VMD-L Mailing List

From: Sara Biocomputation (sarabiocomputation_at_gmail.com)
Date: Mon Jun 27 2011 - 10:39:30 CDT

 The following script was posted by Justin Gullingsrud

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-2279/fit_angle.tcl

  the script does the flowing:

# Set of scripts to:
# fit atoms in a selection to a vector;
# find the angle made by that vector with another vector; and
# do this for all time steps in a trajectory.
#

I am trying to do the same think using his script. The difference is that I
am computing the angle between 25 identical molecules and the Y axis (
vector of coordinates 0 1 0). So I was able to represent each molecule
separate than other identical once using VMD

 So I found out how to select two residues per each molecule. I cant find
out how to do the best fit lines through the two selections per each
molecule ( I have 80 molecules).

 in the script he is doing the the best fit lines through the two
selections. Is it possible to do the same for 80 molecules??

 Also his script shows how to get the angle between two vectors but how do I
adjust it to be able to get the angle between one vector of each molecules
(80 molecules) and the vector with coordinates (0 1 0).

 I will really appreciate your help and any suggestions

 Thank you very much

 Sara