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Azmiri -
>From the point of view of efficiency and convenience in the likely event
that you plan to do this on multiple sets of co-ordinates, it would be
better to transform the matrix rather than the co-ordinates. So in this
example the operation you wish to perform can be written as:
x_new = B.A.B'.x_old
where B is the orthogonalisation matrix appropriate for your cell and
orthogonalisation convention (see e.g. s/r ccp4ccif_cell2mat in
$CLIBS/cciflib.f for definitions), B' is its inverse (i.e. the
fractionalising matrix), and A is your transformation matrix.
The associative law of matrix multiplication allows you to perform this
like so:
x_new = B.(A.(B'.x_old))
which is what has been suggested and which requires 3 passes through the
co-ordinates, or like so:
x_new = (B.A.B').x_old
which requires only one, once you have formed the matrix B.A.B', which
in this case can easily be done by hand calculation, and which needs to
be done only once for any given transformation matrix.
This is of course the way that molecular graphics software does (or
should do!) it, using 4x4 homogeneous matrices to allow concatenation of
both rotation and translation matrices.
-- Ian
> -----Original Message-----
> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On
> Behalf Of Chris Putnam
> Sent: Thursday, March 16, 2006 4:32 PM
> To: Azmiri Sultana
> Cc: [email protected]
> Subject: Re: [ccp4bb]: Problem in rotation in Moleman
>
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> *** CCP4 home page http://www.ccp4.ac.uk ***
>
>
> On Thursday 16 March 2006 01:23 pm, you wrote:
> > Hi,
> > i have a structure that is pseudo-merohedrally twinned and i need to
> > generate the twinned domains of my molecule. The twin
> operator i have
> > is -1 0 0 0 -1 0 1 0 1. But, when i tried to use this
> martix in moleman
> > with the option 'rotate molecule' i get an output that is
> totally distorted
> > and kind of elongated. I also tried PDBset but it complains
> that this
> > matrix is not a rotation matrix. Can anyone please tell me
> how i can get
> > out of this problem?
> > Regards, Azmiri
>
> My quick response is that your twin operator does not define
> a rotation matrix
> using cartesian coordinates (e.g. orthogonal basis vectors).
> So in that
> sense Moleman is correct. Instead this looks like a operator
> that likely
> comes from a trigonal or hexagonal crystal that needs to be
> applied in
> fractional coordinates (e.g. using basis vectors from the crystal).
>
> Thus, you first need to convert model into fractional
> coordinates, apply the
> rotation operator, and then convert back into cartesian
> coordinates. I'm
> pretty sure moleman can do all of that.
>
> Hope this helps.
>
> Chris.
>
>
> --
> Christopher Putnam, Ph.D.
> Ludwig Institute For Cancer Research
>
>
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