[chimerax-users] ATOM has no alt loc B

[Eric Pettersen]

Hi James,
	The problems you are experiencing with your modified structure are indeed fixed in the daily build, so if you get that you will be able to add hydrogens without issue.

--Eric

> On Jul 28, 2021, at 4:12 PM, James Loy <jamesmadiganloy at gmail.com> wrote:
> 
> Eric, Greg-
> 
> Yes, this is a modified CIF file from the pdb-redo service-- sorry I failed to mention that (that was the end of a long day).  I'm attaching the file.
> 
> I'm going to hold off on the bug report for now because my colleague has actually been able to run our pipeline successfully for this pdb code.  It seems like it might be something with my setup?
> 
> I'm sorry to have bothered-- I'll file a bug if we run into this issue again.
> 
> Thanks
> -James
> 
> On Wed, Jul 28, 2021 at 3:27 PM Greg Couch <gregc at cgl.ucsf.edu <mailto:gregc at cgl.ucsf.edu>> wrote:
> 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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> 
> 
> -- 
> James Loy, Ph. D.
> 614.915.9792
> LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>
> <5byl_final.cif>

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