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    Hi Alex,<br>
    <br>
    you need to supply a CIF file with restraints definitions for
    unknown (to Phenix) part of the PDB file. eLBOW or ReadySet are the
    tools to use for this. See documentation for more details.<br>
    <br>
    Pavel<br>
    <br>
    <div class="moz-cite-prefix">On 2/17/16 11:50, Alejandro Virrueta
      wrote:<br>
    </div>
    <blockquote
cite="mid:CAA5EDMR7zJLK3zOCO2-S3d1Mq4M2GRyXKiTDt8umgMMse3rRcA@mail.gmail.com"
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                <div>Hello,</div>
                <div><br>
                </div>
                <div>How can I successfully execute the following
                  command:</div>
                <span class="">
                  <div><br>
                  </div>
                  <div>phenix.refine
                    pdb_1jbe_res_ALA_resID_101_del.pdb 1jbe.mtz
                    main.number_of_macro_cycles=5 output.write_eff_file=False
                    output.write_geo_file=False
                    output.write_def_file=False
                    refinement.input.xray_data.r_free_flags.generate=True
                    --overwrite<br>
                  </div>
                  <div><br>
                  </div>
                  <div>Currently, I am getting the following error:</div>
                  <div><br>
                  </div>
                  Sorry: Fatal problems interpreting model file:<br>
                    Number of atoms with unknown nonbonded energy type
                  symbols: 8<br>
                      Please edit the model file to resolve the problems
                  and/or supply a<br>
                      CIF file with matching restraint definitions,
                  along with<br>
                      apply_cif_modification and apply_cif_link
                  parameter definitions<br>
                      if necessary.
                  <div><br>
                  </div>
                  I'm not a crystallographer, so I don't fully
                  understand the error.
                  <div>I'm simply trying to automate this procedure for
                    many PDBs, and this particular error has come up
                    quite a few times.<br>
                    Can I resolve this issue by providing additional
                    files or command line flags?</div>
                </span>
                <div>Other files I have available are 1jbe.cif and
                  1jbe-sf.cif.</div>
                <div>File 'pdb_1jbe_res_ALA_resID_101_del.pdb' is
                  similar to 1jbe.pdb, except that the occupancies for
                  ALA 101 are set to 0.<br>
                  <div><br>
                  </div>
                  <div>Thanks,<br>
                    Alex</div>
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