+-----------+
			+  Lattice  +
			+-----------+

This package contains the necessary programs to calculate the average
reciprocal unit cell from diffraction data. The average reciprocal unit
cell can be visualized as an electron density map and used to verify 
the lattice, compare resolution bins, examine the spot shape and other
systematic features.

The package consists of a c++ program (lattice_calc), the source 
code and several associated shell- and perl-scripts to prepare
input files, electron density maps and script files for PyMOL.

The associated shell and perl-scripts can be freely modified or extended
to fit individual users need. If modifications are judged to be of benefit
to a wider community please forward the necessary information to the author.

*****************************************************************
menu/lattice_README has description of how to run the programs,
keywords for input files etc
*****************************************************************


INSTALLATION:
 The directory "menu" contains all the necessary scripts and
   executables. For normal use the following alias for the text based
   interface is useful an could be included in the setup 
   (.cshrc, .tcshrc or similar):

 alias lattice 'perl MYPATH/menu/lattice_menu.pl'

  lattice_menu.pl has a definition of the environment lat_home which
  NEEDS TO BE MODIFIED to the local settings

 The source files are present in LINUX/ in case the included binary
   (lattice_calc) has to recompiled. For now other UNIX variants have not
   been tested. If necessary recompilation of lattice_calc can be done:

 cd LINUX
 g++ Lattice01.C -o ../menu/lattice_calc


FOLLOWING PROGRAMS NEED TO BE AVAILABLE:
  mapman, perl, grep, more and nice


LIST OF PROGRAMS IN menu/:
 lattice_calc   
	Calculates the grid based on an input file
 lattice_default.dat
	A default input file
 lattice_denzo.sh
	Shell script for creating two input files from a denzo
	instruction file
 lattice_grid2map.pl
	Convert a grid to an electron density map in XPLOR-format
 lattice_grid_faces.pl
	Add faces to the grid
 lattice_grid_spotshape.pl
	Double the grid in three directions
 lattice_mapman.sh
	Normalize an XPLOR-formated electron density map
 lattice_menu.pl
	Main menu, provides a text based interface to other programs
 lattice_pymol.pl
	Make a PyMOL script
 lattice_README
	Help file with more detailed description of programs


RUNNING THE PROGRAMS:
 If the variable lat_home is set (setenv lat_home MYPATH/menu/) all
   the scripts and programs are accessible directly (example:
   $lat_home/lattice_calc input.dat my.grid).


LIMITATIONS
 Supported detectors: APS3000 (Q315 with 9 ccd chips), QUANTUM4 (with
   4 ccd chips) and RAXIS-IV.
 Unsupported detectors: Please contact the author. If an image and
   experimental details can be made available the detector can quickly
   be tested and included in the list of supported detectors.
 Rhombohedral lattices: This setting is still being tested.


ACKNOWLEDGEMENTS:
 The Authors of Mosflm wrote the code that has been adapted to read 
   all pixels and calculate an HKL-value for each pixel. 
 Mosflm has been developed by the Computational Biology group in the 
   Department of Biological Sciences at Purdue University, W. Lafayette,
   IN by Ingo Steller and Michael G. Rossmann.

 The help and discussions with Michael Sawaya, Duilio Cascio and Todd Yeates
   are also greatfully acknowledged.


REFERENCES:
 In preparation.


Carsten Ryttersgaard
UCLA, January 2004