VMD-L Mailing List

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Wed Feb 25 2009 - 15:45:53 CST

Hi John,

Thanks for your reply! I will just go ahead to decompose the transformation
matrix and extract the angle according to the translation/rotation scheme of
my case.

Best,
Yinglong

On Wed, Feb 25, 2009 at 4:37 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> There isn't any routine to compute angles from an arbitrary
> transformation matrix. The main reason for this is that it's
> problematic since one can have matrices that contain shear/scaling
> components or a destructive warp transformation, and there'd be
> no way to extract angles in such a case. Beyond that, the numerical
> precision for angle extraction would be relatively low. If low precision
> is all you need, then you could write some scripts to attempt to
> either decompose a transformation matrix (on the assumption it only
> has translation/rotation components).
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Feb 25, 2009 at 03:55:27PM -0500, Yinglong Miao wrote:
> > Dear VMD developers/users,
> >
> > >From the user guide, I found matrix routine "transabout" to generate a
> > transformation matrix needed to rotate a molecule around an axis by the
> > given amount, but no routine on the reverse process: calculate the angle
> > from the matrix obtained by fitting structures. Has anyone tried this? It
> > would be great if there is something I missed and ready to use. Or I have
> to
> > do the calculations by myself.
> >
> > Thanks in advance!
> >
> > --
> > Yinglong Miao
> > Ph.D. Candidate
> > Center for Cell and Virus Theory
> > Chemistry Department, Indiana University
> > 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> > Tel: 1-812-856-0981
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981