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<div><span style="background-color: rgba(255, 255, 255, 0);">Hi,<br>
<br>
I have a rather odd model situation, where I’m trying to manually create peptide bond restraints between two alternate conformers in refinement.<br>
<br>
I’m doing this using:<br>
<br>
=======<br>
...<br>
refinement.pdb_interpretation.apply_cif_link {<br>
&nbsp;&nbsp;&nbsp;data_link = TRANS<br>
&nbsp;&nbsp;&nbsp;residue_selection_1 = chain &quot;A&quot; and resid &quot; &nbsp;38 &quot; and altid &quot;B&quot;<br>
&nbsp;&nbsp;&nbsp;residue_selection_2 = chain &quot;A&quot; and resid &quot; &nbsp;39 &quot; and altid &quot;C&quot;<br>
}<br>
refinement.pdb_interpretation.apply_cif_link {<br>
&nbsp;&nbsp;&nbsp;data_link = TRANS<br>
&nbsp;&nbsp;&nbsp;residue_selection_1 = chain &quot;A&quot; and resid &quot; &nbsp;38 &quot; and altid &quot;B&quot;<br>
&nbsp;&nbsp;&nbsp;residue_selection_2 = chain &quot;A&quot; and resid &quot; &nbsp;39 &quot; and altid &quot;D”<br>
}<br>
...<br>
=======<br>
<br>
However, running phenix.refine with this I get the error:<br>
<br>
=======<br>
RuntimeError: Unused apply_cif_link: TRANS ['pdbres=&quot;MET A 38 &quot;', 'pdbres=&quot;GLU A 39 “']<br>
=======<br>
<br>
Given that the alternate conformers have been removed from the labels, I assume that this can only be used to define links between residues, but not between specific conformers?</span></div>
<div id="AppleMailSignature"><span style="background-color: rgba(255, 255, 255, 0);"><br>
</span></div>
<div id="AppleMailSignature"><span style="background-color: rgba(255, 255, 255, 0);">Is there any way to do this?<br>
<br>
Thanks,<br>
Nick</span><br style="font-size: 16px;">
</div>
<div id="AppleMailSignature"><span style="background-color: rgba(255, 255, 255, 0);"><br>
</span></div>
<div id="AppleMailSignature"><span style="background-color: rgba(255, 255, 255, 0);">Nicholas Pearce</span></div>
<div id="AppleMailSignature"><span style="background-color: rgba(255, 255, 255, 0);">Post-doctoral researcher</span></div>
<div id="AppleMailSignature"><span style="background-color: rgba(255, 255, 255, 0);">Universiteit Utrecht</span></div>
<div id="AppleMailSignature"><span style="background-color: rgba(255, 255, 255, 0);"><br>
</span></div>
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