img2r

• Introduction
  
• How it works
  
• Invocation
  
• Input/Output files
  
• Example
  

Introduction

How it works

1. 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).
2. The intensities of pixels from the images are added to (virtual) pixels in the reciprocal lattice
3. The resulting 3-dimensional array of (virtual) pixels is written to a file.

Invocation

• 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
  for all three axes.
• read images
  images is a list of images. Wildcharacters as * and ? are allowed, as are constructions using [], like s0[135]f* or s0[1-5]f*.
• contour name
  This will create:
  • name.cnt
    a cnt file. Basically this file consist of nz 2-dimensional arrays of ny*nx pixels.
  • name.coot
    A coot script which will load the density maps and sets various parameters. You may want to edit this file later.
  • name.rmc
    This file describes the corresponding cnt file. It contains
    • thmax, as used in img2r
    • lambda, the wavelength used in the datacollection
    • scale, the scale factor to map pixel numbers in the cnt file to reciprocal values.
    This file can be used by rmat2pdb, which converts rmatfiles to pdb files .
• exit
  Done.

Input/Output files

Input Files

Output files

• name.cnt
• name.coot
• name.rmc

Example