Subject: Re: CCL:rotate molecules along princliple moments of inertia

From: Xiang Lu <[email-masked]>
Date: Tue, 22 Oct 2002 15:00:55 -0400 (EDT)

Dear Mike:

I believe your problem arises because of the ambiguity in selecting the
"direction" of the eigenvectors. Let the first and second eigenvectors be
whatever you have, you need to make sure the third one is the cross product
of the first two, thus ensuring a right-handed coordinate system.

"rotate_mol", a utility in 3DNA (http://rutchem.rutgers.edu/~xiangjun/3DNA/),
can do this and a bit more, and it is used to get the most extended views
for every structure in the updated Nucleic Acid Database (NDB)
(http://beta-ndb.rutgers.edu/).

Hope this helps.

Xiang-Jun

-- 
Dr. Xiang-Jun Lu            | Tel:   (732) 445 4619 (O)
Department of Chemistry     |
Rutgers University          | Fax:   (732) 445 5958
610 Taylor Road             | Email: [email-masked]
Piscataway, NJ 08854-8087   | URL: http://rutchem.rutgers.edu/~xiangjun/

>>>>> "lala" == lala podibaer <[email-masked]> writes:

lala> Hi all,
lala> I have a problem concerning the alignment of molecules along their principle 
lala> moments of inertia. I read through several papers and use now a singular 
lala> value decomposition for the alignment. At first glance everything seems to 
lala> be ok with the rotated molecules, they are nicely aligned along the axes and 
lala> insensitive to rotation. Unfotunately, at closer inspection of the aligned 
lala> molecules it can be found that some of the molecules are rather mirrored 
lala> than rotated along the principle axes.

lala> I think the problem lies within the sorting routine of the eigenvalues. 
lala> Since the eigenvectors are not sorted according to the largest value in the 
lala> xyz coordinates, multiplication of the original X matrix with the 
lala> eigenvectors doesn't necessarily produce rotated but mirrored molecules.

lala> I am pretty certain that this problem has already been solved, but I was not 
lala> able to find any documentation in terms of formulas which I could use for 
lala> implementation.

lala> I would appreciate every reference or subroutine that might help me with 
lala> this.

lala> Cheers
lala> Mike