[chimerax-users] output mmCIF file

[Greg Couch]

Yes, the rename command does not do what you want.   You need the 
combine command and that just in the daily build for now (sorry, I 
didn't realize that).  So you'll need download and install the ChimeraX 
daily build.  The combine command will be in the upcoming 1.3 release.


The "Not saving entity_poly_seq for non-authoritative sequences" message 
is just a warning.   ChimeraX benefits if the original data includes the 
full sequence information.  Sequence searching is better, gaps can be 
depicted, etc.    In your case, that information is missing.  So the 
mmCIF writer does not put that information in the mmCIF file because it 
wasn't given in the first place.  This is consistent with PHENIX's 
intermediate mmCIF files.  If you want the mmCIF file to have that 
information anyway, use the "bestGuess true" option when saving the 
mmCIF file -- "save snafu.cif bestGuess true".


     -- Greg


On 9/2/2021 9:46 AM, Liu, Xiangan wrote:
> Hi Greg,
> It seems combine command does not work on my chimerax.
> I used rename #1,2 id #3, but when I save them into CIF file, it says 
> "Not saving entity_poly_seq for non-authoritative sequences".
> I think my issue was probably caused by my changing the chain name 
> using "setattr #2.3/b chain chain_id b12".
> The original name for all two 13-units are a or b. I want to name them 
> as a1, b1,a2,b2,...etc.
> Any way to fix the issue?
> Thanks,
> Xiangan
>
> ------------------------------------------------------------------------
> *From:* Greg Couch <gregc at cgl.ucsf.edu>
> *Sent:* Thursday, September 2, 2021 3:05 AM
> *To:* ChimeraX Users Help <ChimeraX-users at cgl.ucsf.edu>
> *Cc:* Liu, Xiangan <Xiangan.Liu at uth.tmc.edu>
> *Subject:* Re: [chimerax-users] output mmCIF file
> **** EXTERNAL EMAIL ****
>
> 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/https://urldefense.proofpoint.com/v2/url?u=http-3A__-5F-5Finit-5F-5F.py&d=DwIDaQ&c=bKRySV-ouEg_AT-w2QWsTdd9X__KYh9Eq2fdmQDVZgw&r=klfWt_GeTa5mjZtvnCjFAvhE4HnIRCWIH1fiSCK0tiQ&m=AX54WX8Vtl6oFIUw3pEZcHYwwW-e2sqqm96Eo1vjksU&s=tt-31xzcBaoG4XaJFjh5-_dSj7MFJqq69hgFrqa6hFw&e= 
> ", 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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