VMD-L Mailing List
Date: Sat Oct 15 2016 - 03:25:48 CDT
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
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