id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2105	mmCIF save: local variable '_1to3' referenced before assignment	Tristan Croll	Greg Couch	"On my Linux machine in the RedHat ChimeraX 0.9 release, attempting to save the attached PDB file causes a segmentation fault. I've pasted the traceback below.

{{{
#0  0x00007ffff74d7207 in raise () at /lib64/libc.so.6
#1  0x00007ffff74d88f8 in abort () at /lib64/libc.so.6
#2  0x00007fffe74817d5 in __gnu_cxx::__verbose_terminate_handler() () at /lib64/libstdc++.so.6
#3  0x00007fffe747f746 in  () at /lib64/libstdc++.so.6
#4  0x00007fffe747f773 in  () at /lib64/libstdc++.so.6
#5  0x00007fffe747f993 in  () at /lib64/libstdc++.so.6
#6  0x00007fffb3fd2091 in std::__throw_out_of_range_fmt(char const*, ...) ()
    at /opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/atomic/lib/libatomstruct.so
#7  0x00007fff3d97993a in compile_links_ssbonds(atomstruct::Structure const*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&) (__s=0x7fff3d98e20c ""basic_string::substr"", __pos=66, this=0x7fffffff98e0)
    at /opt/rh/devtoolset-3/root/usr/include/c++/4.9.2/bits/basic_string.h:324
#8  0x00007fff3d97993a in compile_links_ssbonds(atomstruct::Structure const*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&) (__pos=66, __n=6, this=0x7fffffff98e0) at /opt/rh/devtoolset-3/root/usr/include/c++/4.9.2/bits/basic_string.h:2227
#9  0x00007fff3d97993a in compile_links_ssbonds(atomstruct::Structure const*, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >&) (s=s@entry=0x30a8540, links=std::vector of length 0, capacity 0, ssbonds=std::vector of length 0, capacity 0)
    at pdbio_cpp/PDBio.cpp:235
Python Exception <type 'exceptions.ValueError'> Cannot find type const std::set<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_Rep_type: 
#10 0x00007fff3d97bab2 in write_pdb_file(PyObject*, PyObject*) (polymeric_res_names=
    std::set with 35 elements, h36=true, pqr=false, all_coordsets=<optimized out>, xforms=std::vector of length 1, capacity 1 = {...}, displayed_only=false, selected_only=false, os=..., structures=..., this=<optimized out>, this=<optimized out>, this=<optimized out>, this=<optimized out>, this=<optimized out>)
    at pdbio_cpp/PDBio.cpp:1858
#11 0x00007fff3d97bab2 in write_pdb_file(PyObject*, PyObject*) (args=<optimized out>)
    at pdbio_cpp/PDBio.cpp:2094
#12 0x00007ffff7907739 in _PyMethodDef_RawFastCallKeywords (method=0x7fff3db969e0 <pdbio_functions+32>, self=<optimized out>, args=0x570d0a0, nargs=9, kwnames=<optimized out>) at Objects/call.c:694
#13 0x00007ffff79077f5 in _PyCFunction_FastCallKeywords (func=0x7fffbc43c1f8, args=<optimized out>, nargs=<optimized out>, kwnames=<optimized out>) at Objects/call.c:730
#14 0x00007ffff78e0b87 in _PyEval_EvalFrameDefault (kwnames=0x0, oparg=9, pp_stack=<synthetic pointer>)
    at Python/ceval.c:4568
#15 0x00007ffff78e0b87 in _PyEval_EvalFrameDefault (f=<optimized out>, throwflag=<optimized out>)
    at Python/ceval.c:3093
#16 0x00007ffff79f1d4e in _PyEval_EvalCodeWithName (_co=0x7fffbc483150, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=2, kwnames=0x7fffbc640f00, kwargs=0x5c8b478, kwcount=7, kwstep=1, d-----T---T-----T---T---T---Type <r---Type --

}}}"	defect	closed	major		Input/Output		fixed						all	ChimeraX