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<p>Hi Xavier,</p>
<p>I remember we had a similar case in January and had a long
conversation about it between Nigel, Oleg and me. The solution at
that time was to update Phenix library with that non-standard
amino-acid-like entity so that Phenix produces mmcif file that is
legible by PDB.</p>
<p>In your case it does seem you have "SER plus something" as the
modified residue. I think the easiest way for you to proceed is to
follow Nigel's suggestion.</p>
<p>Pavel<br>
</p>
<div class="moz-cite-prefix">On 4/20/22 14:10, Nigel Moriarty wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANkP=2eg5y1ThT+p=bwjbYocLqE7QUH0d-uaGTi+amt1vp_Qfw@mail.gmail.com">
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<div dir="ltr">Xavier
<div><br>
</div>
<div>I'm sure others can solve this problem but it adds to my
point that if you have a covalently bound ligand to an amino
acid that does not change the main chain, it is generally
"better" to maintain the, in this case SER, and generate the
ligand and links to the side chain.</div>
<div><br>
</div>
<div>Just one of a number of reasons.</div>
<div><br clear="all">
<div>
<div dir="ltr" data-smartmail="gmail_signature">
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<div dir="ltr"><font face="arial, sans-serif">Cheers</font>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Nigel</font>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">---</font></div>
<div><font face="arial, sans-serif">Nigel W.
Moriarty<br>
Building 33R0349, Molecular Biophysics and
Integrated Bioimaging</font></div>
<div><font face="arial, sans-serif">Lawrence
Berkeley National Laboratory</font><br>
<font face="arial, sans-serif">Berkeley, CA
94720-8235</font><br>
<font face="arial, sans-serif">Phone :
510-486-5709 Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a><br>
Fax : 510-486-5909 Web : <a
href="http://CCI.LBL.gov" target="_blank"
moz-do-not-send="true">CCI.LBL.gov</a></font></div>
</div>
<div><font face="arial, sans-serif"><span
style="color:rgb(73,74,76)">ORCID : </span><font
color="#494a4c"><a
href="https://orcid.org/0000-0001-8857-9464"
target="_blank" moz-do-not-send="true">orcid.org/0000-0001-8857-9464</a></font></font><br>
</div>
</div>
</div>
</div>
</div>
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</div>
<br>
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<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Apr 20, 2022 at 2:02
PM Xavier Brazzolotto <<a
href="mailto:xbrazzolotto@gmail.com" target="_blank"
moz-do-not-send="true" class="moz-txt-link-freetext">xbrazzolotto@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear
Phenix users,<br>
<br>
I don’t know if my problem is related to Phenix but for
information I’m running Phenix 1.20.1-4487 under MacOS 12.3.1.<br>
<br>
I’ve finalized a structure where a ligand covalently modified
the protein.<br>
<br>
I’ve generated the modified residue (named SLG for serine
modified by ligand). For this I’ve generated the molecules in
SMILES and used eLBOW to generate the restraints. Then I’ve
modified the cif file defining the molecule as a L-peptide and
replacing the atom names of the Serine part (CA, CB, OG, C, O,
N, and OXT)<br>
In coot (from CCP4 : 0.9.6 EL), I’ve used the modified cif
file and it allowed merging of the modified residue into the
polypeptide chain as expected and further refinements went
without any issue in Phenix (providing the modified cif file
of course). Everything seems well interpreted. So far so good.<br>
<br>
However, now I would like to validate the structure and both
Phenix validation tool and the PDB web server do not accept
the final cif file.<br>
<br>
Checking this file I’ve noticed that the protein seems split
into 3 pieces (chain A, first residue up to the one before the
modified residue; chain B the modified residue by itself
described as HETATM and chain C the rest of the polypeptide up
to the C-ter).<br>
The PDB file presents only one chain A for the whole protein
with the modified residue...<br>
<br>
I don’t know if this is an issue with Phenix generating this
final cif file in this specific case or if I need to modify
this final file by hand ?<br>
<br>
Any help is welcome.<br>
Thanks<br>
<br>
Xavier<br>
<br>
<br>
<br>
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