VMD-L Mailing List

From: amin_at_imtech.res.in
Date: Sat Oct 15 2016 - 03:25:48 CDT

 

Dear All,

I am trying to calculate the angle between two domains of my protein
using fit_angle.tcl. I am getting a value around 60°, but the molecule
is quite straight and value should be more than 120°. I extracted the
two selections and tried calculating the angle using the webserver HINGE
(https://exon.niaid.nih.gov/sis/hinge_file.html). I found the hinge
angle to be 18.4° and angle between minor axes to be 59.7°.

So, it seems to me that fit_angle.tcl is giving me the angle between the
minor axes of the two domains. What am I doing wrong? I am tempted to
calculate the angle between major axes as 180 minus angle given by
fit_angle, but I want to be sure that I am not misunderstanding
something here.

Any help would be highly appreciated.

The procedure I am following is

set domainA "protein and index 1 to 1600"

set domainB "protein and index 1601 to 3200"

sel_sel_angle_frames 0 $domainA $domainB

Regards,

Amin.