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Hi Greg,</div>
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It seems combine command does not work on my chimerax.</div>
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I used rename #1,2 id #3, but when I save them into CIF file, it says "<span style="color: rgb(81, 167, 249);">Not saving entity_poly_seq for non-authoritative sequences</span>".</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
I think my issue was probably caused by my changing the chain name using "<span style="color: rgb(81, 167, 249);">setattr #2.3/b chain chain_id b12</span>".</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
The original name for all two 13-units are a or b. I want to name them as a1, b1,a2,b2,...etc.</div>
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Any way to fix the issue?</div>
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Thanks,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0);">
Xiangan<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Greg Couch <gregc@cgl.ucsf.edu><br>
<b>Sent:</b> Thursday, September 2, 2021 3:05 AM<br>
<b>To:</b> ChimeraX Users Help <ChimeraX-users@cgl.ucsf.edu><br>
<b>Cc:</b> Liu, Xiangan <Xiangan.Liu@uth.tmc.edu><br>
<b>Subject:</b> Re: [chimerax-users] output mmCIF file</font>
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<div class="PlainText">**** EXTERNAL EMAIL ****<br>
<br>
Turns out that this bug is due to the chain ids in separate NMR models <br>
being explicitly changed to be different when they should all be same. <br>
That confuses the mmCIF writing code when it tries to write out the NMR <br>
ensemble, because it can't find the matching chain in different models.<br>
<br>
My guess is what was really wanted is a single model with each chain <br>
having a different chain id. That is easily done by using the combine <br>
command which takes a set of models and produces a new model and <br>
automatically names the chains. Then, when saving the mmCIF file, <br>
explicitly choose the new model. For example, if models #1 and #2 are <br>
the only open models and the one to combine, the command is:<br>
<br>
combine #1,2<br>
<br>
which produces model #3. And the command to save that as a mmCIF file <br>
would be:<br>
<br>
save example.cif models #3<br>
<br>
The backtrace is still a bug that needs to be fixed....<br>
<br>
-- Greg<br>
<br>
On 8/31/2021 2:00 PM, Elaine Meng via ChimeraX-users wrote:<br>
>> On Aug 31, 2021, at 1:50 PM, Liu, Xiangan <Xiangan.Liu@uth.tmc.edu> wrote:<br>
>><br>
>> Hi,<br>
>> 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?<br>
>> Thanks,<br>
>> Xiangan<br>
>> ----------<br>
>> 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<br>
>> mmcif_write.write_mmcif(session, path, **kw)<br>
>> File "src/mmcif_write.pyx", line 145, in chimerax.mmcif.mmcif_write.write_mmcif<br>
>> File "src/mmcif_write.pyx", line 149, in chimerax.mmcif.mmcif_write.write_mmcif<br>
>> File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure<br>
>> KeyError: ('a1', 'RPGMMDSQEFS')<br>
>><br>
>> KeyError: ('a1', 'RPGMMDSQEFS')<br>
>><br>
>> File "src/mmcif_write.pyx", line 542, in chimerax.mmcif.mmcif_write.save_structure<br>
> Hi Xiangan,<br>
> We recommend using the chimerax-users@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.<br>
><br>
> 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.<br>
><br>
> I don't know the answer, so I'm using this address to share your question with the others.<br>
> Best,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D.<br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
><br>
><br>
><br>
><br>
><br>
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