2007.06.07 -- This application has been archived.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.

FREEHELIX

FREEHELIX is a substantially modified version of NEWHELIX, designed specifically for the analysis of radically bent and kinked DNA double helices.

The program was written by Richard E. Dickerson, Molecular Biology Institute, UCLA.

The documentation for this program is avialable as ASCII text. Please note that the documentation was written for the VAX FORTRAN version of the program; input and output designators will be different in this UNIX version which was modified locally. See below for the names of the input and output files.

To use FREEHELIX do the following:

Copy your PDB file containing the DNA coordinates to pdb.inp

Type,
cp /srv/local/freehelix/examples/freehelix.com .
and edit this file according to the documentation above.

Then just type,
./freehelix.com

The main output file from FREEHELIX is freehelix.out. An accessory program called SELECT98 (called from the command file) will summarize the output of FREEHELIX and create a file called freehelix.sel. Other output files from FREEHELIX are helix.crd, the coordinates of the helix, and p-p_o-o.dst, the P-P and O4-O4 distances.

Please Note: If you publish a figure using this program please cite the following:

R. E. Dickerson (1998) DNA Bending: The Prevalence of Kinkiness and the Virtues of Normality. Nucleic Acids Research 26, 1906-1926.