Changes between Initial Version and Version 1 of Ticket #812


Ignore:
Timestamp:
Aug 28, 2017, 11:48:49 AM (8 years ago)
Author:
Eric Pettersen
Comment:

Fixed the hbonds command throwing an error with no structures open, leaving what seems to be a new bug in the graphics-drawing code, so changed the summary and description and re-assigned to T.G.

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  • Ticket #812

    • Property Component Unassigned → Graphics
    • Property Owner changed from Eric Pettersen to Tom Goddard
    • Property Summary hbond command tracebacks → Adding pseudobonds causes graphics error

  • Ticket #812 – Description

    initial v1  
    1 Two traceback buglets: (1) when there are no structure models open, the hbond commands raises "IndexError: list index out of range", and if the "hbond" command is given two times in a row, it raises "ValueError: Cylinder end-point and radii arrays must have same size, got 14 and 14"
     1Finding hydrogen bonds for 1eyg produces:
     2
     3414 hydrogen bonds found
     4Error processing trigger "graphics update"
     5Traceback (most recent call last):
     6File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/triggerset.py", line 126, in invoke
     7return self._func(self._name, data)
     8File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 2230, in _update_graphics_if_needed
     9s[i]._update_graphics_if_needed()
     10File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 309, in _update_graphics_if_needed
     11self._update_graphics(gc)
     12File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 327, in _update_graphics
     13pbg._update_graphics(changes)
     14File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/pbgroup.py", line 143, in _update_graphics
     15d.positions = self._update_positions(pbonds, bond_atoms)
     16File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/pbgroup.py", line 160, in _update_positions
     17return s._halfbond_cylinder_placements(axyz0, axyz1, pbonds.radii)
     18File "/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/structure.py", line 2593, in _halfbond_cylinder_placements
     19half_cylinder_rotations(axyz0, axyz1, radii, p)
     20ValueError: Cylinder end-point and radii arrays must have same size, got 2 and 2