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Hi Nick,<br>
<br>
without seeing files I can only guess.. To me it seems that
selections you provide are not valid (do not select any atoms, for
instance). First, I would remove any quotation marks, that is<br>
<br>
instead of:<br>
<br>
<span style="background-color: rgba(255, 255, 255, 0);">chain "A"
and resid " �38 " and altid "B"<br>
<br>
use:<br>
</span><br>
<span style="background-color: rgba(255, 255, 255, 0);">chain A and
resid 38 and altid B<br>
<br>
You can verify atom selection by running command<br>
<br>
phenix.pdb_atom_selection model.pdb "</span><span
style="background-color: rgba(255, 255, 255, 0);"><span
style="background-color: rgba(255, 255, 255, 0);">chain A and
resid 38 and altid B</span>"<br>
<br>
and it will print selected atoms to the screen.<br>
<br>
If you are still having troubles with this please send me PDB file
and we will investigate.<br>
<br>
Pavel<br>
</span><br>
<div class="moz-cite-prefix">On 1/31/17 09:47, Pearce, N.M. (Nick)
wrote:<br>
</div>
<blockquote cite="mid:1B234486-0DFF-41CC-A899-63050CFE8F91@uu.nl"
type="cite">
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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;">
</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>
<br>
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<br>
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