Marko Hyvonen wrote:
> Hello cooters.
>
> I am trying to compare multiple structures of similar proteins,
> in different crystal forms, and to transform the maps in a script using
> "transform-map-using-lsq-matrix" command. But I am stuck with few
> problems.
>
> This part of the script is essentially as follows:
>
> (no-coot-tips)
> (set-run-state-file-status 0)
> (read-pdb "new.pdb")
> (read-pdb "reference.pdb" )
> (auto-read-make-and-draw-maps "test.mtz")
> (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.
> . See http://www-cryst.bioc.cam.ac.uk/node/199
>
I am not authorized.
> 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?
> Also, I can't seem to find the command how to read a (ccp4) map into coot
> using a script.
http://www.biop.ox.ac.uk/coot/doc/coot.html#Read-Maps
(handle-read-ccp4-map "my.map" 0)
> All I can see is how to read it from the menu, but not the
> scripting command. Ideally I'd read in just a small map carved around the
> area of interest (and then saved).
To carve out a bit of map,
put a water (say) in a new molecule at the centre of the region (make a
note of its molecule-number)
(mask-map-by-molecule map-number water-molecule-number 1)
for some value of map-number and water-molecule-number.
Paul.
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