Opened 7 years ago

Closed 7 years ago

#1249 closed defect (duplicate)

atom spec balloon: index is out of bounds

Reported by: chimerax-bug-report@… 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 Eric Pettersen) 

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.8 (2018-08-09)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.8 (2018-08-09)  
OpenGL version: 4.1 INTEL-10.36.19  
OpenGL renderer: Intel(R) HD Graphics 6000  
OpenGL vendor: Intel Inc.  
How to cite UCSF ChimeraX  

lighting simple

open 2bbv format mmCIF fromDatabase pdb

Summary of feedback from opening 2bbv fetched from pdb  
---  
notes | Used PDBx fixed column width tables to speed up reading mmCIF file  
Used PDBx keywords to speed up reading mmCIF file  
  
2bbv title: The refined three-dimensional structure of an insect virus at 2.8
angstroms resolution [more&nbspinfo...;]  
Chain information for 2bbv #1  
---  
Chain | Description  
A B C | protein (black beetle virus capsid protein)  
D E F | protein (black beetle virus capsid protein)  
N | RNA (5'-R(*up*cp*up*up*ap*up*ap*up*cp*U)-3')  
  
2bbv mmCIF Assemblies | 1| complete icosahedral assembly | 2| icosahedral
asymmetric unit | 3| icosahedral pentamer | 4| icosahedral 23 hexamer | 5|
icosahedral asymmetric unit, std point frame | 6| crystal asymmetric unit,
crystal frame  
Opened mmCIF data containing 7817 atoms and 7813 bonds  

lighting simple

lighting simple

lighting simple

ui mousemode rightMode translate

ui mousemode rightMode translate

ui mousemode rightMode translate

ui mousemode rightMode translate

ui mousemode rightMode zoom

ui mousemode rightMode translate

open /Users/inshaqari/Desktop/ChimeraX/PDB/1hwk.pdb

Opened PDB data containing 12296 atoms and 12256 bonds  
| Chain information for 1hwk.pdb #2  
---  
Chain | Description  
A B C D | hmg-coa reductase  
  

show selAtoms surfaces

show selAtoms surfaces

lighting simple

lighting simple

lighting shadows true

lighting simple

show selAtoms surfaces

lighting soft

show selAtoms surfaces

ui mousemode rightMode translate selected models

hide selAtoms surfaces

show selAtoms surfaces

show selAtoms surfaces

hide selAtoms surfaces

show selAtoms

show selAtoms surfaces

show selAtoms

show selAtoms surfaces

hide selAtoms

hide selAtoms

hide selAtoms

hide selAtoms surfaces

hide selAtoms surfaces

show selAtoms surfaces

show selAtoms surfaces

hide selAtoms

show selAtoms

lighting simple

hide selAtoms surfaces

show selAtoms surfaces

close

open /Users/inshaqari/Desktop/ChimeraX/PDB/1hwk.pdb

Opened PDB data containing 12296 atoms and 12256 bonds  
Chain information for 1hwk.pdb #1  
---  
Chain | Description  
A B C D | hmg-coa reductase  
  

show selAtoms surfaces

hide selAtoms surfaces

Traceback (most recent call last):  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
    s.ui.mouse_modes.mouse_pause_tracking()  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 290, in mouse_pause_tracking  
    self._mouse_pause()  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 376, in _mouse_pause  
    m.pause(self._mouse_pause_position)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 844, in pause  
    p = picked_object(x, y, self.view)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 584, in picked_object  
    p = picked_object_on_segment(xyz1, xyz2, view, max_transparent_layers =
max_transparent_layers)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 588, in picked_object_on_segment  
    p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=unpickable)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 785, in
first_intercept_on_segment  
    p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 888, in first_intercept  
    p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 904, in
first_intercept_children  
    p = d.first_intercept(cxyz1, cxyz2, exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1546, in first_intercept  
    ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2,
exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1567, in _position_intercepts  
    p = d.first_intercept(xyz1, xyz2)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1982, in first_intercept  
    atom = self.visible_atoms[anum]  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molarray.py", line 154, in __getitem__  
    v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 776 is out of bounds for axis 0 with size 776  
  


[multiple copies of the error deleted]

IndexError: index 776 is out of bounds for axis 0 with size 776  
  
File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molarray.py", line 154, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

Traceback (most recent call last):  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
    s.ui.mouse_modes.mouse_pause_tracking()  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 290, in mouse_pause_tracking  
    self._mouse_pause()  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 376, in _mouse_pause  
    m.pause(self._mouse_pause_position)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 844, in pause  
    p = picked_object(x, y, self.view)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 584, in picked_object  
    p = picked_object_on_segment(xyz1, xyz2, view, max_transparent_layers =
max_transparent_layers)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 588, in picked_object_on_segment  
    p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=unpickable)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 785, in
first_intercept_on_segment  
    p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 888, in first_intercept  
    p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 904, in
first_intercept_children  
    p = d.first_intercept(cxyz1, cxyz2, exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1546, in first_intercept  
    ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2,
exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1567, in _position_intercepts  
    p = d.first_intercept(xyz1, xyz2)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1982, in first_intercept  
    atom = self.visible_atoms[anum]  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molarray.py", line 154, in __getitem__  
    v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 776 is out of bounds for axis 0 with size 776  
  

IndexError: index 776 is out of bounds for axis 0 with size 776  
  
File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molarray.py", line 154, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  

Traceback (most recent call last):  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback  
    s.ui.mouse_modes.mouse_pause_tracking()  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 290, in mouse_pause_tracking  
    self._mouse_pause()  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 376, in _mouse_pause  
    m.pause(self._mouse_pause_position)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 844, in pause  
    p = picked_object(x, y, self.view)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 584, in picked_object  
    p = picked_object_on_segment(xyz1, xyz2, view, max_transparent_layers =
max_transparent_layers)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/mousemodes.py", line 588, in picked_object_on_segment  
    p2 = p = view.first_intercept_on_segment(xyz1, xyz2, exclude=unpickable)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/view.py", line 785, in
first_intercept_on_segment  
    p = self.drawing.first_intercept(xyz1, xyz2, exclude=exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 888, in first_intercept  
    p = self.first_intercept_children(self.child_drawings(), mxyz1, mxyz2,
exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/graphics/drawing.py", line 904, in
first_intercept_children  
    p = d.first_intercept(cxyz1, cxyz2, exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1546, in first_intercept  
    ppicks = self._position_intercepts(self.positions[pn], mxyz1, mxyz2,
exclude)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1567, in _position_intercepts  
    p = d.first_intercept(xyz1, xyz2)  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/structure.py", line 1982, in first_intercept  
    atom = self.visible_atoms[anum]  
  File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molarray.py", line 154, in __getitem__  
    v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
IndexError: index 776 is out of bounds for axis 0 with size 776  
  

IndexError: index 776 is out of bounds for axis 0 with size 776  
  
File
"/private/var/folders/mx/76n0n04j0_g5ps8ryp66k7540000gn/T/AppTranslocation/5E0A9AD0-3DC2-4293-98DB-B1DB02D7708E/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/molarray.py", line 154, in __getitem__  
v = self._object_class.c_ptr_to_py_inst(self._pointers[i])  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 4.1 INTEL-10.36.19
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.

Change History (2)

comment:1 by Eric Pettersen, 7 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 → atom spec balloon: index is out of bounds

comment:2 by Eric Pettersen, 7 years ago

Resolution: → duplicate
Status: assigned → closed
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