From: Jeremiah Babcock (zhc605_at_my.utsa.edu)
Date: Tue Nov 05 2013 - 10:24:27 CST

It worked well. Thank you!

On Tue, Nov 5, 2013 at 3:46 AM, Joaquim Rui de Castro Rodrigues <
joaquim.rodrigues_at_ipleiria.pt> wrote:

> Hi,
>
> You must set the current frame for your "protein" and "ligand" selections
> inside the loop, right after $all frame $j:
> $protein frame $j
> $ligand frame $j
>
> Hope this helps,
> J Rui Rodrigues
>
> ________________________________________
> De: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] Em Nome De Jeremiah
> Babcock [zhc605_at_my.utsa.edu]
> Enviado: terša-feira, 5 de Novembro de 2013 3:55
> Para: vmd-l_at_ks.uiuc.edu
> Assunto: vmd-l: measuring angles between principal axes through multiple
> frames
>
> Hello,
> I built a fluorophore covalently linked N-terminus to a protein and
> ran simulations. I want to compare the segmental motion of the ligand to
> the protein inertial frame by calculating rotation angles between principal
> axes of both protein and ligand throughout my simulation timeframe. I used
> the Orient plugin and designed the included script. The problem is is that
> in my loop, the principal axes command is not calculating new axes for each
> new trajectory frame: it calculates the first frame and afterwards it stays
> constant. I know this isn't correct, as manually selecting a frame returns
> different axial values for different frames. Am I doing something
> incorrect?
>
>
> # Script to find rotation angles between principal axes
> package require Orient
> namespace import Orient::orient
>
> # Open a file to save inertial axes angles to
> # Select protein atoms without the ligand
> # Select ligand atoms
> # Select protein and ligand atoms together
>
> set file [open InertialAngles.dat w]
> set protein [atomselect top "protein and not index 0 to 46"]
> set ligand [atomselect top "index 0 to 46"]
> set all [atomselect top "protein"]
> set nfram [molinfo 0 get numframes]
>
> # Label output file for the 4 x 1 matrix of time and axial rotation angles
> put $file "Time Th_x Th_y Th_z"
>
> # Create a loop through all DCD frames to find first the principal axes of
> the
> # protein without ligand, and then the ligand principal axes. Then find the
> # angle of rotation between protein and ligand axes.
>
> for {set j 0} {$j < $nfram } { incr j } {
> $all frame $j
> $all update
>
> # update frame number
> put "Frame $j"
>
> # convert frame number to time (ns)
> set time [expr $j*(.001)]
>
> # Find protein and ligand principal axes
> set Ip [Orient::calc_principalaxes $protein]
> set Il [Orient::calc_principalaxes $ligand]
>
>
> # Find rotation angles between protein and ligand principal axes
> set Ax [Orient::orient $all [lindex $Ip 0] [lindex $Il 0]]
> set Ay [Orient::orient $all [lindex $Ip 1] [lindex $Il 1]]
> set Az [Orient::orient $all [lindex $Ip 2] [lindex $Il 2]]
>
> # Create results list and print to file
> set type [list $time $Ax $Ay $Az]
> put $file "$type"
> }
> close $file
>
> Thank you for your help.
>
> --
> Jeremiah Babcock
> PhD Candidate, Molecular Biophysics
> Department of Physics and Astronomy
> University of Texas at San Antonio
> AET 3.206, One UTSA Circle
> San Antonio, TX 78249
> Voice: (210) 458-6191
> Email: zhc605_at_my.utsa.edu<mailto:zhc605_at_my.utsa.edu>
>

-- 
Jeremiah Babcock
PhD Candidate, Molecular Biophysics
Department of Physics and Astronomy
University of Texas at San Antonio
AET 3.206, One UTSA Circle
San Antonio, TX 78249
Voice: (210) 458-6191
Email: zhc605_at_my.utsa.edu