2007.06.07 -- This application has been archived. Local users, see a CSB staff member for help if you need to run this program in the Core.

A tool to extract or replace DNA/RNA fragments

To use FRAGMENT in the CSB core, type the following on an SGI:

setup fragment (or source /srv/local/setup/fragment.set)
fragment &

Contents of the FRAGMENT package:
file.dat : X data file

dict/ : residue database

nahelix : Construction of regular helices (*.hd format)

hd2pdb : Translator *.hd format => *.pdb format
usage: hd2pdb inputfile.hd outputfile.pdb [title]

pdb2hb : Translator *.pdb format => *.hd format
usage: pdb2hd inputfile.pdb outputfile.hd

extend : Addition of missing phosphates at the 5' end of strand
usage: extend inputfile.hd outputfile.hd [list of residues numbers to extend]

makefgm : Translator *.hd format => *.fgm format
needed by the program fragment

fragment : Replacement of residues from a *.fgm file