VMD-L Mailing List

From: Cesar Millan (pachequin_at_gmail.com)
Date: Wed Oct 04 2006 - 15:35:33 CDT

thank you so much.

On 10/4/06, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> 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
> 

-- 
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