id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
771	"""hb salt true"" causes traceback on 5o3o"	Elaine Meng	Eric Pettersen	"open 5o3o format mmcif fromDatabase pdb
Summary of feedback from opening 5o3o fetched from pdb
notes	Used PDBx fixed column width tables to speed up reading mmCIF file
Used PDBx keywords to speed up reading mmCIF file
Chain information for 5o3o #1
Chain	Description
A B C D E F G H I J	Microtubule-associated protein τ
Opened mmCIF data containing 11360 atoms and 11450 bonds

hbonds saltOnly true
Traceback (most recent call last):
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/cmd_line/tool.py"", line 178, in execute
cmd.run(cmd_text)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/commands/cli.py"", line 2395, in run
result = ci.function(session, **kw_args)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/hbonds/cmd.py"", line 70, in cmd_hbonds
sb_donors, sb_acceptors = salt_preprocess(hbonds)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/hbonds/cmd.py"", line 304, in salt_preprocess
coord_group = s.pseudobond_group(s.PBG_METAL_COORDINATION, create_type=None)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/molobject.py"", line 1658, in pseudobond_group
return object_map(pbg, PseudobondGroup)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/molobject.py"", line 2146, in object_map
_object_map[p] = o = object_type(p)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/pbgroup.py"", line 26, in __init__
PseudobondGroupData.__init__(self, pbg_pointer)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/molobject.py"", line 551, in __init__
set_c_pointer(self, pbg_pointer)
File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/molc.py"", line 160, in set_c_pointer
self._c_pointer = cp = ctypes.c_void_p(int(pointer))
TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'

TypeError: int() argument must be a string, a bytes-like object or a number, not 'NoneType'

File ""/Users/chimera/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/core/atomic/molc.py"", line 160, in set_c_pointer
self._c_pointer = cp = ctypes.c_void_p(int(pointer))

See log for complete Python traceback."	defect	closed	major		Structure Analysis		fixed						all	ChimeraX