From: Leonardo Palmieri (
Date: Fri Jun 10 2022 - 11:15:34 CDT


I'm using Calc. RMSD function of Timeline plugin to analyze
trajectories. If I use it from the VMD GUI, results seems correct.
But, if I use it in a script, for eg., the script proposed in titin
Timeline tutorial "titin-per-res-rmsd.tcl" to generate a .tml file, I
can't get the same results.

RMSD values for some residues in some frames increases too much, not
corresponding to what is happening in the molecule trajectory.

The calculation part of the script that I'm using is the same from
tutorial "titin-per-res-rmsd.tcl":

  ::timeline::writeDataFileHeader $outDataFile $molid $dataTitle $numFrames \
     $numSelectionGroups $usesFreeSelection

  set chain $theChain
  set seg $theSeg
  for {set r $firstRes} {$r <= $lastRes} {incr r} {
    set sela [atomselect $molid "resid $r"]
    set selb [atomselect $molid "resid $r"]
    $sela frame 0
    for {set f $firstFrame} {$f<=$lastFrame} {incr f} {
      $selb frame $f
      display update
      set val [measure rmsd $sela $selb]
      set resid $r
      puts $outDataFile "$resid $chain $seg $f $val"

eg of RMSD values:

with GUI:

95 CYS frame 211: 6.64
95 CYS frame 212: 6.845

with script:

95 CYS frame 211: 8.54
95 CYS frame 212: 20.75

Is there something wrong with my script? Did I miss something?

Thanks in advance!

Leonardo Palmieri
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