VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 04 2006 - 00:12:59 CDT

If you use "$sel move $matrix" you can set $matrix to any 4x4 transformation,
so you can apply any rotation you want. You just have to populate the matrix
with the right rotation transformation for the purpose you have in mind.
The "transaxis" and other commands that help with this are described
in the User's Guide, but if you need something they don't provide you may
need to make your own 4x4 transformation matrix (which is what those
commands do anyway...)

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 03, 2006 at 03:32:17PM -0500, Cesar Millan wrote:
> hi! thanks for your reply, the moveby and moveto worked, thank you. I just
> have another question, i want to rotate my molecule using the principal axis
> of it as the Z-axis and rotate it around this axis, if I use "trans x ..."
> it rotate around an axis that is not what I wanted. How can I move or change
> the rotation axis so the Z axis fits (and the rotation) on the principal
> axis of my molecule? Thank you again
>
> On 10/3/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> >Hi,
> > I think you'll find it much easier to use the built-in
> >'$sel moveby' and '$sel move' subcommands, rather than creating your own.
> >See the examples in the bottom half of the User's Guide page here:
> > http://www.ks.uiuc.edu/Research/vmd/current/ug/node181.html#14252
> >
> >Your moveby proc looks like it's from that page, but the later
> >examples are the better way to do it.
> >
> >For your rotations, you'll need to use the '$sel move [transaxis x 90]'
> >way of doing things. The 'rotate x by 45' doesn't actually affect the
> >atom coordinates, it only rotates the _view_ of the structure, and thus
> >will not affect the structure you're saving.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Oct 03, 2006 at 02:02:41PM -0500, Cesar Millan wrote:
> >> Hi everyone, I trying to move a coordinates and save the changes on a
> >new
> >> file but when I look on the new coordinates, the coordinate values are
> >the
> >> same :S, here is what I'm doing:
> >>
> >> ###
> >> animate read pdb lig1.pdb
> >>
> >> proc moveby {sel offset} {
> >> foreach coord [$sel get {x y z}] {
> >> lappend newcoords [vecadd $coord $offset]
> >> }
> >> $sel set {x y z} $newcoords
> >> }
> >>
> >> set sel [atomselect top "all"]
> >>
> >> set v 1
> >> while { $v <= 5 } {
> >> moveby $sel "5 0 0"
> >> set $sel [atomselect top "all"]
> >> $sel writepdb lig1_${v}.pdb
> >> rotate z by 45
> >> moveby $sel "-5 0 0"
> >> incr v
> >> }
> >>
> >> when I watch the coordinates on lig1_*.pdb, they are the same as the
> >> original, does anyone know what happend?
> >>
> >> thank you so much.
> >>
> >> --
> >> César Millán Pacheco
> >> Facultad de Ciencias
> >> Universidad Autonoma del Estado de Morelos
> >> Tel: 777 3297020
> >> Fax: 777 3207040
> >> email: cmp_at_servm.fc.uaem.mx
> >> pachequin_at_gmail.com
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
>
>
> --
> César Millán Pacheco
> Facultad de Ciencias
> Universidad Autonoma del Estado de Morelos
> Tel: 777 3297020
> Fax: 777 3207040
> email: cmp_at_servm.fc.uaem.mx
> pachequin_at_gmail.com 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078