[chimerax-users] output mmCIF file

[Greg Couch]

Turns out that this bug is due to the chain ids in separate NMR models 
being explicitly changed to be different when they should all be same.  
That confuses the mmCIF writing code when it tries to write out the NMR 
ensemble, because it can't find the matching chain in different models.

My guess is what was really wanted is a single model with each chain 
having a different chain id.  That is easily done by using the combine 
command which takes a set of models and produces a new model and 
automatically names the chains.  Then, when saving the mmCIF file, 
explicitly choose the new model.  For example, if models #1 and #2 are 
the only open models and the one to combine, the command is:

     combine #1,2

which produces model #3.  And the command to save that as a mmCIF file 
would be:

     save example.cif models #3

The backtrace is still a bug that needs to be fixed....

     -- Greg

On 8/31/2021 2:00 PM, Elaine Meng via ChimeraX-users wrote:
>> On Aug 31, 2021, at 1:50 PM, Liu, Xiangan <Xiangan.Liu at uth.tmc.edu> wrote:
>>
>> Hi,
>> I have issue to output the models I build in pdb formation to mmCIF formation. I did not provide the sequences in orginal pdb files. Could please let me know what is the problem and how to fix it?
>> Thanks,
>> Xiangan
>> ----------
>>    File "/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/mmcif/__init__.py", line 89, in save
>>      mmcif_write.write_mmcif(session, path, **kw)
>>    File "src/mmcif_write.pyx", line 145, in chimerax.mmcif.mmcif_write.write_mmcif
>>    File "src/mmcif_write.pyx", line 149, in chimerax.mmcif.mmcif_write.write_mmcif
>>    File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure
>> KeyError: ('a1', 'RPGMMDSQEFS')
>>
>> KeyError: ('a1', 'RPGMMDSQEFS')
>>
>> File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure
> Hi Xiangan,
> We recommend using the chimerax-users at cgl.ucsf.edu address for questions (CC'd on this message, so you don't need to do anything this time).  The address you used is just for commercial licensing.
>
> Actually, if you get a traceback like this, you can usually use ChimeraX menu: Help... Report a Bug instead of sending e-mail.  You may need to attach your session file so that we can reproduce the problem.
>
> I don't know the answer, so I'm using this address to share your question with the others.
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
>
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