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#2721 closed defect (fixed)

Index out of bounds showing interface contact residues

Reported by:	leygkn@…	Owned by:	Tom Goddard
Priority:	normal	Milestone:
Component:	Surface/Binding Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)
I tried Interfaces -> select contact residue~~ or Residue plot ...
and this error occured

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/leygk/OneDrive/구조 모델링 관련 자료/VHL mutation (4wqo).cxs"

opened ChimeraX session  

> graphics silhouettes false

> lighting full

> toolshed show "Side View"

> select clear

> graphics silhouettes true

> rainbow

Unknown command: clor /a red  

> color /a red

> color /c green

> color bychain

> color byhetero

> color byhetero

> color bychain

> interfaces ~solvent

3 buried areas: A C 1001, D C 965, A D 340  

> show sel atoms

> color sel byatom

> label sel

> label sel size 100

> label sel size 200

> label sel size 30

> label sel size 50

> help help:user

> label sel height 100 size 50

> label sel height 10 size 50

> label sel height 1 size 50

> label sel height 0.5 size 100

> toolshed show "Command Line Interface"

> toolshed show "Basic Actions"

> label sel height 0.5 size 200

> label sel height 0.5

> label sel height 0.5 color purple

> label sel height 0.5 color red

> select clear

> show sel atoms

> label sel height 0.5 color red

> label sel height 0.5 color yellow

> label sel height 0.5 color blue

> color sel byatom

> select clear

> hide /D target c

Alignment identifier is 1.A  
Alignment identifier is 1.C  
Alignment identifier is 1.D  

> select clear

> delete sel

> select clear

Alignment identifier is 1.A  
Alignment identifier is 1.C  
Alignment identifier is 1.D  

> select clear

> interfaces ~solvent

3 buried areas: D C 965, C A 902, D A 340  

> color red

> color sel red

> undo

> color sel red

> undo

> select /C:89

9 atoms, 8 bonds, 1 model selected  

> hide sel atoms

> label

> save session "C:/Users/leygk/OneDrive/구조 모델링 관련 자료/VHL - Cul2.cxs"

> select clear

> select /A:191

10 atoms, 10 bonds, 1 model selected  

> select /A:190

8 atoms, 7 bonds, 1 model selected  

> select /A:189

9 atoms, 8 bonds, 1 model selected  

> select /A:188

8 atoms, 7 bonds, 1 model selected  

> select /A:184

8 atoms, 7 bonds, 1 model selected  

> select /a

470 atoms, 476 bonds, 1 model selected  

> show sel surfaces

> undo

> hide sel surfaces

> select /A:184

8 atoms, 7 bonds, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select /A:187

8 atoms, 7 bonds, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select /A:191

10 atoms, 10 bonds, 1 model selected  

> show sel surfaces

> delete sel

> select /c

739 atoms, 755 bonds, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select /C:68

10 atoms, 10 bonds, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select /C:64

9 atoms, 8 bonds, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select /C:65

8 atoms, 7 bonds, 1 model selected  

> show sel surfaces

> show sel surfaces

> select /C:65

8 atoms, 7 bonds, 1 model selected  

> select /C:66

7 atoms, 7 bonds, 1 model selected  

> select /C:66

7 atoms, 7 bonds, 1 model selected  

> select /C:74

6 atoms, 5 bonds, 1 model selected  

> select clear

> select /C:64

9 atoms, 8 bonds, 1 model selected  

> show sel surfaces

> select /C:38@O

1 atom, 1 model selected  

> select /C:38@CG2

1 atom, 1 model selected  

> select /c

739 atoms, 755 bonds, 1 model selected  

> hide sel surfaces

> select /C:38

7 atoms, 6 bonds, 1 model selected  

> show sel surfaces

> select /C:64

9 atoms, 8 bonds, 1 model selected  

> select /C:65

8 atoms, 7 bonds, 1 model selected  

> show sel surfaces

> color sel red

> select /c

739 atoms, 755 bonds, 1 model selected  

> show sel surfaces

> select clear

> delete sel

> undo

Undo failed, probably because structures have been modified.  

> select /c

368 atoms, 377 bonds, 1 model selected  

> hide sel surfaces

> select clear

> save session "C:/Users/leygk/OneDrive/구조 모델링 관련 자료/VHL - Cul2 (Core).cxs"

> toolshed show "Command Line Interface"

> ui favorite true "Command Line Interface"

> help help:user

> help help:user/tools/cli.html

> ui dockable false "Command Line Interface"

> ui dockable true "Command Line Interface"

> ui dockable false "Command Line Interface"

> select /c

368 atoms, 377 bonds, 1 model selected  

> show sel surfaces

> hide sel surfaces

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\graph.py", line 416, in <lambda>  
a.triggered.connect(lambda checked, cb=callback, args=args: cb(*args))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\tool.py", line 240, in _show_residue_plot  
self._show_interface_residues(c, g)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\tool.py", line 218, in _show_interface_residues  
af = c.contact_residue_atoms(gf, min_area)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\cmd.py", line 264, in contact_residue_atoms  
res = self.contact_residues(group, min_area)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\cmd.py", line 274, in contact_residues  
res, rareas = group.atoms[i].residue_sums(areas)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 158, in __getitem__  
ptrs = self._pointers[i].copy()  
IndexError: index 428 is out of bounds for axis 0 with size 368  
  
IndexError: index 428 is out of bounds for axis 0 with size 368  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 158, in __getitem__  
ptrs = self._pointers[i].copy()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\graph.py", line 416, in <lambda>  
a.triggered.connect(lambda checked, cb=callback, args=args: cb(*args))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\tool.py", line 240, in _show_residue_plot  
self._show_interface_residues(c, g)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\tool.py", line 218, in _show_interface_residues  
af = c.contact_residue_atoms(gf, min_area)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\cmd.py", line 264, in contact_residue_atoms  
res = self.contact_residues(group, min_area)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\cmd.py", line 274, in contact_residues  
res, rareas = group.atoms[i].residue_sums(areas)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 158, in __getitem__  
ptrs = self._pointers[i].copy()  
IndexError: index 428 is out of bounds for axis 0 with size 368  
  
IndexError: index 428 is out of bounds for axis 0 with size 368  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 158, in __getitem__  
ptrs = self._pointers[i].copy()  
  
See log for complete Python traceback.  
  
Exception ignored in: <function Drawing.__del__ at 0x000001FDEBE5DC18>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1113, in __del__  
self.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1122, in delete  
c.make_current() # Make OpenGL context current for deleting OpenGL resources.  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 128, in make_current  
qc = self._initialize_context()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 157, in _initialize_context  
window.setFormat(fmt)  
RuntimeError: wrapped C/C++ object of type QWindow has been deleted  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "position" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "normal" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "tex_coord" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function _DrawShape.__del__ at 0x000001FDEBE5EC18>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1577, in __del__  
self.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1586, in delete  
self.element_buffer.delete_buffer()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2488, in delete_buffer  
self.release_buffer()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2497, in release_buffer  
GL.glDeleteBuffers(1, [self.opengl_buffer])  
File "src\latebind.pyx", line 32, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDeleteBuffers,  
pyArgs = (  
1,  
<OpenGL.arrays.lists.c_ulong_Array_1 object at 0x000001FD8C4826C8>,  
),  
cArgs = (  
1,  
<OpenGL.arrays.lists.c_ulong_Array_1 object at 0x000001FD8C4826C8>,  
),  
cArguments = (  
1,  
<OpenGL.arrays.lists.c_ulong_Array_1 object at 0x000001FD8C4826C8>,  
)  
)  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 Bindings.__del__ at 0x000001FDEC33B708>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2319, in __del__  
raise OpenGLError('OpenGL vertex array object was not deleted before
core.graphics.Bindings destroyed')  
chimerax.core.graphics.opengl.OpenGLError: OpenGL vertex array object was not
deleted before core.graphics.Bindings destroyed  
Exception ignored in: <function Drawing.__del__ at 0x000001FDEBE5DC18>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1113, in __del__  
self.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1122, in delete  
c.make_current() # Make OpenGL context current for deleting OpenGL resources.  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 128, in make_current  
qc = self._initialize_context()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 157, in _initialize_context  
window.setFormat(fmt)  
RuntimeError: wrapped C/C++ object of type QWindow has been deleted  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "position" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "normal" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "tex_coord" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function _DrawShape.__del__ at 0x000001FDEBE5EC18>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1577, in __del__  
self.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1586, in delete  
self.element_buffer.delete_buffer()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2488, in delete_buffer  
self.release_buffer()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2497, in release_buffer  
GL.glDeleteBuffers(1, [self.opengl_buffer])  
File "src\latebind.pyx", line 32, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDeleteBuffers,  
pyArgs = (  
1,  
<OpenGL.arrays.lists.c_ulong_Array_1 object at 0x000001FD8C496C48>,  
),  
cArgs = (  
1,  
<OpenGL.arrays.lists.c_ulong_Array_1 object at 0x000001FD8C496C48>,  
),  
cArguments = (  
1,  
<OpenGL.arrays.lists.c_ulong_Array_1 object at 0x000001FD8C496C48>,  
)  
)  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 Bindings.__del__ at 0x000001FDEC33B708>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2319, in __del__  
raise OpenGLError('OpenGL vertex array object was not deleted before
core.graphics.Bindings destroyed')  
chimerax.core.graphics.opengl.OpenGLError: OpenGL vertex array object was not
deleted before core.graphics.Bindings destroyed  
Exception ignored in: <function Drawing.__del__ at 0x000001FDEBE5DC18>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1113, in __del__  
self.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1122, in delete  
c.make_current() # Make OpenGL context current for deleting OpenGL resources.  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 128, in make_current  
qc = self._initialize_context()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 157, in _initialize_context  
window.setFormat(fmt)  
RuntimeError: wrapped C/C++ object of type QWindow has been deleted  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "position" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "normal" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, in __del__  
% self.shader_variable_name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "tex_coord" was not
deleted before core.graphics.Buffer destroyed  
Exception ignored in: <function _DrawShape.__del__ at 0x000001FDEBE5EC18>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1577, in __del__  
self.delete()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\drawing.py", line 1586, in delete  
self.element_buffer.delete_buffer()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2488, in delete_buffer  
self.release_buffer()  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2497, in release_buffer  
GL.glDeleteBuffers(1, [self.opengl_buffer])  
File "src\latebind.pyx", line 32, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1282,  
description = b'invalid operation',  
baseOperation = glDeleteBuffers,  
pyArgs = (  
1,  
<OpenGL.arrays.lists.c_ulong_Array_1 object at 0x000001FD8C496E48>,  
),  
cArgs = (  
1,  
<OpenGL.arrays.lists.c_ulong_Array_1 object at 0x000001FD8C496E48>,  
),  
cArguments = (  
1,  
<OpenGL.arrays.lists.c_ulong_Array_1 object at 0x000001FD8C496E48>,  
)  
)  
Exception ignored in: <function Buffer.__del__ at 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 0x000001FDEC33BB88>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2483, 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 Bindings.__del__ at 0x000001FDEC33B708>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2319, in __del__  
raise OpenGLError('OpenGL vertex array object was not deleted before
core.graphics.Bindings destroyed')  
chimerax.core.graphics.opengl.OpenGLError: OpenGL vertex array object was not
deleted before core.graphics.Bindings destroyed  
Exception ignored in: <function Texture.__del__ at 0x000001FDEC33DD38>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2861, in __del__  
raise OpenGLError('OpenGL texture was not deleted before core.graphics.Texture
destroyed')  
chimerax.core.graphics.opengl.OpenGLError: OpenGL texture was not deleted
before core.graphics.Texture destroyed  
Exception ignored in: <function Texture.__del__ at 0x000001FDEC33DD38>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2861, in __del__  
raise OpenGLError('OpenGL texture was not deleted before core.graphics.Texture
destroyed')  
chimerax.core.graphics.opengl.OpenGLError: OpenGL texture was not deleted
before core.graphics.Texture destroyed  
Exception ignored in: <function Texture.__del__ at 0x000001FDEC33DD38>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\graphics\opengl.py", line 2861, in __del__  
raise OpenGLError('OpenGL texture was not deleted before core.graphics.Texture
destroyed')  
chimerax.core.graphics.opengl.OpenGLError: OpenGL texture was not deleted
before core.graphics.Texture destroyed  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\graph.py", line 416, in <lambda>  
a.triggered.connect(lambda checked, cb=callback, args=args: cb(*args))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\tool.py", line 219, in _show_interface_residues  
ab = c.contact_residue_atoms(gb, min_area)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\cmd.py", line 264, in contact_residue_atoms  
res = self.contact_residues(group, min_area)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\cmd.py", line 274, in contact_residues  
res, rareas = group.atoms[i].residue_sums(areas)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 158, in __getitem__  
ptrs = self._pointers[i].copy()  
IndexError: index 428 is out of bounds for axis 0 with size 368  
  
IndexError: index 428 is out of bounds for axis 0 with size 368  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 158, in __getitem__  
ptrs = self._pointers[i].copy()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\graph.py", line 416, in <lambda>  
a.triggered.connect(lambda checked, cb=callback, args=args: cb(*args))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\tool.py", line 167, in _select_contact_residues  
atoms = c.contact_residue_atoms(g, min_area)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\cmd.py", line 264, in contact_residue_atoms  
res = self.contact_residues(group, min_area)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\interfaces\cmd.py", line 274, in contact_residues  
res, rareas = group.atoms[i].residue_sums(areas)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 158, in __getitem__  
ptrs = self._pointers[i].copy()  
IndexError: index 428 is out of bounds for axis 0 with size 368  
  
IndexError: index 428 is out of bounds for axis 0 with size 368  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\atomic\molarray.py", line 158, in __getitem__  
ptrs = self._pointers[i].copy()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 440.97
OpenGL renderer: GeForce GTX 1070 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
File attachment: VHL - Cul2 (Core).cxs

VHL - Cul2 (Core).cxs

Attachments (1)

VHL - Cul2 (Core).cxs (2.4 MB ) - added by leygkn@… 6 years ago.: Added by email2trac

Change History (3)

by leygkn@…, 6 years ago

Attachment:	VHL - Cul2 (Core).cxs added

Added by email2trac

comment:1 by Eric Pettersen, 6 years ago

Component:	Unassigned → Surface/Binding Analysis
Owner:	set to Tom Goddard
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Index out of bounds showing interface contact residues

Reported by Yongkwan Lee

comment:2 by Tom Goddard, 6 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed.

The error resulted from making an interfaces plot and then deleting half the atoms used in the plot. The interface plot does not know how to update when atoms have been deleted. I have made the code delete the plot if some of its atoms are deleted.

To avoid this problem in older ChimeraX, delete atoms first, and then make the interfaces plot.

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