Hi Bradely, If you don'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? http://cctbx.sourceforge.net/sbgrid2008/tutorial.html If you do need the restraints the main way to speed up processing is to use multiple cpus. Ralf On Tue, Dec 6, 2011 at 1:24 PM, Bradley Hintze wrote:

Developers,

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

Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 46 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files).

Is there a way around this without creating a CIF file or another tool to cut pdbs?

Thanks, Bradley

-- Bradley J. Hintze Duke University Graduate Student Department of Biochemistry

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