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

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