img2r is a program which reads a set of images,
converts all pixels to points in reciprocal space, sums all the
intensitites and creates a so-called cnt file.
This file can be displayed with the contour
command in view.
The file can also be converted by
a CCP4 density map which in its turn can be displayed with
- img2r reads the images. Every pixel is
assumed to be the
impact of an outray of the diffaction experiment. Using the settings
of the goniostat and the position and orientation of the detector,
every outray can be transformed to a reciprocal lattice vector.
This vector lives in the laboratory system ( x pointing to xray source,
z pointing up (zenith) and y completing the righthanded coordinate system).
- The intensities of pixels from the images are added to (virtual) pixels
in the reciprocal lattice
- The resulting 3-dimensional array of (virtual) pixels is written to
You will need a file distorpol.vic to describe the
distortion of the detector. This file can be created using the program view:
view read imagename save distorpol = exit
If a file detalign.inp exists, it will be used by img2r
- thmax f
Sets the maximum resolution to f degrees.
- maxdim n
Sets the dimension of the reciprocal map. The result will be
a map of -n:n
all three axes.
- read images
images is a list of images.
Wildcharacters as * and ?
are allowed, as are constructions using , like s0f* or s0[1-5]f*.
- contour name
This will create:
a cnt file. Basically
this file consist of nz 2-dimensional arrays of ny*nx pixels.
A coot script which will load the density
maps and sets various parameters. You may want to edit this file later.
This file describes the corresponding cnt file. It contains
This file can be used by rmat2pdb, which
converts rmatfiles to pdb files .
- thmax, as used in
- lambda, the wavelength used in
- scale, the scale factor to map
pixel numbers in the cnt file to reciprocal values.
images, for example s01f0001 s01f002...
from images to density map
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