From: Rinky Parakra (
Date: Mon May 21 2018 - 19:32:48 CDT

Dear VMD users,

I have a problem in calculating or getting a 2D plot for RMSF calculation.
I can get a 3D plot for RMSF from the VMD>Extensions>Timeline. However, it
gives RMSF value for 1000 trajections for every 104 residues. I need to get
average RMSF for all 1000 trajectories.

I have tried to load the trajectory file and aligned it using
VMD>Extensions>Analysis>RMSD trajectory tool> Align. Thereafter, in
VMDExtensions>TK console>File>Load the script. However, I could not get the
output file.

The script I got for RMSF is
*> proc rmsf_all_ca {} { *
*> set file_name "Calfa-rmsf.dat" *
*> set outfile [open $file_name w]; *
*> set sel [atomselect top "resid 1 to 104 and name CA"] *
*> set mol [$sel molindex] *
*> for {set i 0} {$i < [$sel num]} {incr i} { *
*> set rmsf [measure rmsf $sel] *
*> puts $outfile "[expr {$i+1}] [lindex $rmsf $i]" *
*> } *
*> close $outfile. *

*It would be of immense help if I can get this script corrected and make a
way out to work RMSF in 2D plot. [RMSF (nm/Angstroms) in y-axis and
 Residues (carbon alpha) in x-axis].*

*Many thanks in advance, *

*Kind regards,*
*Rinky Parakra*
*Assistant Research Fellow,*
*University of Otago, *
*New Zealand.*