VMD-L Mailing List

From: Stephanie Held (e-mail_at_stephanie-held.de)
Date: Mon Sep 28 2009 - 09:57:08 CDT

Am Monday 28 September 2009 16:35:25 schrieb Axel Kohlmeyer:
> hi stephanie,
>
> On Mon, Sep 28, 2009 at 9:39 AM, Stephanie Held
>
> <e-mail_at_stephanie-held.de> wrote:
> > Hello!
> >
> > I have a problem concerning vectors in vmd. What I'm trying to do is draw
> > a cylinder using vmd console which works nicely when I do it like this:
> >
> > graphics top cylinder {-12.3400001526 73.4120025635 46.4959983826}
> > {-6.99599981308 63.8670005798 67.9349975586} radius 0.5 resolution 60
> > filled yes
> >
> > Since I have to draw many cylinders I would like to give the positions as
> > variables instead of numbers in the command:
>
> this is not how programming or script languages like tcl work. you would
> have to use something more obscure like APL to make these things work,
> but that is a way you don't want to go.
>
> the solution is very simple: use a loop!
> see below for an example.
>
> > set a1 [atomselect 0 "resid 33 and type CA"]
> > set x1 [$a1 get {x y z}]
> >
> > I did the same for x2 and then tried to draw the cylinder by typing:
> >
> > graphics top cylinder {$x1} {$x2} radius 0.5 resolution 60 filled yes
>
> foreach x1 [$a1 get {x y z}] x2 [$a2 get {x y z}] {
> graphics top cylinder $x1 $x2 radius 0.5 resolution 60 filled yes
> }
>
> other than that, i stronly suggest to have a look at the excellent tcl
> tutorial that ships with tcl 8.5 and can be found at www.tcl.tk which
> has many great examples of how to deal with lists (which is what
> a "vector" really is in tcl syntax).
>
> cheers,
> axel.
>
> > But that doesn't work. vmd tells me "need three numbers for a vector"
> > which doesn't make sense to me because x1 and x2 are actually vectors of
> > three numbers which I checked:
> >
> > puts $x1
> > {-12.3400001526 73.4120025635 46.4959983826}
> >
> > Does anyone know what to do about this? I'd be very happy about any
> > advice!
> >
> > Best regards
> >
> > Stephanie

Thank you very much! Now it works! That saves a lot of time.

Best regards

Stephanie