NAME

xmd3 - analyze 3DNA archive files

SYNOPSIS

xmd3 [ options ] -d desf

DESCRIPTION

Open the descriptor file desf which should be properly tagged as a 3DNA model. Then xmd3 waits for the user to enter commands.

xmd3 supplements exam which is a general utility to analyze archive files. xmd3 adds analyses that are specifically for DNA supercoiling such as the calculation of writhing number.

The options are:

-n N_atom: specify the number of atoms as N_atom. This should not be necessary as the number of atoms is recorded in both the descriptor and archive files and the numbers recorded in the two places must match. If N_atom is specified however, then the descriptor and the archives must have these number of atoms.

-a arcf: open the archive file arcf and read the first archive record into memory. You can also use the equivalent xmd3 command to read in an archive.

EXAMPLES

xmd3 -d plasmid.ds -a circle.ar

Analyze the 3DNA archive file circle.ar with the descriptor plasmid.ds. When both files are read, xmd3 will load the first archive record into memory and wait for the user to type commands.

FILES

SEE ALSO

mkd3c, mkd3d, exam, xmd3 commands

DIAGNOSTICS

BUGS

NOTES

xmd3 is one of three programs specifically designed for the 3DNA model. In this model, the base pairs of a DNA double helix is represented by only three masses. This reduces the size of the problem by one to two orders of magnitude allowing large pieces of DNA to be studied.