VMD-L Mailing List

From: Rebeca García Fandiño (regafan_at_hotmail.com)
Date: Wed Feb 20 2013 - 04:07:55 CST

It works perfectly now!!
Thanks a lot very very much.
Best wishes,
Rebeca.

> Date: Wed, 20 Feb 2013 11:03:54 +0100
> Subject: Re: vmd-l: rotate a selection of a molecule and write rotated coordinates
> From: akohlmey_at_gmail.com
> To: regafan_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu
>
> On Wed, Feb 20, 2013 at 10:38 AM, Rebeca García Fandiño
> <regafan_at_hotmail.com> wrote:
> > Hi,
> > thanks a lot for your help. However, when I tried
> >
> > set sel [atomselect top "resid 10"]
> > set matrix [transaxis z 45]
> > $sel move $matrix
> >
> > I do not obtain a rotated residue around z axis, it is translated long away
> > my main molecule...
>
> it works for me.
>
> > My main molecule is a nanotube and it is aligned to principal axes.
> > Do you have any idea of the reason for this problem?
>
> there is one thing that you may be overlooking.
> by applying a rotation matrix to the coordinates of the selection, you
> rotate around the origin of your _coordinate system_ not your
> viewpoint. those two may be far away from each other and thus the
> rotation may appear as a translation. to rotate about the center of
> mass of an object you have to extend the Tcl code as follows:
>
> set sel [atomselect top "resid 10"]
> set com [measure center $sel weight mass]
> set matrix [transaxis z 45]
>
> $sel moveby [vecscale -1.0 $com]
> $sel move $matrix
> $sel moveby $com
>
> axel.
>
> > Thanks a lot again for your help.
> > Best wishes,
> > Rebeca.
> >
> >
> >
> >
> >> Date: Tue, 19 Feb 2013 17:07:23 +0100
> >> Subject: Re: vmd-l: rotate a selection of a molecule and write rotated
> >> coordinates
> >> From: akohlmey_at_gmail.com
> >> To: regafan_at_hotmail.com
> >> CC: vmd-l_at_ks.uiuc.edu
> >
> >>
> >> On Tue, Feb 19, 2013 at 3:45 PM, Rebeca García Fandiño
> >> <regafan_at_hotmail.com> wrote:
> >> > Hello,
> >> > I am trying to rotate a part of an assembled molecule, consisting on
> >> > several
> >> > residues, so I want to rotate only one of these residues, for example,
> >> > residue 10. I have tried different combinations:
> >> >
> >> > set sel [atomselect top "resid 10"]
> >> > $sel rotate z by 45
> >> >
> >> > $sel [rotate z by 45]
> >> >
> >> > $sel rotate [z by 45]
> >> >
> >> > But I always get errors.
> >>
> >> yes, because none of this is not a supported syntax. please have a look
> >> at:
> >> http://www.ks.uiuc.edu/Research/vmd/current/ug/node121.html
> >>
> >> > By the other hand, when I have tried to rotate the whole molecule
> >> >
> >> > set sel [atomselect top "resid 10"]
> >> > rotate z by 45
> >> >
> >> > It works, but when I try to write the coordinates using:
> >> >
> >> > $sel writepdb file.pdb
> >> >
> >> > they are identical to the first ones!
> >>
> >> yes, because the rotate command rotates the *view* (i.e. the camera),
> >> it doesn't change the coordinates. please check out:
> >> http://www.ks.uiuc.edu/Research/vmd/current/ug/node146.html
> >>
> >>
> >> what you need is:
> >>
> >> $sel move $matrix
> >>
> >> and the rotation matrix can be computed beforehand with:
> >>
> >>
> >
> >
> >>
> >> check out:
> >> http://www.ks.uiuc.edu/Research/vmd/current/ug/node191.html
> >>
> >>
> >> HTH,
> >> axel.
> >>
> >> > Please, could anyone help me to rotate a selection in a molecule and to
> >> > save
> >> > its rotated coordinates?
> >>
> >> > Thanks a lot for your help in advance.
> >> >
> >> > Best wishes,
> >> >
> >> > Rebeca.
> >> >
> >> >
> >> >
> >> >
> >> > Dr Rebeca García
> >> > Universidad de Santiago de Compostela
> >> > Spain
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.