Hello,<div><br></div><div>I am trying to refine PDB 1YEW using the default phenix settings. </div><div><br></div><div>$phenix.refine 1yew.pdb 1yew.mtz</div><div><br></div><div>yields:</div><div>&#39;&#39;&#39;</div><div><div>
Sorry: Fatal problems interpreting PDB file:</div><div>  Number of atoms with unknown nonbonded energy type symbols: 6</div><div>    Please edit the PDB file to resolve the problems and/or supply a</div><div>    CIF file with matching restraint definitions, along with</div>
<div>    apply_cif_modification and apply_cif_link parameter definitions</div><div>    if necessary.</div></div><div>&#39;&#39;&#39;</div><div><br></div><div>$ phenix.ready_set 1YEW_H.pdb</div><div><meta charset="utf-8"><div>
<br class="Apple-interchange-newline">yields:</div><div>&#39;&#39;&#39;</div></div><div><div>Sorry:</div><div>    Atoms in the input are supposed to be bound</div><div>     </div><div>    CU1(CUA) - CU2(CUA) = 2.58</div><div>
<br></div><div>    Fix the input file and retry</div></div><div>&#39;&#39;&#39;</div><div><br></div><div>I assume this means that the Cu atoms in CUA are at an inappropriate distance. Is there an easy way to find out what the appropriate distance is? Can I fix this in coot?</div>
<div><br></div><div>Thanks,</div><div>Bradley</div>