VMD-L Mailing List
From: Turman, Cheri M (Cheri.M.Turman_at_uth.tmc.edu)
Date: Wed Mar 29 2006 - 19:34:29 CST
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Hi all,
I am having trouble with the rmsd-fullthrottle.tcl script. I am able to run the residue_rmsd.tcl script but not this one. I really would like to show B values by the coloring method in VMD from a simulated annealing trajectory I ran in NAMD. I have the .dcd, .pdb and .psf files loaded in VMD and next go to the tcl script page. I type: source rmsd-fullthrottle.tcl and get the output: Calculating rmsd for frame 0 ...
measure rmsd: No atoms selected
Here is the rmsd-fullthrottle.tcl script I am calling:
# $Id: rmsd-fullthrottle.tcl,v 1.3 2005/03/29 17:58:52 sotomayo Exp $
# This script contains a procedure called rmsd_residue_over_time that calculates the average RMSD for each residue in a selection over all frames in a trajectory. The procedure is called as:
# rmsd_residue_over_time mol sel_resid
#where mol is the molecule in VMD and sel_resid is a list of the residue numbers in that selection.
#You can use the procedure for any residue or list of residues. Here, as an example, we will make a selection for all residues in the protein. Note that this will take a long time to calculate:
set sel_resid [[atomselect top "protein and alpha"] get resid]
#The procedure is presented below. It also sets the B value to the value calculated, so you can color the protein by RMSD. The call for the procedure is at the end of the file.
proc rmsd_residue_over_time {{mol top} res} {
# use frame 0 for the reference
set reference [atomselect $mol "protein" frame 0]
# the frame being compared
set compare [atomselect $mol "protein"]
#make a selection with all atoms
set all [atomselect top all]
#get the number of frames
set num_steps [molinfo $mol get numframes]
foreach r $res {
set rmsd($r) 0
}
#loop over all frames in the trajectory
for {set frame 0} {$frame < $num_steps} {incr frame} {
puts "Calculating rmsd for frame $frame ..."
# get the correct frame
$compare frame $frame
$all frame $frame
# compute the transformation
set trans_mat [measure fit $compare $reference]
# do the alignment
$all move $trans_mat
# compute the RMSD
#loop through all residues
foreach r $res {
set ref [atomselect $mol "chain U and resid $r and noh" frame 0]
set comp [atomselect $mol "chain U and resid $r and noh" frame $frame]
set rmsd($r) [expr $rmsd($r) + [measure rmsd $comp $ref]]
$comp delete
$ref delete
}
}
set ave 0
foreach r $res {
set rmsd($r) [expr $rmsd($r)/$num_steps]
# print the RMSD
puts "RMSD of residue $r is $rmsd($r)"
set res_b [atomselect $mol "resid $r"]
$res_b set beta $rmsd($r)
$res_b delete
set ave [expr $ave + $rmsd($r)]
}
set ave [expr $ave/[llength $res]]
puts " Average rmsd per residue: $ave"
}
#Call the procedure
rmsd_residue_over_time top $sel_resid
Has anyone seen a problem in the script or know of a better way?
Cheers,
Cheri
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