Notes on MRC IMAGE PROCESSING software 2000 installation.	13.02.2001
--------------------------------------------------------


	The MRC Image Processing package is currently freely available to 
academic workers, and although it is helpful if bugs are reported, no support 
or instruction is available. A list of users is kept, so please do not just 
copy the system without informing us. These notes are not completely 
comprehensive, but should assist you in the installation of the package.

	Use of the programs is described in published papers which are 
referred to in our publication Crowther, Henderson and Smith, J. Struct. Biol.
(1996) 116, 9-16. If you do require instruction from someone, the file :
image2000/doc/outside_users.doc contains a list of users, so you should find 
someone close to you and ask to visit them so that you can learn from them.


					Jude Smith. 
						jms@mrc-lmb.cam.ac.uk


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	This release has a plot library which produces postscript format files 
rather than the .plt files as in the old system which required reformatting 
before printing. 

	It is also LINUX compliant and machine architecture independent and 
provided that they were created on a matching-endian machine, the programs are 
still able to read old-style MRC Image format files. i.e. little-endian 
old-style maps can be read correctly on a little-endian (e.g. DEC/Alpha), but 
not on a big-endian computer (e.g. SGI). Old-style maps of a different 
architecture may be converted by the byte_swap_map program. Some programs need 
to write information into the header e.g. autocorrlk, backautok, and in this 
case will require new-style, architecture compatible maps. If the map is 
new-style, but architecture incompatible, or if it is old style but 
architecture compatible, then the program image_convert will correctly 
reformat them. In the case where the map is old-style and 
architecture-incompatible, then byte_swap_map followed by image_convert 
would need to be run first. Newly created files will always be written in 
the new-style format which carries a machine stamp in the header along with 
a rms deviation, a three-dimensional origin in a shifted position and 
symmetry data. 

To summarise :

Old style, different endian maps ........... no read, no write
			: use byte_swap_map followed by image_convert

Old style, compatible endian maps .......... read, no write
			: use image_convert

New style, different endian maps ........... read, no write
			: use image_convert

New style, compatible endian maps .......... read, write

The new format is 
described in more detail in :    image2000/doc/image.doc.

Although the original MRC image processing package is still available, 
upgrades will be confined to the new 2000 version. 


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1) Prerequisites
  --------------

F77  and C compilers and X11/R6 (or X11/R5).

Edit the first executable line in the file image2000/com/image.login 
to suit your system. For example, if you have loaded the uncompressed 
tar file into /disk7/public then change the line to :

  setenv IMAGE_PUBLIC /disk7/public/image2000

Edit each users .login and .cshrc to source the files image.login and 
image.cshrc needed to make the required links. In the example above, users
.login and .cshrc files should include :

  source /disk7/public/image2000/com/image.login

and 

  source /disk7/public/image2000/com/image.cshrc

respectively.


2) Installation of software :
   ------------------------

If you are running on a DEC/Alpha computer, run  :
                  ../image2000/rebuild_image_alpha
                  ../image/laserlinks

If you are running on a Silicon Graphics computer, run :
                  ../image2000/rebuild_image_sgi 

  NB : if you are installing on IRIX6.5 you will first need to edit the
         file image2000/lib/rebuild_genlib_sgi. Replace "-Olimit 1500"
         with "-OPT:Olimit=1500"

If you are running on a PC under LINUX, run
                   ../image2000/rebuild_image_linux

  NB : This version has been tested on RedHat LINUX 6.2. Higher versions
       have problems, in particular the version of XFree86 which comes with
       RedHat LINUX 7.0 has a bug which affects Ximdisp. 06.04.2001

It is wise to redirect the output to a log file and check the installation
has run to completion.

Note : If the error 'file not found' occurs, it may be necessary to type 
the following, or put it in your .login :

setenv PATH .:$PATH



3) Test the installation :
   ---------------------

First :
source ../image2000/com/image.login 
source ../image2000/com/image.cshrc

Run the command scripts in ../image2000/test  :

  a) allspace.com reads allspace.data to test allspace.exe, log file
     for comparison in allspace.log

  b) fftir.com sets up files for job2000.com which tests many programs. 
     Log files in fftir.log and job2000.log for comparison.

  c) ctfg000.com tests ctfapply which tests the plot2k routines.

  d) Helical programs can be tested by using the instructions described in 
     ../image2000/test/hlxtest_scheme

  e) Frealign is distributed with this package and can be tested by running
    ../image2000/frealign/test301.com.alpha, or if you are usingan SGI :
    ../image2000/frealign/test301.com.sgi


Notes :

If you are running on an SGI, you may need to use the command unlimit


4) Documentation :
   -------------

Documentation on the programs is found as a plain text file in :
	../image2000/doc/improc.doc


5) Man pages for laserwriter programs :
   ----------------------------------

Either read the plain text in :
	../laser/postscript/lasertext.doc
	../laser/postscript/lasertone.doc

or copy :
	../laser/postscript/lasertext.1
	../laser/postscript/lasertone.1

to e.g. /usr/local/man/man1

Note : to  make laser links correctly
cd local
ln -sf ${IMAGE_LASER}/lasertext.exe lasertext
ln -sf ${IMAGE_LASER}/lasertone.exe lasertone
