[chimerax-users] ATOM has no alt loc B

[James Loy]

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
LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>
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