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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.