[phenixbb] pdbtools

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Tue Dec 6 13:30:46 PST 2011

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


If you do need the restraints the main way to speed up processing is to use
multiple cpus.


On Tue, Dec 6, 2011 at 1:24 PM, Bradley Hintze <bradley.hintze at duke.edu>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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