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Opened 6 years ago
Closed 6 years ago
#2419 closed defect (can't reproduce)
Model.positions is None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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: <function Buffer.__del__ at 0x7fc972d1f5f0>
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: <function Buffer.__del__ at 0x7fc972d1f5f0>
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: <function Buffer.__del__ at 0x7fc972d1f5f0>
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: <function Buffer.__del__ at 0x7fc972d1f5f0>
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: <function Buffer.__del__ at 0x7fc972d1f5f0>
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: <function Buffer.__del__ at 0x7fc972d1f5f0>
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: <function Buffer.__del__ at 0x7fc972d1f5f0>
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 <lambda>
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: <function Buffer.__del__ at 0x7fc972d1f5f0>
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: <function Buffer.__del__ at 0x7fc972d1f5f0>
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 "<class
'chimerax.atomic.structure.AtomicStructure'>": '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 <lambda>
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 "<class
'chimerax.atomic.structure.AtomicStructure'>": '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 "<class
'chimerax.atomic.structure.AtomicStructure'>": '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 <lambda>
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 "<class
'chimerax.atomic.structure.AtomicStructure'>": '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
Attachments (1)
Change History (3)
by , 6 years ago
| Attachment: | Screenshot from 2019-09-18 10-49-06.png added |
|---|
comment:1 by , 6 years ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Model.positions is None |
comment:2 by , 6 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
This error saving a ChimeraX session is because something was referencing the closed atomic models. We have seen this before but don't know what is holding the reference to the closed model. So a week ago we put in code that reports where the reference is that causes the session save error. But you are running an older ChiemraX (July 2019) so your bug report does not tell us where the problem is. If you see this again in a recent ChimeraX build we will be able to fix it, so please report it again if it happens.
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