4adx won't open

[Greg Couch]

Neither as either a PDB nor a mmCIF file. Interrupting the process shows that it might be an infinite loop in atomstruct::_constrained(). Backtrace from opening as a PDB:

(gdb) where
#0  0x000000328ea787a0 in _int_free () from /lib64/libc.so.6
#1  0x00007fffe72f83c9 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#2  0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#3  0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#4  0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#5  0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#6  0x00007fffe72f91c8 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#7  0x00007fffe72f91c8 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#8  0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#9  0x00007fffe72f91c8 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#10 0x00007fffe72f91c8 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#11 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#12 0x00007fffe72f91c8 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#13 0x00007fffe72f91c8 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#14 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#15 0x00007fffe72f91c8 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#16 0x00007fffe72f91c8 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#17 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#18 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#19 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#20 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#21 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#22 0x00007fffe72f91c8 in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#23 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#24 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<in---Type <return> to continue, or q <return> to quit---
t> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#25 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#26 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#27 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#28 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#29 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#30 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#31 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#32 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#33 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#34 0x00007fffe72f975d in atomstruct::_constrained(std::vector<char, std::allocator<char> > const&, atomstruct::AssocParams&, std::vector<int, std::allocator<int> >&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#35 0x00007fffe72fa33e in atomstruct::constrained_match(std::vector<char, std::allocator<char> > const&, atomstruct::StructureSeq const&, atomstruct::AssocParams const&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#36 0x00007fffe72fb18c in atomstruct::try_assoc(atomstruct::Sequence const&, atomstruct::StructureSeq const&, atomstruct::AssocParams const&, unsigned int) ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#37 0x00007fffe72ad479 in atomstruct::AtomicStructure::make_chains() const ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/bin/../lib/libatomstruct.so
#38 0x00007fffe75a2402 in structure_num_chains ()
   from /home/socr/a/gregc/src/chimerax/ChimeraX.app/lib/python3.5/site-packages/chimerax/core/atomic/libmolc.so
#39 0x00007fff454dce40 in ffi_call_unix64 ()
    at /home/socr/a/gregc/src/chimerax/build/tmp/Python-3.5.1/Modules/_ctypes/libffi/src/x86/unix64.S:76
#40 0x00007fff454dbc61 in ffi_call (cif=cif@entry=0x7fffffffc0d0,
    fn=fn@entry=0x7fffe75a23b0 <structure_num_chains>,
    rvalue=rvalue@entry=0x7fffffffbfe0, avalue=avalue@entry=0x7fffffffbfb0)
    at /home/socr/a/gregc/src/chimerax/build/tmp/Python-3.5.1/Modules/_ctypes/libffi/src/x86/ffi64.c:525
#41 0x00007fff454d35df in _call_function_pointer (argcount=3,
    resmem=0x7fffffffbfe0, restype=<optimized out>, atypes=<optimized out>,
    avalues=0x7fffffffbfb0, pProc=0x7fffe75a23b0 <structure_num_chains>,
    flags=4357)
    at /home/socr/a/gregc/src/chimerax/build/tmp/Python-3.5.1/Modules/_ctypes/callproc.c:811
#42 _ctypes_callproc (pProc=pProc@entry=0x7fffe75a23b0 <structure_num_chains>,
    argtuple=argtuple@entry=0x7fffdcac2ee8, flags=4357,
    argtypes=argtypes@entry=0x7fffe9ce1d38, restype=0x9c7918, checker=0x0)
    at /home/socr/a/gregc/src/chimerax/build/tmp/Python-3.5.1/Modules/_ctypes/callproc.c:1149

[Eric Pettersen]

Not an infinite loop, but close!

Problem was in the handling of CA-only chains