Opened 6 years ago

Closed 6 years ago

#2383 closed defect (fixed)

surface close causes OpenGL buffer delete error

Reported by: goddard@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Tom Goddard) 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-05)
Description
"surface close" command generated this error.  Had molecular surfaces shown on 5 of 10 chains colored by bfactor.

Log:
UCSF ChimeraX version: 0.91 (2019-09-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6h6b format mmCIF fromDatabase pdb

6h6b title:  
Structure of alpha-synuclein fibrils [more info...]  
  
Chain information for 6h6b #1  
---  
Chain | Description  
A B C D E F G H I J | Alpha-synuclein  
  
  

> hide atoms

> show cartoons

> set bgColor white

> lighting simple

> graphics silhouettes true

> save /Users/goddard/Desktop/image1.png supersample 3

> close

> open 6h6b format mmCIF fromDatabase pdb

6h6b title:  
Structure of alpha-synuclein fibrils [more info...]  
  
Chain information for 6h6b #1  
---  
Chain | Description  
A B C D E F G H I J | Alpha-synuclein  
  
  

> save /Users/goddard/Desktop/image1.png supersample 3

> hide atoms

> show ribbons

> save /Users/goddard/Desktop/image1.png supersample 3

> show /A only

> show /A ribbons only

> hide /A

> show ribbons

> show /A ribbons only

> show ribbons

> save /Users/goddard/Desktop/image1.png supersample 3

> select clear

> color /D,E,F,I,J tan

> color /A,B,C,G,H pink

> save /Users/goddard/Desktop/image1.png supersample 3

> select /A

806 atoms, 808 bonds, 1 model selected  

> show /A ribbons only

> select clear

> save /Users/goddard/Desktop/image1.png supersample 3

> show /A atoms

> style stick

Changed 8060 atom styles  

> color byhetero

> save /Users/goddard/Desktop/image1.png supersample 3

> log metadata #1

Metadata for 6h6b #1  
---  
Title | Structure of alpha-synuclein fibrils  
Citation | Guerrero-Ferreira, R., Taylor, N.M., Mona, D., Ringler, P., Lauer,
M.E., Riek, R., Britschgi, M., Stahlberg, H. (2018). Cryo-EM structure of
alpha-synuclein fibrils. Elife, 7. PMID: 29969391. DOI: 10.7554/eLife.36402  
Gene source | Homo sapiens  
Experimental method | Electron microscopy  
Resolution | 3.4Å  
  
> sequence chain #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J

Alignment identifier is 1  

> select clear

> color sel orange

> color /D,E,F,I,J tan

> color /A,B,C,G,H pink

> color byhetero

> select clear

Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1666, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 549, in close_request  
tool_instance.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.alignment.detach_viewer(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 110, in destroy_alignment  
alignment._destroy()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
KeyError: <chimerax.atomic.molobject.Chain object at 0x129c06550>  
  
KeyError:  
  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
  
See log for complete Python traceback.  
  

> save /Users/goddard/Desktop/seqbug.cxs

> sequence chain #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J

Alignment identifier is 1  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1666, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 549, in close_request  
tool_instance.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.alignment.detach_viewer(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 110, in destroy_alignment  
alignment._destroy()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
KeyError: <chimerax.atomic.molobject.Chain object at 0x129c06550>  
  
KeyError:  
  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
  
See log for complete Python traceback.  
  

> sequence chain #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J

Alignment identifier is 1  

> select clear

> select /A:52

16 atoms, 15 bonds, 1 model selected  

> select up

144 atoms, 144 bonds, 1 model selected  

> graphics selection width 4

> save /Users/goddard/Desktop/image1.png supersample 3

> select clear

> select strand

3540 atoms, 3500 bonds, 1 model selected  

> select clear

> label /A

> label height 1.4

> hide atoms

> show /A

> graphics silhouettes false

> hide H

> save /Users/goddard/Desktop/image1.png supersample 3

> save /Users/goddard/Desktop/image1.png supersample 3

> usage label

label [objects] [objectType] [text text] [offset offset] [color color]
[bgColor bgColor] [size size] [height height] [font a text string] [onTop true
or false]  
— Create atom labels  
objects: an objects specifier or nothing  
objectType: one of atoms, bonds, pseudobonds, or residues  
text: default or a text string  
offset: default or some numbers  
color: default or a color  
bgColor: none or a color  
size: default or an integer  
height: fixed or a number

label delete [objects] [objectType]  
— Delete atom labels  
objects: an objects specifier or nothing  
objectType: one of atoms, bonds, pseudobonds, or residues

label listfonts  
— List available fonts

label orient [orient]  
— Set label orientation updating  
orient: a number  

> label delete

> cofr

Center of rotation: 121.58 120.4 94.561 front center  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1666, in <lambda>  
dw.closeEvent = lambda e, tw=tool_window, mw=mw: mw.close_request(tw, e)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 549, in close_request  
tool_instance.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 495, in delete  
self.alignment.detach_viewer(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 325, in detach_viewer  
self.session.alignments.destroy_alignment(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 110, in destroy_alignment  
alignment._destroy()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
KeyError: <chimerax.atomic.molobject.Chain object at 0x129c06550>  
  
KeyError:  
  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 498, in _destroy  
aseq.match_maps[sseq].mod_handler.remove()  
  
See log for complete Python traceback.  
  

> cofr frontCenter

> show ribbons

> lighting simple

> graphics silhouettes true

> hbonds

295 hydrogen bonds found  

> hide atoms

> save /Users/goddard/Desktop/image1.png supersample 3

> ~hbonds

> usage hbonds

hbonds [atoms] [makePseudobonds true or false] [radius a number] [color a
color] [showDist true or false] [restrict restrict] [interSubmodel true or
false] [interModel true or false] [intraModel true or false] [intraMol true or
false] [intraRes true or false] [cacheDa a number] [relax true or false]
[distSlop a number] [angleSlop a number] [twoColors true or false] [slopColor
a color] [reveal true or false] [retainCurrent true or false] [saveFile name
of a file to save/write] [log true or false] [namingStyle namingStyle] [batch
true or false] [dashes dashes] [saltOnly true or false] [name a text string]
[coordsets true or false]  
— Find hydrogen bonds  
atoms: an atoms specifier or nothing  
restrict: one of any, both, or cross or an atoms specifier  
namingStyle: one of command, serial, or simple  
dashes: an integer ≥ 0  

> usage ~hbonds

~hbonds [name a text string]  
— Clear hydrogen bonds  

> show surfaces

> lighting soft

> lighting full

> save /Users/goddard/Desktop/image1.png supersample 3

> color bfactor

8060 atoms, 580 residues, 10 surfaces, atom bfactor range 19.1 to 60.1  

> mlp

Map values for surface "6h6b_A SES surface": minimum -28.32, mean -4.205,
maximum 22.28  
Map values for surface "6h6b_B SES surface": minimum -28.29, mean -4.234,
maximum 22.78  
Map values for surface "6h6b_C SES surface": minimum -28.69, mean -4.206,
maximum 22.63  
Map values for surface "6h6b_D SES surface": minimum -28.48, mean -4.227,
maximum 22.65  
Map values for surface "6h6b_E SES surface": minimum -28.67, mean -4.197,
maximum 22.18  
Map values for surface "6h6b_F SES surface": minimum -28.2, mean -4.217,
maximum 22.35  
Map values for surface "6h6b_G SES surface": minimum -27.92, mean -4.26,
maximum 23.73  
Map values for surface "6h6b_H SES surface": minimum -28.31, mean -4.211,
maximum 22.08  
Map values for surface "6h6b_I SES surface": minimum -28.39, mean -4.225,
maximum 23.02  
Map values for surface "6h6b_J SES surface": minimum -28.76, mean -4.2,
maximum 22.47  
Exception ignored in: <function Drawing.__del__ at 0x1027124d0>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1113, in __del__  
self.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1700, in delete  
Model.delete(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 80, in delete  
Drawing.delete(self)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 1129, in delete  
self.remove_all_drawings()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 318, in remove_all_drawings  
self.remove_drawings(cd, delete)  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 311, in remove_drawings  
d.delete()  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1867, in delete  
self.volume._surfaces.remove(self)  
ValueError: list.remove(x): x not in list  

> save /Users/goddard/Desktop/image1.png supersample 3

> hide /A,B,C,G,H surfaces

> color /A,B,C,G,H pink

> hide ribbons

> show atoms

> hide atoms

> show ribbons

> hide /A,B,C ribbons

> save /Users/goddard/Desktop/image1.png supersample 3

> color bfactor

8060 atoms, 580 residues, 10 surfaces, atom bfactor range 19.1 to 60.1  

> save /Users/goddard/Desktop/image1.png supersample 3

> show /G,H atoms

> save /Users/goddard/Desktop/image1.png supersample 3

> surface close

Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "vcolor" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "instance_placement"
was not deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x102cda560>  
Traceback (most recent call last):  
File "/Users/goddard/Desktop/ChimeraX Sep 5
2019.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2460, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer
"instance_shift_and_scale" was not deleted before core.graphics.Buffer
destroyed  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Tom Goddard, 6 years ago

Component: Unassigned → Graphics
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → surface close causes OpenGL buffer delete error

comment:2 by Tom Goddard, 6 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

OpenGL buffers not deleted due to indentation error. Bug introduced 3 weeks ago when changing element buffer creation when number of triangles is 0.

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