Re: [COOT] Transforming maps

[Paul Emsley]

Marko Hyvonen wrote:

(transform-map-using-lsq-matrix 1 "A" 1 200 0 "A" 1 200 2 (molecule-centre 1) 10)

All seems to go fine, except that the map matches correctly only part of the transformed molecule, and it looks like when the map is extended by symmetry, things fail

Yes, the transformed map only makes sense 10A around the centre of molecule 1.

Make sense, but it does not quite do the correct thing. If I use:

(read-pdb "test.pdb")
(read-pdb "reference.pdb" )
(auto-read-make-and-draw-maps "test.mtz")

(transform-map-using-lsq-matrix 1 "A" 118 349 0 "A" 118 349 2 (molecule-centre 1) 10)

(set-rotation-centre 34.07    26.71   0.6102)# centre of molecule 1

the result is: http://www-cryst.bioc.cam.ac.uk/node/199

still can't see anything (other than window dressing).

This is centred on the point around which the map is created (based on coot output), and you can see clearly density is lacking from one side of the image, very close to the centre.

that sound like the radius is too big.

I am sure there is trivial solution to this, but I can't think of it now.

Use a bigger radius? Dynamically set the position to which you transform maps?

Dynamically? Me? That would be great.

Hmm...

Can I centre on a residue or calculate a centre from a set of atoms?

Yes.

go-to-atom-chain-residue-atom-name

molecule-centre

Also, is the lsq matrix from the transform-map-using-lsq-matrix stored anywhere,

No, sadly not.  It returns the new molecule number of the map.

You can generate an lsq matrix using:

(clear-lsq-matches)
(add-lsq-match bla bla..)
(define my-matrix (apply-lsq-matches imol-ref imol-mov))

and can I use it for other transformations?

Yes, indeed.