VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Wed Apr 06 2016 - 20:54:17 CDT

Hi,

What you need to do is define Helix 1 (H1) and Helix 2 (H2). After that -
get two points on each helix (such that a line through those two points run
along the helix i,e, H1(p1) and H1(p2)). Subtract one point on H1 from the
other point on H1 to get the vector (Vh1) describing the line running along
H1. Repeat the same for H2 (Vh2). Now you have two vector one for H1 and
one for H2. The dot product of these divided by the magnitude of the
individual vectors will give you the cosine of the angle between the two
vectors inverse of which will then give you the angle you want i.e. between
the helices.

use -- in TCL

"vecsub" to subtract the two points on each helix i.e. H1(p1) and H1(p2) to
> get the vector of the line running through those two point.

"vecdot" to get the dot product of the Vh1 and Vh2.

"veclength" to get the magnitude of each vector Vh1 and Vh2

"acos " to take the inverse of the angle

Note that the angle returned is in radians.

Hope this helps.

p.s. A previous posts that can possibly be related:

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3898.html

On Thu, Apr 7, 2016 at 8:09 AM, Anjela Manandhar <anjelamanandhar_at_gmail.com>
wrote:

> Hi,
> I want to determine angle between two helices. For that, I want to define
> each helix by a vector and measure the angle between those vectors. How
> can i do it? Thank you.
> Sincerely,
> Anjela Manandhar
> Graduate Student
> Biochemistry Program
> Graduate Center, City University of New York
> 365 Fifth Avenue, NY-10016, USA
> 

-- 
Best,
/A