(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
(corrected permssions, sorry about that)
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.
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. Can I centre on a residue or
calculate a centre from a set of atoms? Also, is the lsq matrix from the
transform-map-using-lsq-matrix stored anywhere, and can I use it for other
transformations?
(handle-read-ccp4-map "my.map" 0)
Aah, of course. Thanks.
Marko
_____________________________________
Marko Hyvonen
Department of Biochemistry, University of Cambridge
[email protected]
http://www-cryst.bioc.cam.ac.uk/groups/hyvonen
tel: +44-(0)1223-766 044/760 468
mobile: +44-(0)7796-174 877
fax: +44-(0)1223-766 002
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