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An alternative way of doing this..<br>
<br>
You can make a file with a content like this<br>
<br>
refinement {<br>
geometry_restraints.edits {<br>
bond {<br>
atom_selection_1 = chain A and resseq 123 and name CA<br>
atom_selection_2 = chain Z and resseq 321 and name N<br>
distance_ideal = 1.3<br>
sigma = 0.02<br>
}<br>
angle {<br>
atom_selection_1 = chain A and resseq 123 and name CA<br>
atom_selection_2 = chain A and resseq 321 and name N<br>
atom_selection_3 = chain A and resseq 234 and name O<br>
angle_ideal = 120.<br>
sigma = 2.5<br>
}<br>
bond {<br>
atom_selection_1 = chain A and resseq 1 and name CA<br>
atom_selection_2 = chain Z and resseq 2 and name N<br>
distance_ideal = 1.3<br>
sigma = 0.02<br>
}<br>
angle {<br>
atom_selection_1 = chain A and resseq 1 and name CA<br>
atom_selection_2 = chain A and resseq 2 and name N<br>
atom_selection_3 = chain A and resseq 3 and name O<br>
angle_ideal = 120.<br>
sigma = 2.5<br>
}<br>
}<br>
<br>
and load it with all the other files in the GUI or provide in the
command line, whichever you use.<br>
<br>
It is true that many non-standard links can be created automatically
or by specialized stand-alone tools. However, these tools use a lot
of heuristics and are highly reliant on input model geometry.<br>
<br>
To make sure a particular bond was created, try to find it in .*geo
file that refinement always outputs. If it is there -- you all good!<br>
<br>
Don't use graphic programs to check if a particular bond was used in
refinement. Why? Here is the answer:<br>
<br>
<a
href="http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10">http://phenix-online.org/newsletter/CCN_2016_01.pdf#page=10</a><br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 4/15/20 03:44, Xavier Brazzolotto
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:03F7FCD7-9390-44E8-9517-BA0B20EC9926@chemdef.fr">
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2 solutions that I use
<div class=""><br class="">
</div>
<div class="">A first one consists in designing your residue
linked to your ligand (under ChemDraw / MarvinSketch) then
prepare the restraints under eLBOW (from smiles for examples).
You will have to modify some atom names into the generated cif
file (C, O, CA, N, CB, etc… depending of the modified residue)
and above all change the nature of this molecule to L-peptide.
Then you can use it in coot as a modified residue and use the
modified cif file in Phenix. You can adjust the modification by
tuning the occupancy of the atoms corresponding to the ligand
and keep the occupancy to 1 for the atoms of the residue. Here
you will have a nice covalent bond.</div>
<div class=""><br class="">
</div>
<div class="">The second solution would be to restrain the
distance between the atom of your residue and the atom of the
ligand to a covalent bond (C-C distance or whatever it is).
Certainly, angles should be restraint too.</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">Le 15 avr. 2020 à 00:59, Muhammad Bashir Khan
<<a href="mailto:mbk@ualberta.ca" class=""
moz-do-not-send="true">mbk@ualberta.ca</a>> a écrit :</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hi All;
<div class=""><br class="">
</div>
<div class="">I have a protein molecule and a ligand
structure. I want to make a covalent bond between the
ligand and protein molecule, could somebody explain to
me how I can do that using phenix.</div>
<div class=""> I used the </div>
<div class=""><br class="">
</div>
<div class="">" <i style="" class="">phenix.ligand_linking
pdb_file_name" commond</i>
<div class=""><br class="">
</div>
<div class="">It creates </div>
<div class="">apply_link.def<br class="">
</div>
<div class="">and </div>
<div class="">data_link.cif<br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I did refine the structure again giving
the above file as well but did not see any covalent
bond created between the protein and ligand.</div>
<div class=""><br class="">
</div>
<div class="">Thanks for your help</div>
<div class=""><br class="">
</div>
<div class="">Bashir</div>
-- <br class="">
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<span style="font-family: Helvetica;
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<br style="font-family: Helvetica; font-size:
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<span style="font-family: Helvetica;
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