VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 13 2006 - 10:17:25 CST

Andrea,
  On Unix systems you can use the "-e" command line flag of VMD to execute
scripts at startup (equivalent to using the "play" command inside VMD).
This is described more fully in the User's Guide.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 13, 2006 at 11:19:55AM +0100, andrea spitaleri wrote:
> Hi Johns,
> the only way to run a own script is first to source it and then use it?
> May vmd load it at start up the script without put it in the $vmddir/script?
> I couldn't find it any answer ......
>
> Reagards,
>
> andrea
>
>
>
> John Stone wrote:
>
> >Hi Lily,
> > Yes, there are various little scripts that can do things like this.
> >Take one of these and cut out the stuff you don't need, as all of these
> >probably do more than you're looking for.
> >
> >Here's one that loads a numerically named sequence of PDB files:
> > http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/
> >
> >Here's another that loads all of the PDB files in a particular
> >directory using filename globbing (wildcards), which I've used to
> >load the entire PDB into VMD at once, for example:
> >
> >##
> >## Example:
> >## load_all_pdb "/Scr/pdb/data/structures/all/pdb/*.Z" 32000
> >##
> >
> >proc load_all_pdb { pdbfilespec maxcount } {
> > puts "Gathering candidate files."
> > set filelist [glob -types f -- $pdbfilespec]
> > set numfiles [llength $filelist]
> > set count 0
> >
> > if { $numfiles > 0 } {
> > puts "Searching $numfiles PDB files..."
> > foreach {file} $filelist {
> > incr count
> > if {$count > $maxcount} {
> > break;
> > }
> >
> ># puts "$count/$numfiles, loading $file ..."
> >
> > # detect compressed PDB entry by filename, uncompress, and load
> > if { [string match "*.ent.Z" $file] } {
> > file delete /tmp/loadpdb.pdb
> > exec zcat $file > /tmp/loadpdb.pdb
> > mol new /tmp/loadpdb.pdb waitfor all
> ># mol rename top $file
> > } elseif { [string match "*.ent" $file] } {
> > mol new $file type pdb waitfor all
> > } elseif { [string match "*.pdb" $file] } {
> > mol new $file waitfor all
> > } else {
> > # Skip unrecognized structure file formats and PDB files without
> > coords
> > continue;
> > }
> > }
> > puts "Completed loading $numfiles PDB files..."
> > } else {
> > puts "No PDB files found"
> > }
> >}
> >
> >
> >
> >
> >On Fri, Mar 10, 2006 at 11:41:03AM -0800, lily jin wrote:
> >
> >
> >>In the .VMD file, I have :
> >> mol addfile 1.pdb type pdb type pdb waitfor all
> >> mol addfile 2.pdb type pdb type pdb waitfor all
> >> mol addfile 3.pdb type pdb type pdb waitfor all
> >> mol addfile 4.pdb type pdb type pdb waitfor all
> >> mol addfile 5.pdb type pdb type pdb waitfor all
> >> mol addfile 6.pdb type pdb type pdb waitfor all
> >> mol addfile 7.pdb type pdb type pdb waitfor all
> >> mol addfile 8.pdb type pdb type pdb waitfor all
> >> mol addfile 9.pdb type pdb type pdb waitfor all
> >> mol addfile 10.pdb type pdb type pdb waitfor all
> >> Is there a way to do the same in a loop? Thanks!
> >>
> >>
> >>Lily
> >>
> >>---------------------------------
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> >>
> >>
>
> --
> -------------------------------
> Andrea Spitaleri
> Dulbecco Telethon Institute
> c/o DIBIT Scientific Institute
> Biomolecular NMR, 1B4
> Via Olgettina 58
> 20132 Milano (Italy)
> ------------------------------- 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078