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<p>Hi Jorge and Nigel,</p>
<p>indeed, defining the bond across symmetry is trivial (using
refinement.geometry_restraints.edits) and defining the angle is
not implemented in Phenix. To check if the bond you defined was
actually created and used, please inspect the .geo file that, in
case of success, should list that bond. </p>
<p>As Nigel said, please feel free to reach us off list with the
model file and we will help if needed.</p>
<p>All the best!<br>
Pavel<br>
</p>
<div class="moz-cite-prefix">On 12/15/23 18:15, Nigel Moriarty
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CANkP=2cSPAO=UNv6LcWvhHkJfRGtk5fj-KLNVd-b+gBLa_+PSw@mail.gmail.com">
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<div dir="ltr">Jorge
<div><br>
</div>
<div>It is not possible to specify a symmetry related angle in
an unambiguous fashion. Using the bond edit should give a
result. If you send the model directly to me and Pavel Afonine
(not the list) we will take a closer look.</div>
<div><br>
</div>
<div>NB. Any files sent to me will be held in strictest
confidence.<br>
</div>
<div><br clear="all">
<div>
<div dir="ltr" class="gmail_signature"
data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<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">Email :
<a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a></font></div>
<div><font face="arial, sans-serif">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>
</div>
</div>
<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Dec 15, 2023 at
7:55 AM Jorge Iulek <<a href="mailto:iulek@uepg.br"
moz-do-not-send="true" class="moz-txt-link-freetext">iulek@uepg.br</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
all,<br>
<br>
I am working currently on a structure that should be
"peptide bond" <br>
between chains, but the "second" part of the chain is in a
symmetry <br>
related peer. Numbering is continuous and there are
justifications to <br>
why the chains are separately named with different chain ID's.
By the <br>
way, this "connection" is "full of glycines" so a kind of
flexible, but <br>
a continuous stretch can be seen at "reasonable" density (and
despite <br>
low resolution).<br>
To better explain, say I have chain C residue x to be
bound to chain K, <br>
at symm operation -x-1,y-1/2,-z-1/2, residue x + 1.<br>
I would prefer to really refine the presence of these
"connecting" <br>
glycines, of course with due geometrical restraints imposed
(precious at <br>
this low resolution).<br>
phenix.refine offers:<br>
<br>
refinement.geometry_restraints.edits<br>
<br>
at<br>
<br>
bond<br>
<br>
with the possibility to indicate the<br>
<br>
symmetry_operation<br>
<br>
for the "second atom" within the bond. But this
"symmetry_operation" <br>
indication is not available (?) for the other
geometry_restraints edits, <br>
like angle, dihedral, etc. (eventually, planarity might also
make <br>
easier). Do I miss anything here?<br>
Currently, I see 3 possibilities:<br>
a) somehow (how?) I can add angle, dihedral restraints in
involving <br>
chains in symmetry related operations<br>
b) I bring the symmetry related chain to its non "symmetry
related" <br>
position and change chains names/residues ID, etc., so I go
into this <br>
go/return of naming at each step of the refinement
work/analysis<br>
c) I add "extra" ( + - like alternate conformation residues)
residues to <br>
each end of the connection, such that these extra residues
will receive <br>
due conventional geometrical restraints (as phenix.refine does
for <br>
contiguous residues in a chain) but I force them to be on the
same <br>
position (and probably declare 0.5 occupancy for these
overlying residues).<br>
"a" should be the easiest, if available somehow; "b"
would be <br>
cumbersome during the refinement/analysis process; "c" seems
to be the <br>
most complex but maybe the best if it works. Nevertheless,
someone might <br>
have an easier suggestion.<br>
Thanks,<br>
<br>
Jorge<br>
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