From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 28 2011 - 09:55:40 CDT

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.