Greetings,<div><br></div><div>I have a few structures I am trying to refine that have density for ligands, and I&#39;m having trouble getting phenix to refine them properly. There are two unique scenarios, so I&#39;ll go in order of difficulty.</div>


<div><br></div><div>1) There are non-water solvent molecules (i.e. probably PEGs) that are here and there in the structure. I used phenix.elbow with SMILES notation to build the requested ligands and placed / real space refined them into the density using COOT. Now I cannot get phenix to refine the structure, every time I get the message &quot;Number of atoms with unknown nonbonded energy type symbols: XX<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>    Also note that phenix.ready_set and phenix.elbow are available</div><div>    for creating restraint definitions (CIF files).</div><div><br></div><div>where XX can be any variation of a number, depending on how I set up the phenix.refine run. This is what I&#39;ve tried:</div>


<div><br></div><div>a) adding the .cif files into my .def file I&#39;m using for refinement parameters</div><div>b) adding the .cif files on the command line</div><div>c) running phenix.ready_set to generate .cif files for the unknown ligands and then inputing the .cif files from that on the command line</div>


<div>d) running phenix.elbow with --add_all and the pdb to generate .cif files for unknown ligands, then doing as in (c) from the command line</div><div><br></div><div>None of these seem to get phenix.refine to skip the error mentioned above and start refining. There are 3 different ligands, one of which is repeated 4x, but each has its own chain number in the same chain (I&#39;ve even tried them each with their own unique chain). Any advice on getting these ligand restraints into phenix so it will happily refine?</div>


<div><br></div><div>2) I have an intramolecular crosslink in another structure, basically I crosslinked two cysteines with 1,3-dichloroacetone, giving a Cys-S-CH2C(=O)CH2-S-Cys linkage. How can I get restraints for this crosslink so it will refine as one covalent chain? So far, I&#39;ve placed the acetone in between the two Cysteines, but it would be nice for it to be a part of the chain so I can refine it in real space, the density is not so good since the crosslink adds flexibility to the bond as apposed to just a disulfide. Any ideas here? I thought maybe the best way to do it is to just modify one of the cys to contain the extra atoms and call it a new residue, then add bond restraints for the 2nd link, however, then I&#39;m still stuck with the extra hydrogen.</div>


<div><br></div><div>Thanks!</div><div>Geoff</div><div><br></div><br clear="all"><br>-- <br>Geoffrey K. Feld<br><br>Department of Chemistry<br>492 Stanley Hall<br>University of California, Berkeley<br><br>&quot;Vigilia pretium libertatis&quot;<br>



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