VMD-L Mailing List

From: andrea spitaleri (spitaleri.andrea_at_hsr.it)
Date: Mon Mar 13 2006 - 04:19:55 CST

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)
-------------------------------