Hi folks-
I'm trying to add hydrogens to an mmCIF file (5byl) using the addh command. However, every time I try, I encounter the following error:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/ChimeraX_main.py", line 712, in init
run(sess, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/run.py", line 36, in run
results = command.run(text, log=log, return_json=return_json)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/core/commands/cli.py", line 2852, in run
result = ci.function(session, **kw_args)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 63, in cmd_addh
add_h_func(session, structures, template=template, in_isolation=in_isolation, **prot_schemes)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 170, in hbond_add_hydrogens
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas, hydrogen_totals,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 214, in add_hydrogens
_attach_hydrogens(atom, altloc_hpos_info, bonding_info)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/hbond.py", line 895, in _attach_hydrogens
add_altloc_hyds(atom, altloc_hpos_info, invert, bonding_info, total_hydrogens, naming_schema)
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 862, in add_altloc_hyds
h = new_hydrogen(atom, i+1, total_hydrogens, naming_schema,
File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/addh/cmd.py", line 882, in new_hydrogen
metal_pos = metal.get_alt_loc_coord(alt_loc)
File "atomic_cpp/cymol.pyx", line 587, in chimerax.atomic.cymol.CyAtom.get_alt_loc_coord
ValueError: Atom /A MG 702 MG has no alt loc B
I'm using ucsf-chimerax_1.2.5-1_amd64.deb installed on Ubuntu 20.04. I've done some digging, and I cannot figure out what is going on. Any help would be appreciated.
Thanks in advance!
-James
--
James Loy, Ph. D.
614.915.9792