## VMD-L Mailing List

**From:** Axel Kohlmeyer (*akohlmey_at_gmail.com*)

**Date:** Tue Jun 28 2011 - 09:55:40 CDT

**Next message:**J. Nathan Scott: "Changing representations on a per-atom per-timestep basis"**Previous message:**Axel Kohlmeyer: "Re: VMD-I: rsmd calculation"**In reply to:**Sara Biocomputation: "Re: best fit lines through two selections per each molecule ( I have 80 molecules) and the angle with another vector for each molecule"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

On Mon, Jun 27, 2011 at 11:44 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
*

*> id 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??
*

yes. you just need to do two selections for each molecule. ;)

you can either store them in an array or do it in a loop.

*> 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).
*

{0 1 0} _is_ a vector in Tcl (note the curly braces), so where is the

problem? ;)

cheers,

axel.

*>
*

*> 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
*

*>
*

-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.

**Next message:**J. Nathan Scott: "Changing representations on a per-atom per-timestep basis"**Previous message:**Axel Kohlmeyer: "Re: VMD-I: rsmd calculation"**In reply to:**Sara Biocomputation: "Re: best fit lines through two selections per each molecule ( I have 80 molecules) and the angle with another vector for each molecule"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]