[phenixbb] pdbtools

[Ralf Grosse-Kunstleve]

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 <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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>
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