[chimerax-users] ATOM has no alt loc B

[Greg Couch]

I was unable to reproduce this on a Ubuntu 20.04 system with ChimeraX 
1.2.5.  So something weird is going on.   Please use the Help / Report a 
Bug dialog to provide us with information about your system.  And in 
your bug report, please include your 5byl.cif file 
(~/Downloads/ChimeraX/PDB/5byl.cif file if you didn't modify it).  There 
is also a chance that this is a hardware error, but let's start with the 
bug report.

     -- Greg


On 7/28/2021 12:00 PM, Eric Pettersen via ChimeraX-users wrote:
> 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 <mailto: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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>
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