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.
