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<p>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.<br>
</p>
<p><br>
</p>
<p>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".</p>
<p><br>
</p>
<p> -- Greg<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 9/2/2021 9:46 AM, Liu, Xiangan
wrote:<br>
</div>
<blockquote type="cite"
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<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Hi Greg,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
It seems combine command does not work on my chimerax.</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
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>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Any way to fix the issue?</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Thanks,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif;
font-size: 12pt; color: rgb(0, 0, 0);">
Xiangan<br>
</div>
<div style="font-family:Calibri,Arial,Helvetica,sans-serif;
font-size:12pt; color:rgb(0,0,0)">
<br>
</div>
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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 <a class="moz-txt-link-rfc2396E" href="mailto:gregc@cgl.ucsf.edu"><gregc@cgl.ucsf.edu></a><br>
<b>Sent:</b> Thursday, September 2, 2021 3:05 AM<br>
<b>To:</b> ChimeraX Users Help
<a class="moz-txt-link-rfc2396E" href="mailto:ChimeraX-users@cgl.ucsf.edu"><ChimeraX-users@cgl.ucsf.edu></a><br>
<b>Cc:</b> Liu, Xiangan <a class="moz-txt-link-rfc2396E" href="mailto:Xiangan.Liu@uth.tmc.edu"><Xiangan.Liu@uth.tmc.edu></a><br>
<b>Subject:</b> Re: [chimerax-users] output mmCIF file</font>
<div> </div>
</div>
<div class="BodyFragment"><font size="2"><span
style="font-size:11pt">
<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
<a class="moz-txt-link-rfc2396E" href="mailto:Xiangan.Liu@uth.tmc.edu"><Xiangan.Liu@uth.tmc.edu></a> 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/<a class="moz-txt-link-freetext" href="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=">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=</a>
", 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 <a class="moz-txt-link-abbreviated" href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>
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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