous position = 0.195 degrees atoms outside contour = 2808, contour level = 0.015 Position of 190915_mRNA-tRNA_rs_eRF1-301-coot-18.pdb (#7) relative to mask_40S_refine.mrc (#6) coordinates: Matrix rotation and translation 0.99999443 0.00065353 0.00327173 -0.77807613 -0.00065583 0.99999954 0.00069937 0.04409013 -0.00327127 -0.00070151 0.99999440 0.93400596 Axis -0.20546140 0.95963875 -0.19203925 Axis point 286.45139505 0.00000000 236.87276391 Rotation angle (degrees) 0.19532726 Shift along axis 0.02280940 > hide #!7 models > select #7/v:34-37 #7/k:1053-1055 159 atoms, 175 bonds, 1 model selected > show selAtoms > show #!7 models > select #7 5029 atoms, 5295 bonds, 2 pseudobonds, 2 models selected > hide selAtoms > hide selAtoms ribbons > select #7/v:34-37 #7/k:1053-1055 159 atoms, 175 bonds, 1 model selected > show selAtoms > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 159 atom styles > hide #!4 models > show #!4 models > close #7 > hide #!4 models > nucleotides selAtoms fill > style nucleic & selAtoms stick Changed 118950 atom styles > show #!4 models > show #!6 models > hide #!6 models > lighting simple > lighting soft > lighting simple > lighting full > lighting simple > select #7/v:34-37 #7/k:1052-1055 Nothing selected > select #4/v:34-37 #4/k:1052-1055 181 atoms, 200 bonds, 1 model selected > surface zone #6 nearAtoms sel distance 1.5 > show #!6 models > color zone #6 near sel distance 1.5 > color zone #6 near sel distance 1.2 > color zone #6 near sel distance 1.0 > hide #!6 models > show #!6 models > surface zone #6 nearAtoms sel distance 1.0 > surface zone #6 nearAtoms sel distance 1.2 > surface zone #6 nearAtoms sel distance 1.4 > surface zone #6 nearAtoms sel distance 1.5 > color zone #6 near sel distance 1.5 > select clear > select #4/k:1052@O5' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > hide selAtoms > select #4/v:38@N6 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > hide selAtoms Exception ignored in: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2421, in __del__ % self.shader_variable_name) chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer ""None"" was not deleted before core.graphics.Buffer destroyed > select #4/v:34-37 #4/k:1052-1054 161 atoms, 178 bonds, 1 model selected > surface zone #6 nearAtoms sel distance 1.5 > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > surface zone #6 nearAtoms sel distance 1.5 > color zone #6 near sel distance 1.5 > select clear > view all > volume #6 subdivideSurface true > volume #6 subdivideSurface false > volume #6 subdivideSurface true > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190918_ASL_34-37_mesh.tif width 842 height 726 > hide #!6 models > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190918_ASL_34-37.tif width 842 height 726 > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > nucleotides selAtoms atoms > style nucleic & selAtoms stick Changed 159 atom styles > select clear > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190918_ASL_34-37_open.tif width 842 height 726 > show #!6 models > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190918_ASL_34-37_open_mesh.tif width 842 height 726 > hide #!6 models > select #4/v:34@OP1 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 1 model selected > select clear > select #4/v:34@OP1 1 atom, 1 model selected > hide selAtoms > hide selAtoms > hide selAtoms > hide selAtoms > hide selAtoms > hide selAtoms > hide selAtoms > show #!6 models > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > surface zone #6 nearAtoms sel distance 1.5 > color zone #6 near sel distance 1.5 > select clear > hide #!6 models > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/Core_region/190918_ASL_34-37_open_1.tif width 842 height 726 > show #!6 models > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/ASL/190918_ASL_34-37_open_1_mesh.tif width 842 height 726 > select up Nothing selected > select #4/v:34-37 #4/k:1053-1055 159 atoms, 175 bonds, 1 model selected > hbonds sel intraModel false 39 hydrogen bonds found > hide #!7 models > show #!7 models > hbonds sel 56 hydrogen bonds found > select #7 56 pseudobonds, 1 model selected > ~select #7 Nothing selected > hide selAtoms > hide selAtoms surfaces > select clear > hide sel pseudobonds > hide sel pseudobonds > hide sel pseudobonds > hide sel pseudobonds > hide sel pseudobonds > hide sel pseudobonds > select clear > hide sel pseudobonds > hide #!7 models > show #!7 models > hide #!6 models > save image /media/HDD5/Wenfei/190327_NPN/Model/Figures/ASL/190918_ASL_34-37_open_1_hbond.tif width 842 height 726 > save session /media/HDD5/Wenfei/190327_NPN/Model/Figures/ASL/190918_ASL_34-37_open_hbond.cxs Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2407, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py"", line 271, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 763, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 532, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2407, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py"", line 271, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 855, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 595, in file_save_cb self.save_dialog.display(self, session) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 138, in display fmt.save(session, filename) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 1056, in save run(session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2646, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 950, in save_session save(session, filename, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 763, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 532, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. > save session /media/HDD5/Wenfei/190327_NPN/Model/Figures/ASL/190918_ASL_34-37_open_hbond.cxs includeMaps true Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2407, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py"", line 271, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 763, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 532, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 255, in process data = sm.take_snapshot(obj, session, self.state_flags) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 2407, in take_snapshot 'structure state': Structure.take_snapshot(self, session, flags), File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/atomic/structure.py"", line 164, in take_snapshot data = {'model state': Model.take_snapshot(self, session, flags), File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py"", line 271, in take_snapshot 'positions': self.positions.array(), AttributeError: 'NoneType' object has no attribute 'array' During handling of the above exception, another exception occurred: Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 855, in save_action.triggered.connect(lambda arg, s=self, sess=session: s.file_save_cb(sess)) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 595, in file_save_cb self.save_dialog.display(self, session) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py"", line 138, in display fmt.save(session, filename) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 1056, in save run(session, cmd) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2646, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 950, in save_session save(session, filename, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/commands/save.py"", line 61, in save fmt.export(session, filename, fmt.nicknames[0], **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/io.py"", line 213, in export result = self.export_func(session, path, **kw) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 763, in save session.save(output, version=version, include_maps=include_maps) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 532, in save mgr.discovery(self._state_containers) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 234, in discovery self.processed[key] = self.process(obj) File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 258, in process raise RuntimeError(msg) RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' RuntimeError: Error while saving session data for """": 'NoneType' object has no attribute 'array' File ""/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/session.py"", line 258, in process raise RuntimeError(msg) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.67 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation File attachment: Screenshot from 2019-09-18 10-49-06.png }}} [attachment:""Screenshot from 2019-09-18 10-49-06.png""] " defect closed normal Core can't reproduce all ChimeraX