FFJOIN (CCP4: Supported Program)

NAME

   ffjoin - Fffear Fragment JOINing, release 1.0.0, 06/06/00

SYNOPSIS

   ffjoin XYZIN foo.pdb [XYZIN1 foo.pdb] [XYZIN2 foo.pdb] XYZOUT
   bar.pdb
   [Keyworded input]

REFERENCE

     * K. Cowtan (1998), Acta Cryst. D54, 750-756. Modified phased
       translation  functions and their application to molecular
       fragment location.

DESCRIPTION

   `ffjoin' takes files of fragments output from `fffear' and merges
   linked  fragments  to  create  longer fragments (with greater
   confidence values). Fragments running in opposite directions may
   optionally be merged. Overlapping fragments which cannot be merged
   may  optionally be identified and the fragment with the lower
   confidence value removed. Since fragments of opposite direction may
   be merged, the output file will only contain alpha Carbons.

   `ffjoin' does not know about crystal symmetry or repeat, so all
   input fragments should be calculated in `fffear' using the same
   `CENTRE' keyword.

  `ffjoin' Recepies

ffjoin xyzin alpha-helix-10-rot.pdb xyzout alpha-helix-10-rot-join.pdb
 << eof

eof

INPUT/OUTPUT FILES

  XYZIN

   Input pdb file. This should contain a list of fragments output from
   `fffear'.

  XYZIN1

   Input pdb file. Additional fragments to be merged, e.g. from a
   different search model.

  XYZIN2

   Input pdb file. Additional fragments to be merged, e.g. from a
   different search model.

  XYZOUT

   Output pdb file. This contains the CA coordinates for the merged
   fragments. The B-factors will contain updated confidence values
   which will be lower for those fragments which appear many times.

KEYWORDS

   Input is keyworded. Available keywords are: JOIN, BUMP.

BASIC KEYWORDS

   (All keywords are optional.)

JOIN [RADIUS <joinrad>] [OVERLAP <overlap>] [NOREVERSE]

   <joinrad>
          Maximum allowed CA separation for fragments to be considered
          mergeable. If any pair of corresponding CA atoms in a pair
          of fragments are beyond this spacing then the fragments will
          not be merged. Default=2.0A

   <overlap>
          Minimum number of overlapping CA atoms for fragments to be
          considered mergeable. Reduce this to 2 when trying to join
          unlike fragments, e.g. helices to strands. Default=3 CA
          atoms.

   NOREVERSE
          Do not merge fragments running in opposite directions.

BUMP [RADIUS <bumprad>] [NOBUMP]

   <bumprad>
          Maximum CA separation for fragments which are considered as
          clashing. If any pair of corresponding CA atoms in a pair of
          fragments are within this spacing after all other merging is
          complete, then the fragment with the lower confidence value
          will be removed. Default=3.0A

   NOBUMP
          Do not perform bump checking and fragment removal.

OUTPUT

          New fragments are assembled using an internal numbering
          scheme from the input fragments which are described by their
          chain name and segid for the first input file only. Merged
          fragments are then eliminated by bumping according to their
          internal numbers.

AUTHOR

          Kevin D. Cowtan, Department of Chemistry, University of York
          email: cowtan@ysbl.york.ac.uk

REFERENCES

    1. K. Cowtan (1998), Acta Cryst. D54, 750-756. Modified phased
       translation functions and their application to molecular
       fragment location.
    2. Kleywegt G. J., Jones T. A. (1997) Acta Cryst., D53, 179-185.
       Template convolution to enhance or detect structural features
       in macromolecular electron-density maps.

SEE ALSO

   fffear