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<p>Hi Yufan,</p>
<p>I suggest you generate CIF for each individual non-standard item
in your PDB file first. If you are using recent Phenix it should
link them together automatically (link_ligands=True is responsible
for this, and it is the default).</p>
<p>Make sure it linked them all correct. It relies on input model
geometry, so if geometry is suboptimal it may not link them
correctly.</p>
<p>Alternatively, you can use custom bond restraints that allow you
to link any pair of atoms, any number of pairs:</p>
<p><a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles">http://phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles</a></p>
<p>You can compose a file like shown in above link and give it to
phenix.refine GUI or command line, whatever you use.</p>
<p>LINK records are not recognized and used by phenix.refine.</p>
<p>Let me know if you have any questions or need help!</p>
<p>Pavel<br>
</p>
<br>
<div class="moz-cite-prefix">On 6/30/16 08:28, Yufan Wu wrote:<br>
</div>
<blockquote
cite="mid:D8959ACB-0A82-4969-A514-35C6003112BC@bioc.uzh.ch"
type="cite">Dear Phenix Developers/Users,
<div class=""><br class="">
</div>
<div class="">I have a question regarding how to generate a
correct restrain for a whole nonstandard peptide and how do run
refinement correctly.</div>
<div class=""><br class="">
</div>
<div class="">The nonstandard peptide in my structure is pepstatin
A (IVA Val Val STA Ala STA).</div>
<div class=""><br class="">
</div>
<div class="">I manually put the pepstatin A in the density and
generated the cif files for IVA and STA and run the refinement
with them.�</div>
<div class=""><br class="">
</div>
<div class="">After refinement, the whole pepstatin A explored as
pieces, which I guess the program treated the pepstatin A as
single amino acids.�</div>
<div class=""><br class="">
</div>
<div class="">By the way, I also manual input the �LINK�
information in the input pdb file as below,</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">LINK � � � � C � VAL L � 3 � � � � � � � � N � STA
L � 4 � � 1555 � 1555 � � � �</div>
<div class="">LINK � � � � N � ALA L � 5 � � � � � � � � C � STA
L � 4 � � 1555 � 1555 � � � �</div>
<div class="">LINK � � � � C � ALA L � 5 � � � � � � � � N � STA
L � 6 � � 1555 � 1555</div>
</div>
<div class=""><br class="">
</div>
<div class="">And also, when I use the �Real Space Refine Zone� by
clicking two atoms for the whole pepstatin A in coot, it
exploded again, although I input the same cif file in coot as
well.</div>
<div class=""><br class="">
</div>
<div class="">The data quality is not good (2.9 A with CC1/2=12),
thus it is difficult to place amino acid individually to fit the
destiny.</div>
<div class=""><br class="">
</div>
<div class="">In the PDB, there are several structures containing
the pepstatin A, such as 4TVG, 4AUC. They have the pepatatin A
sequence as VVVXAX, but none of them lists the constrains.</div>
<div class=""><br class="">
</div>
<div class="">Would you please help me and let me know how can I
continue with refinement? Please let me know if you need more
information.</div>
<div class=""><br class="">
</div>
<div class="">Thank you vey much!</div>
<div class=""><br class="">
</div>
<div class="">Yufan Wu</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<br class="">
<br class="">
<div class="">
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color="#999999">Regards,</font></span></div>
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</span></div>
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