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Hi Ralf and Pavel,<br><br>Thanks so much for the quick response and advice.<br><br>I have tried both of your suggestions: To assign different altloc identifiers, with the same res ID, chain ID and different resnames (Ralf) and with the same resname (Pavel). I had thought of this but was afraid it would cause confusion with the associated .cif files. Unfortunately, this appears to be the case. <br><br>For your strategy Ralf, the .cif and .pdb files created by "phenix.ready_set modified.pdb"<br><br> and <br><br>the .cif file created by "phenix.elbow modified.pdb" were all accepted by phenix.refine, however the two molecules were still driven away from each other =(<br><br>For your strategy Pavel, I could not get phenix.refine to run with either the pehnix.ready_set, or the phenix.elbow outputs. It consistently gives the following .cif file error:<br><br>Sorry: Fatal problems interpreting PDB file:<br> Number of atoms with unknown nonbonded energy type symbols: 52<br> Please edit the PDB 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.<br> Also note that phenix.ready_set and phenix.elbow are available<br> for creating restraint definitions (CIF files).<br><br><br>I will send to you the appropriate sections of both modified pdb files off list and the associated .cif files.<br><br>Thanks so much again to both of you for all of your help.<br><br>Cheers,<br><br>Joe.<br><br><br><br>                                            <br /><hr />Looking for a hot date? <a href='http://clk.atdmt.com/NMN/go/150855801/direct/01/' target='_new'>View photos of singles in your area!</a></body>
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