VMD-L Mailing List

From: Stef (steletch_at_free.fr)
Date: Thu Mar 03 2005 - 04:37:05 CST

Le mercredi 02 mars 2005 à 12:18 +0100, Eduard Schreiner a écrit :
> Stef wrote:
> > Over a trajectory, i'd like to pick up snapshot containing certain
> > particularities (for instance distance < cutoff, ...).
> >
> > I'd like to display the 'sub-trajectory' and also to be able to keep the
> > trace of snapshot number (for instance i'd like to see from the whole
> > trajectory all snapshots containing dist1 <4.0 angstroems AND dihedral

> if i understood You correctly, You have a trajectory where only steps
> should be displayed having some specific features whereas the others
> should be removed. Additionally You want to know the the correct
> (original) time step. Right?

The best thing would be to generate a sub-trajectory from the original
one (and have a way to link frame 1 of sub-trajectory to fram <x> of the
original one).

> You could try the following:
> One could go through the trajectory checking whether the current time
> step contains atoms in the specified selection.This one could check by

Something missing here ?

> If a given step matches one writes its number in one array (the name of
> the array is, say, OK) if not in an other.
> Something like:

I've just adapted a little the script you sent me :
label add Dihedrals 0/159 0/162 0/182 0/187
set ts 0
set OK 0
foreach dihed [label graph Dihedrals 0] {
     incr ts
        if {$dihed < 75.0} {
            lappend OK $ts
      }
}

foreach i $OK {
animate goto $i
graphics text {x y z} "$i" [size s]
}

But when i launch it, i get :
vmd > source prune_trajec.tcl
invalid command name "size"

Although on the website this command seems correct (and i've tried to
change [size s] to anything without more luck).
As described on the website :

http://www.ks.uiuc.edu/Research/vmd/current/ug/node114.html
The documentation is may be out-of-date or i'm not understanding it
correctly.

> I hope this will be useful for You.

Thanks a lot for the help, you gave me useful directions !
>
> Eduard Schreiner

Stéphane Teletchéa 

-- 
http://www.steletch.org
Fingerprint: 1E83 26EE A2F1 87E5 5865 4DBF F2B4 9083 F44C AE88
GPG key @ http://www.steletch.org/article.php3?id_article=13
Mandrakelinux release 10.1 (Official) @ http://www.mandrakesoft.com/
11:30:33 up 2:35, 1 user, load average: 0.57, 0.64, 0.48