[phenixbb] PDB Tools and CNS formatted structure factors

Nathaniel Echols nechols at lbl.gov
Wed Sep 22 07:09:09 PDT 2010

On Wed, Sep 22, 2010 at 3:39 AM, Joseph Noel <noel at salk.edu> wrote:
> Is there anyway with the PDB Tools to renumber protein chains? I have a
> model that doesn't correspond to the actual sequence, off by a couple of
> residues and just looking for a quick way to change that. Also, which module
> in Phenix is used to read in and convert CNS formatted ascii structure
> factors to the mtz read by phenix other then using ccp4.

The reflection file editor in the GUI is the easiest tool for format
conversions (there are also a couple of command-line utilities like
phenix.reflection_file_converter).  However, most of the programs will
quite happily take a CNS file as input (the exception I believe is a
few of the tools which use Resolve directly, like fit_loops or
find_helices_strands).  Some of these will export the reflections as
an MTZ file too - for instance, phenix.refine will write out a file


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