Opened 6 years ago

Closed 6 years ago

#2389 closed defect (duplicate)

Graphics buffer deletion problem for "split" after "surface"

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

Description 

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-03)
Description
error using "split" after "surface"

open 1zik
surf
split

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  

> open startup.cxc

> alias reset view orient; view initial

> alias vmc view selAtoms|selMaps; cofr front

> alias toggle sel ##display; hide sel models; show ~sel models; ~sel

> alias stoggle sel ##display; hide sel & $1 models; show ~sel & $1 models;
~sel

executed startup.cxc  
UCSF ChimeraX version: 0.91 (2019-09-03)  
© 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  
  
  

> split

Chain information for 6h6b A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 6h6b B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 6h6b C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 6h6b D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 6h6b E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 6h6b F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 6h6b G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 6h6b H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 6h6b I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for 6h6b J #1.10  
---  
Chain | Description  
J | No description available  
  
Split 6h6b (#1) into 10 models  

> 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  
  
  

> surface

> split

Chain information for 6h6b A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 6h6b B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 6h6b C #1.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 6h6b D #1.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 6h6b E #1.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 6h6b F #1.6  
---  
Chain | Description  
F | No description available  
  
Chain information for 6h6b G #1.7  
---  
Chain | Description  
G | No description available  
  
Chain information for 6h6b H #1.8  
---  
Chain | Description  
H | No description available  
  
Chain information for 6h6b I #1.9  
---  
Chain | Description  
I | No description available  
  
Chain information for 6h6b J #1.10  
---  
Chain | Description  
J | No description available  
  
Split 6h6b (#1) into 10 models  
Exception ignored in: <function Buffer.__del__ at 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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  

> version

UCSF ChimeraX version: 0.91 (2019-09-03)  
© 2016-2019 Regents of the University of California. All rights reserved.  

> close

> open 1zik

1zik title:  
GCN4-leucine zipper core mutant ASN16LYS In the dimeric state [more info...]  
  
Chain information for 1zik #1  
---  
Chain | Description  
A B | general control protein GCN4  
  
  

> surface

> split

Chain information for 1zik A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 1zik B #1.2  
---  
Chain | Description  
B | No description available  
  
Split 1zik (#1) into 2 models  
Exception ignored in: <function Buffer.__del__ at 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 0x10a139050>  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.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 INTEL-12.10.12
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by pett, 6 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Graphics buffer deletion problem for "split" after "surface"

comment:2 by Tom Goddard, 6 years ago

Resolution: → duplicate
Status: assigned → closed

Fixed yesterday but last night's builds failed.

Duplicate of #2383.

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