Hi Bradely,<div><br><div>If you don&#39;t need the geometry restraints it is much faster to work with the pdb.hierarchy directly (from Python). Are you aware of the iotbx pdb tutorial?</div><div><br></div><div><a href="http://cctbx.sourceforge.net/sbgrid2008/tutorial.html">http://cctbx.sourceforge.net/sbgrid2008/tutorial.html</a><br>
<br>If you do need the restraints the main way to speed up processing is to use multiple cpus.</div><div><br></div><div>Ralf</div><div><br><div class="gmail_quote">On Tue, Dec 6, 2011 at 1:24 PM, Bradley Hintze <span dir="ltr">&lt;<a href="mailto:bradley.hintze@duke.edu">bradley.hintze@duke.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Developers,<div><br></div><div>I am doing some automated analysis on many pdbs. My analysis is contained to a single chain in a given pdb. Aa such, to cut down on computing time I am generating many pdbs cut to the desired chain. When using pdbtools I get the following</div>


<div><br></div><div><div>Sorry: Fatal problems interpreting PDB file:</div><div>  Number of atoms with unknown nonbonded energy type symbols: 46</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>    Also note that phenix.ready_set and phenix.elbow are available</div>


<div>    for creating restraint definitions (CIF files).</div></div><div><br></div><div><br></div><div>Is there a way around this without creating a CIF file or another tool to cut pdbs?</div><div><br></div><div>Thanks,</div>


<div>Bradley</div><span class="HOEnZb"><font color="#888888"><div><div><br></div>-- <br><div>Bradley J. Hintze</div><div>Duke University</div><div>Graduate Student</div><div>Department of Biochemistry</div><br>
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<br></blockquote></div><br></div></div>