[phenixbb] pdbtools

Bradley Hintze bradley.hintze at duke.edu
Tue Dec 6 13:24:49 PST 2011


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?


Bradley J. Hintze
Duke University
Graduate Student
Department of Biochemistry
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