VMD-L Mailing List

From: Schreiner Eduard (eschrein_at_ks.uiuc.edu)
Date: Sun Jul 27 2008 - 01:52:20 CDT

Hi Roman,

maybe you would like to take a look at the

move [trans bond ....]

command (just search for "move [ trans bond" in the manual. In the
current from the vmd web page it is on pp 160f).
instead of "bond", you also can specify an axis like

$sel move [trans bond {0.0 1.0 0.0} {0.0 0.0 0.0} 90 deg]

Using something similart, you should be able to rotate your system in
the appropriate way.
Since you have already positioned one of the atoms at the correct
position, you will have to determine the angle for the rotation and
the axis of rotation. However, may get quite tricky. Maybe there is a
simpler solution.

eddi

On Jul 26, 2008, at 11:31 PM, Roman Petrenko wrote:

> I have two identical molecules (described by the same psf file), but
> with different coordinates. Each molecule has some inner bond CA-CB,
> the question is how to align molecule2 with molecule1, so that the
> specified bond in both molecules have EXACTLY the same coordinates.
>
> I tried fit - method and it didn't work.
>
> So far i've managed only to bring two CA atoms from each molecule to
> the same spot.
>
> Thanks.
>
> --
> Roman Petrenko.
> Physics Department
> University of Cincinnati