VMD-L Mailing List

From: Cesar Millan (pachequin_at_gmail.com)
Date: Tue Oct 03 2006 - 15:32:17 CDT

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