id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2184	Problematic mmCIF file	Tristan Croll	Greg Couch	"Will attach the offending .cif file (it's an unpublished and likely high-profile model from a colleague who's given me permission to share it but asks that it remain confidential). Attempting to load it on ChimeraX start (i.e. with `ChimeraX RCLH1LH2.cif`) causes a segmentation fault with the traceback below. Loading it after ChimeraX starts doesn't crash, but a whole lot of residues are simply missing. The log reports:

{{{
skipping chem_comp category: Missing column 'type' near line 108
Unknown polymer entity '?' near line 160
Skipping residue with duplicate label_seq_id 3 in chain AQ
Skipping residue with duplicate label_seq_id 5 in chain AQ
Skipping residue with duplicate label_seq_id 7 in chain AQ
Skipping residue with duplicate label_seq_id 9 in chain AQ
Skipping residue with duplicate label_seq_id 11 in chain AQ
644 messages similar to the above omitted
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
skipping chem_comp category: Missing column 'type' near line 45377
skipping chem_comp category: Missing column 'type' near line 45404
skipping chem_comp category: Missing column 'type' near line 46309
skipping chem_comp category: Missing column 'type' near line 47201
skipping chem_comp category: Missing column 'type' near line 47228
}}}

Traceback:

{{{
#0  0x00007fffe2a649d0 in std::_Hash_bytes(void const*, unsigned long, unsigned long) () from /lib64/libstdc++.so.6
#1  0x00007fff3e4d456b in std::_Hash_impl::hash (__seed=3339675911, __clength=<optimized out>, __ptr=<optimized out>)
    at /usr/include/c++/4.9/bits/functional_hash.h:131
#2  std::hash<std::string>::operator() (this=<optimized out>, __s=
    ""01;\005\000\000\000\000\000\240\063\a\000\000\000\000\220\031\371\004\000\000\000\000@1;\005\000\000\000\000ph\370\003"", '\000' <repeats 12 times>, ""\300\000\000\000\000\000\000\000A\000\000\000\000\000\000\000p\255\001\005\000\000\000\000\020\004F\005"", '\000' <repeats 20 times>, ""`\253%\006\000\000\000\000}\f\000\000\000\000\000\000@\000\000\000\000\000\000\000Q\000\000\000\000\000\000\000\200[3\005\000\000\000\000\262\000\000\000\000\000\000\000\263\000\000\000\000\000\000\000CD\000\000\000\000\000\000\350\346\065\005\000\000\000\000\270\344\065\005\000\000\000\000 \000\000\000\000\000\000\000\200\353\065\005\000\000\000\000V%\306\060\271\332\327\301""...) at /usr/include/c++/4.9/bits/basic_string.h:3084
#3  mmcif::ExtractMolecule::hash_ResidueKey::operator() (this=<optimized out>, k=...) at mmcif_cpp/mmcif.cpp:332
#4  std::__detail::_Hash_code_base<mmcif::ExtractMolecule::ResidueKey, std::pair<mmcif::ExtractMolecule::ResidueKey const, atomstruct::Residue*>, std::__detail::_Select1st, mmcif::ExtractMolecule::hash_ResidueKey, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, true>::_M_hash_code (this=<optimized out>, __k=...)
    at /usr/include/c++/4.9/bits/hashtable_policy.h:1261
#5  std::_Hashtable<mmcif::ExtractMolecule::ResidueKey, std::pair<mmcif::ExtractMolecule::ResidueKey const, atomstruct::Residue*>, std::allocator<std::pair<mmcif::ExtractMolecule::ResidueKey const, atomstruct::Residue*> >, std::__detail::_Select1st, std::equal_to<mmcif::ExtractMolecule::ResidueKey>, mmcif::ExtractMolecule::hash_ResidueKey, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >::find (__k=..., this=<optimized out>) at /usr/include/c++/4.9/bits/hashtable.h:1302
#6  std::unordered_map<mmcif::ExtractMolecule::ResidueKey, atomstruct::Residue*, mmcif::ExtractMolecule::hash_ResidueKey, std::equal_to<mmcif::ExtractMolecule::ResidueKey>, std::allocator<std::pair<mmcif::ExtractMolecule::ResidueKey const, atomstruct::Residue*> > >::find (__x=..., this=0x523b3d0) at /usr/include/c++/4.9/bits/unordered_map.h:574
#7  mmcif::ExtractMolecule::finished_parse (this=0x7fffffffb040) at mmcif_cpp/mmcif.cpp:813
#8  0x00007fff3e4f1d1c in readcif::CIFFile::internal_parse(bool) ()
}}}"	defect	closed	major		Input/Output		fixed						all	ChimeraX