[chimerax-users] ATOM has no alt loc B

[Eric Pettersen]

Hi James,
	Is this somehow a modified version of 5byl?  I don't get this error with 5byl in the 1.2.5 release, though I am using Mac and not Linux (shouldn't matter AFAIK).  At any rate, try getting the daily build and trying that.  It has some fixes related to adding hydrogens to structures with alt locs.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jul 27, 2021, at 9:54 PM, James Loy via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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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