VMD tutorial scripting

Scripting VMD

This page is a placeholder, or under current development; it is here principally to establish the logical framework of the site. The material on this page is correct, but incomplete.

One of the most powerful features of VMD is the ability to complete control all aspects of the program with scripts. The scripting language used is tcl.

 

Introductory reading

 

Contents

Coloring by RMSD

(RMSD by John Stone - colouring needs to be added)

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]
    #open file for writing
    set fil [open residue_rmsd.dat w]
    #write title to file
    #puts $fil "residue \t rmsd"
    

    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
	# 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]]
	    #puts [measure rmsd $comp $ref]
	}
    }
    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)"
	    puts $fil " $r \t $rmsd($r)"
	    [atomselect $mol "resid $r"] set beta $rmsd($r)
	    set ave [expr $ave + $rmsd($r)]
	    
	}
    set ave [expr $ave/[llength $res]]
    puts " Average rmsd per residue:   $ave"
    close $fil
}

   

Further reading and resources