VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 03 2005 - 09:52:15 CST

Stephane,
  The "size" command should just be added at the end of the command line,
not put into brackets. The typographic conventions in the User's Guide
are primarily to indicate which parameters are required, and which ones
are optional. When you see a parameter surrounded by brackets [], that
indicates the parameter is optional. The syntax you use when specifying
the optional parameter to Tcl is _without_ the brackets, as they have
special meaning in Tcl (evluate command). e.g.:

graphics top text {0 0 0} "Test" size 24

Here's an example of how you would use the brackets in Tcl:

set x 0
set y 0
set z 0
set s 10
set i 2048
graphics top text [list $x $y $z] "$i" size $s

  John

On Thu, Mar 03, 2005 at 11:37:05AM +0100, Stef wrote:
> 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
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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