Hi Natasha,
On Mon, 15 Sep 2008 08:15:45 -0700, Natasha Keith <[log in to unmask]>
wrote:
> I'm sorry if this question is somewhat basic...
>
> I'm comparing three homologous proteins, and I'd like to determine a
> number of facts to be able to rigorously compare them... I'd like to
> know the angle formed by two crossed helices, the angle of kinking in
> a kinked helix, and the distance between two separated helices that
> are nearly parallel to one another along the y axis, but not parallel
> along any other axis.
>
> Could anyone recommend any software to rigorously determine distances
> and angles in differently oriented helices? My guess is that I'd need
> some kind of a program that can draw vectors through the helices, and
> find minimum distances between the vectors, or to use them to define
> angles...
Just to add to the answers, I have a python program that calculates the angle
and distance between pairs of helices. It requires that the numpy python
module be installed as well. It should work with both alpha-helices and DNA
helices.
The input is on the command line in the form of:
file.pdb A 153 170 B 271 291
Where one would calculate the angle and distance between the helices defined
as chain A, residues 153-170 and chain B, residues 271-291.
The output should be self-explanatory and is more verbose than necessary.
That could easily be modified, of course.
Cheers,
Rob
--
Robert L. Campbell, Ph.D.
Senior Research Associate/Adjunct Assistant Professor
Botterell Hall Rm 644
Department of Biochemistry, Queen's University,
Kingston, ON K7L 3N6 Canada
Tel: 613-533-6821 Fax: 613-533-2497
<[log in to unmask]> http://pldserver1.biochem.queensu.ca/~rlc
|