VMD-L Mailing List

From: andrea spitaleri (spitaleri.andrea_at_hsr.it)
Date: Tue Mar 14 2006 - 05:05:00 CST

Hi Axel,
thanks for your reply. So if I undestood well *everytime* I add a script
in /usr/local/lib/vmd/scripts/vmd I need to add the lines done by
auto_mkindex in tclIndex file, is it right?

Thanks
Reagards

andrea

Axel Kohlmeyer wrote:

>On Mon, 13 Mar 2006, andrea spitaleri wrote:
>
>AS> Hi Johns,
>AS> the only way to run a own script is first to source it and then use it?
>AS> May vmd load it at start up the script without put it in the $vmddir/script?
>AS> I couldn't find it any answer ......
>
>andrea,
>you also can use standard TCL techniques to have scripts autoloaded.
>
>please have a look at:
>http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part1.html#chap3_sect3
>
>to make a directory autoloadable, you only need to generate an index
>file i use the following trivial script for it:
>
>#!/usr/bin/tclsh
>
>auto_mkindex . *.tcl
>
>
>note, that the draw extensions (and similar functions) _have_
>to be sourced before they are recognized. but the URL from above
>shows how to do this in a generic way.
>
>regards,
> axel.
>
>AS>
>AS> Reagards,
>AS>
>AS> andrea
>AS>
>AS>
>AS>
>AS> John Stone wrote:
>AS>
>AS> >Hi Lily,
>AS> > Yes, there are various little scripts that can do things like this.
>AS> >Take one of these and cut out the stuff you don't need, as all of these
>AS> >probably do more than you're looking for.
>AS> >
>AS> >Here's one that loads a numerically named sequence of PDB files:
>AS> > http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/
>AS> >
>AS> >Here's another that loads all of the PDB files in a particular
>AS> >directory using filename globbing (wildcards), which I've used to
>AS> >load the entire PDB into VMD at once, for example:
>AS> >
>AS> >##
>AS> >## Example:
>AS> >## load_all_pdb "/Scr/pdb/data/structures/all/pdb/*.Z" 32000
>AS> >##
>AS> >
>AS> >proc load_all_pdb { pdbfilespec maxcount } {
>AS> > puts "Gathering candidate files."
>AS> > set filelist [glob -types f -- $pdbfilespec]
>AS> > set numfiles [llength $filelist]
>AS> > set count 0
>AS> >
>AS> > if { $numfiles > 0 } {
>AS> > puts "Searching $numfiles PDB files..."
>AS> > foreach {file} $filelist {
>AS> > incr count
>AS> > if {$count > $maxcount} {
>AS> > break;
>AS> > }
>AS> >
>AS> ># puts "$count/$numfiles, loading $file ..."
>AS> >
>AS> > # detect compressed PDB entry by filename, uncompress, and load
>AS> > if { [string match "*.ent.Z" $file] } {
>AS> > file delete /tmp/loadpdb.pdb
>AS> > exec zcat $file > /tmp/loadpdb.pdb
>AS> > mol new /tmp/loadpdb.pdb waitfor all
>AS> ># mol rename top $file
>AS> > } elseif { [string match "*.ent" $file] } {
>AS> > mol new $file type pdb waitfor all
>AS> > } elseif { [string match "*.pdb" $file] } {
>AS> > mol new $file waitfor all
>AS> > } else {
>AS> > # Skip unrecognized structure file formats and PDB files without coords
>AS> > continue;
>AS> > }
>AS> > }
>AS> > puts "Completed loading $numfiles PDB files..."
>AS> > } else {
>AS> > puts "No PDB files found"
>AS> > }
>AS> >}
>AS> >
>AS> >
>AS> >
>AS> >
>AS> >On Fri, Mar 10, 2006 at 11:41:03AM -0800, lily jin wrote:
>AS> >
>AS> >
>AS> >>In the .VMD file, I have :
>AS> >> mol addfile 1.pdb type pdb type pdb waitfor all
>AS> >> mol addfile 2.pdb type pdb type pdb waitfor all
>AS> >> mol addfile 3.pdb type pdb type pdb waitfor all
>AS> >> mol addfile 4.pdb type pdb type pdb waitfor all
>AS> >> mol addfile 5.pdb type pdb type pdb waitfor all
>AS> >> mol addfile 6.pdb type pdb type pdb waitfor all
>AS> >> mol addfile 7.pdb type pdb type pdb waitfor all
>AS> >> mol addfile 8.pdb type pdb type pdb waitfor all
>AS> >> mol addfile 9.pdb type pdb type pdb waitfor all
>AS> >> mol addfile 10.pdb type pdb type pdb waitfor all
>AS> >> Is there a way to do the same in a loop? Thanks!
>AS> >>
>AS> >>
>AS> >>Lily
>AS> >>
>AS> >>---------------------------------
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>AS> >>
>AS>
>AS>
>
>
> 

-- 
-------------------------------
Andrea Spitaleri 
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
-------------------------------