VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Apr 12 2006 - 12:16:30 CDT

Dear Margaret,
you can do this by using the VMD matrix routines, documented at
http://www.ks.uiuc.edu/Research/vmd/current/ug/node172.html.

For example, for your case, if the long axis of your molecule is along
the vector {a b c}, you can rotate it to align it with the z axis as
follows:

set sel [atomselect top all]
set M [transvecinv {a b c}]
$sel move $M
set M [transaxis y -90]
$sel move $M

This performs your task in two steps: transvec inv rotates your vector
to be along the x axis, and then transaxis rotates about the y axis to
align your vector with z.

Hopefully this will work for you.
Best,
Peter

Margaret Shun Cheung wrote:

> Dear Peter,
>
> Thank you for your email. I knew the vector of the long axis of my
> molecule. I would like to rotate/transform my molecule so that
> eventually
> this vector will align with (0,0,z). After the transformation, I can
> use this new set of coordinates as an input file in NAMD for pulling
> at (0,0,z) direction.
> Thank you very much!
> Sincerely,
> Margaret
>
> On Wed, 12 Apr 2006, Peter Freddolino wrote:
>
>> Dear Margaret,
>> to be clear, do you know what the long axis is and just want to know
>> how to move things right, or do you not know what the longest axis is?
>> Peter
>>
>> Margaret Shun Cheung wrote:
>>
>>>
>>> Dear VMD wizards,
>>>
>>> I want rotate my aspherical molecule such that its long axis will be
>>> aligned to the z- axis. Is there a VMD script that can be used for
>>> this purpose?
>>> Thank you very much!
>>> Sincerely,
>>> Margaret S. Cheung,
>>> Ph. D. Postdoctoral Fellow,
>>>
>>> ------------------------------------------------------------
>>> Room 2117 Tel: (301) 405-4892
>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>> University of Maryland http://glue.umd.edu/~mscheung
>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>> ------------------------------------------------------------
>>
>>
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------