VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 17 2001 - 14:00:10 CDT

Elizabeth,
  All of us VMD developers are out of town at conferences or giving
tutorials this week, but we'll try to get back to you on this asap when
we return next week.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 15, 2001 at 02:03:11PM -0600, Elizabeth K. White wrote:
> I modified the RMSD calculator to align parts of a protein over multiple
> frames, in order to see what regions might be folding. The calculations
> are going suspiciously slowly, and VMD often crashes without finishing
> them. I am writing the files to a huge disk, so space shouldn't be a
> problem. Can anyone suggest what is wrong? I am running VMD 1.6 on a DEC
> Alpha using Linux. The script follows.
>
> Thanks, Elizabeth
>
> # Prints the RMSD of the protein atoms between each timestep
> # and the first timestep for the given molecule id (default: top)
> proc overlap_rmsd {aminos dir seglength {mol top}} {
> puts "$aminos aminos, $dir subdir, $seglength seglength"
> set file1 [molinfo top get {source filename}]
> set file2 [molinfo top get {source filename2}]
> # note the filename of the molecule
> exec echo ".parm file is $file1" > thisframe.out
> exec cat thisframe.out >> header.out
> exec echo ".crd file is $file2" > thisframe.out
> exec cat thisframe.out >> header.out
> set num_steps [molinfo $mol get numframes]
> set maxk [expr $aminos - $seglength + 2]
> for {set frame 0} {$frame < $num_steps} {incr frame} {
> for {set k 1} {$k < $maxk} {incr k} {
> set m [expr $k + $seglength - 1]
> # use frame 0 for the reference
> set reference [atomselect $mol "protein and resid
> $k to $m" frame 0]
> # the frame being compared
> set compare [atomselect $mol "protein and resid $k
> to $m"]
> # get the correct frame
> $compare frame $frame
> # compute the transformation
> set trans_mat [measure fit $compare $reference]
> # do the alignment
> $compare move $trans_mat
> # compute the RMSD
> set rmsd [measure rmsd $compare $reference]
> set spc "_"
> set output "$seglength$spc$frame"
> # puts "output is $output"
> # print the RMSD
> puts "frame=$frame k=$k m=$m $rmsd=rmsd"
> set x [expr ($k + $m) / 2.0]
> exec echo "$x $rmsd" > thisframe.out
> exec cat thisframe.out >>
> /home/ri/ekwhite/rmsd/$dir/$output
> }
> }
> puts "Okay, done"
> }
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078