VMD-L Mailing List

From: Sara Biocomputation (sarabiocomputation_at_gmail.com)
Date: Mon Jun 27 2011 - 10:44:48 CDT

The following script was posted by Justin Gullingsrud

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/att-2279/fit_angle.tclid
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 timesteps in a trajectory.

I am trying to do the same think using his script. The difference is that I
am computing the angle between 80 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

On Mon, Jun 27, 2011 at 11:39 AM, Sara Biocomputation <
sarabiocomputation_at_gmail.com> wrote:

>
>
> 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
>