Hi Matthew,<br><br>Did you try to run phenix like that (see below)? for instance:<br><pre class="literal-block">phenix.refine data.hkl model.pdb elbow._you_ligand_name.pdb.001.cif<br><br>I mean, supplying the cifs file in the same line?
<br></pre>Regards,<br><br>Joao Muniz.<br><br><div><span class="gmail_quote">On 3/15/07, <b class="gmail_sendername">Matthew Bowler</b> &lt;<a href="mailto:mwb@mrc-dunn.cam.ac.uk">mwb@mrc-dunn.cam.ac.uk</a>&gt; wrote:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear All,<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;I am trying to run phenix.refine but I keep getting the message:<br><br>
<br>Sorry: Fatal problems interpreting PDB file:<br>&nbsp;&nbsp; Number of atoms with unknown nonbonded energy type symbols: 308<br>&nbsp;&nbsp; Please edit the PDB file to resolve the problems and/or supply a<br>&nbsp;&nbsp; CIF file with matching restraint definitions. Note that
<br>&nbsp;&nbsp; elbow.builder is available to create restraint definitions.<br><br>I have run my ligands through elbow and used the output .cif but I<br>still get the same message.&nbsp;&nbsp;I can find no info on this problem in<br>the manual or the BB, can anyone help?&nbsp;&nbsp;Thanks in advance, yours, Matt.
<br><br><br><br><br><br>Matthew Bowler<br>MRC Dunn Human Nutrition Unit<br>Wellcome Trust / MRC Building<br>Hills Road<br>Cambridge CB2 2XY<br>Tel: 0044 (0) 1223 252826<br>Fax: 0044 (0) 1223 252825<br><br>_______________________________________________
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