NAME

mkd3c - generate 3DNA coordinates in various trajectories

SYNOPSIS

mkd3c [ options ] -n N_bp -a arcfile

DESCRIPTION

The 3DNA coordinates are generated for the shape and dimensions specified in options for N_bp base pairs and written to an archive file arcfile. The generated file is a binary format archive file.

The options are:

-r rise: specify the rise to be riseÅ. The preset value is 3.4Å.

-t twist: specify the twist to be twist degrees. The preset value is 36 degrees. Negative angles are legal and acceptable. Acceptable values are within ±180 degrees.

-open: to create an open 3DNA model, i.e., the ends of the DNA are not connected. The preset action is to create a closed circular model.

-link: estimate the linking number for the generated model. This may take some time.The estimate assumes a closed circular model by connecting the first and the last base pairs even when an open model is specified.

Only one of the following remaining options may be specified.

-circle: place the 3DNA coordinates in a flat circle sized to fit all the base pairs. This is the preset shape.

-linear: place the 3DNA coordinates in a straight path. Obviously -open is implied.

-template f: read the 3DNA coordinates from the file f, then trace the center spine of the template DNA and lay new 3DNA coordinates on the trace. The template and the desired model need not be of the same size. The template will be scaled by an interpolation to fit the base pairs of the desired model.

-arc r: generate the 3DNA coordinates in an arc of radius rÅ. If r is not large enough the generated coordinates will trace out a full circle and possibly overlap itself. There is no warning when this happens. The user should specify a radius that is large enough to accommodate all the base pairs without any overlap.

-spiral r p: generate the 3DNA trajectory to fit a right handed spiral of radius rÅ and pitch pÅ. To generate a left-handed spiral specify a negative pitch dimension.

EXAMPLES

mkd3c -n 1500 -a circ15k.ar

Generate a flat circular trajectory (preset shape) with the rise at 3.4Å (preset value), the twist at 36 degrees (preset value), for 1500 base pairs and write to a file circ15k.ar.

mkd3c -a ramp.ar -spiral 194.8 -50.0 -n 1200 -open

Generate an open left-handed spiral trajectory with a pitch of 50Å and a radius of 194.8Å for a 1200 base pair model and write the coordinates to the file ramp.ar. There will be just over three turns in the spiral.

FILES

SEE ALSO

mkd3d, xmd3, the archive file format.

DIAGNOSTICS

BUGS

NOTES

mkd3c 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.