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.
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