From: crockett c.h. (chc2g16) (
Date: Thu Dec 12 2019 - 12:43:26 CST


I’m trying to use a script (like the one below) to measure the RMSF (for all residues) of my dcd trajectory file. I know that there are lots of errors in this but the most concerning is the ‘can’t read “rmsf”: no such variable’ and then subsequently ‘measure rmsf: invalid syntax, no such keyword: atomselect0’ When this ‘measure rmsf’ command is done in the tcl window of VMD is there a source script which I would need to manually source in this case?

Many thanks, and any input appreciated as always,

proc rmsf_resid { frame } {
    global outfile sel frame0 nf sel
    $sel mve [measure fit $sel $frame0]
    puts "$frame: [measure rmsf $sel first 1 last 210021 step]"
puts $outfile "$frame [measure rmsf $sel first 1 last 210021 step]"
source bigdcd.tcl
set outfile [open rmsf.dat w]
set mol [mol new 2gbu_wbn.psf type psf waitfor all]
mol addfile 2gbu_6.dcd type dcd waitfor all
set nf [molinfo top get numframes]
set frame0 [atomselect top "protein and backbone and noh" frame 0]
set sel [atomselect top "protein and backbone and noh"]
$frame0 global
$sel global
$outfile global
for {set i 0} {$i < [$sel num]} {incr i} {
   puts $outfile "[expr {$i+1}] [lindex $rmsf $i]"

bigdcd rmsf_resid 2gbu_6.dcd
puts $outfile "[measure rmsf $sel first 1 last 210021 step]"
close $outfile

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