Ribbon: list index out of range

[Tom Goddard]

Error showing ribbon produced by the following two commands.

open 5a5b
ribbon

graphics update callback raised error
Traceback (most recent call last):

File "/Users/goddard/ucsf/chimera2/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/chimera/core/graphics/view.py", line 600, in _call_callbacks

cb()

File "/Users/goddard/ucsf/chimera2/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/chimera/core/atomic/structure.py", line 183, in _update_graphics_if_needed

self._create_ribbon_graphics()

File "/Users/goddard/ucsf/chimera2/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/chimera/core/atomic/structure.py", line 392, in _create_ribbon_graphics

back_c, back_t, back_n = ribbon.segment(i, ribbon.FRONT, seg)

File "/Users/goddard/ucsf/chimera2/Chimera2.app/Contents/Library/Frameworks/Python.framework/Versions/3.4/lib/python3.4/site-packages/chimera/core/atomic/ribbon.py", line 120, in segment

xc = self.coefficients[0][seg]

IndexError: list index out of range

[Conrad Huang]

It worked with my latest code, which I just committed.  Can you please 
pull and give it another try?

Conrad

On 9/23/15 7:48 PM, Chimera2 wrote:

[goddard@…]

Works with 5a5b.pdb but not 5a5b.cif

[Conrad Huang]

Fixed!

The problem was that the ribbon code was not ignoring unused residues in 
a ribboned chain.  The mmcif version of 5a5b has an MSE which has not CA 
and therefore is not used for the ribbon; the pdb version must not have 
that residue, or it was not grouped as part of the same chain.  The code 
now properly regenerates a residue list from the list of atoms used for 
the ribbon.

As a side effect, I found the bug that caused the infinite loop on 
traceback.  I wrongly accused the logger. It was the ribbon code.  On 
redraw, if m._gc_ribbon is True, m._create_ribbon_graphics() is called 
and then _gc_ribbon is cleared.  When an exception is thrown in the 
ribbon code, _gc_ribbon is not cleared, so it goes into a state where it 
keeps trying to rebuild the ribbon on every redraw.

Both fixes have been committed.

Conrad

On 9/24/15 3:59 PM, Tom Goddard wrote:

[goddard@…]

Thanks!

[pett]

The PDB version doesn’t make the inter-residue bond from the (singleton) N in /8:500 to /8:499 whereas the mmCIF version does.  I will investigate improving the PDB version at some point.

—Eric