Associating structure with sequence alignment leads to crash

[Tom Goddard]

Opening the nup84.ihm file (attached), and then expanding the "Sequence alignments" model in model panel and clicking the show checkbutton for nup84_3ikoC_3jroC_3f3fG.fa (#1.3.1) causes the fasta file to be loaded and the 3 PDB models to be loaded and associated with the sequence. ChimeraX Jan 6 2017 nightly build then crashes, while ChimeraX Dec 22 2016 works correctly. If I comment out the ihm code (bundles/ihm/ihm.py) that forces the association of the structures (this also prevents aligning the structures) then no crash occurs.

The crash gives a Python traceback to the shell indicating it is drawing ribbons.

Fatal Python error: Segmentation fault

Thread 0x000070000fbdd000 (most recent call first):

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 297 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 549 in wait
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 1178 in run
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 914 in _bootstrap_inner
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/threading.py", line 882 in _bootstrap

Current thread 0x00007fffd3c213c0 (most recent call first):

File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/molc.py", line 37 in get_prop
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/structure.py", line 800 in _create_ribbon_graphics
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/structure.py", line 272 in _update_graphics_if_needed
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/atomic/structure.py", line 1883 in _update_graphics_if_needed
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/triggerset.py", line 126 in invoke
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/triggerset.py", line 186 in activate
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/triggerset.py", line 321 in activate_trigger
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/graphics/view.py", line 220 in check_for_drawing_change
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/updateloop.py", line 39 in draw_new_frame
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/ui/graphics.py", line 83 in _redraw_timer_callback
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/chimerax/core/ui/gui.py", line 166 in event_loop
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/ChimeraX_main.py", line 547 in init
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/ChimeraX_main.py", line 638 in <module>
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/runpy.py", line 85 in _run_code
File "/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/runpy.py", line 170 in _run_module_as_main

Segmentation fault: 11

[Tom Goddard]

Don't use nup84.cif -- does not have the FASTA data. Use nup84.ihm in nup84.zip and it will use the FASTA from the extra_data directory in the zip file.

[Tom Goddard]

The Mac crash dump indicates ChimeraX is in a ctypes call but does not indicate what call (presumably in m.ribbon_tether_scale, line 800 of structure.py from the traceback). This seems unlikely to be the real cause of the crash -- possibly memory corruption occurring during sequence association.

[Tom Goddard]

I tried making a simpler test case opening just the PDB models and fasta file, but it fails to auto-associate 2 of the 3 PDB files and no crash is observed. The IHM code uses the "force" option in making the structure / sequence association (look for "a.associate(...)" in bundles/ihm/ihm.py.

[Eric Pettersen]

The StructSequence.residue_at method was returning an Atom instead of a Residue.