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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>
data_link = TRANS<br>
residue_selection_1 = chain "A" and resid " 38 " and altid "B"<br>
residue_selection_2 = chain "A" and resid " 39 " and altid "C"<br>
}<br>
refinement.pdb_interpretation.apply_cif_link {<br>
data_link = TRANS<br>
residue_selection_1 = chain "A" and resid " 38 " and altid "B"<br>
residue_selection_2 = chain "A" and resid " 39 " and altid "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="MET A 38 "', 'pdbres="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;">
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<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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