Notes on MRC IMAGE PROCESSING software 2010 installation.	05.05.2011
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	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 publications Crowther, Henderson and Smith, J. Struct. 
Biol. (1996) 116, 9-16 and Smith, J. Struct. Biol. (1999) 125, 223-228.

If you do require instruction from someone, the file :
image2010/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.
However do contact me if you have problems you cannot solve this way.


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


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

. Any version of the LINUX operating system, 32-bit or 64-bit.

. G77 or GFORTRAN

. C compilers 

. X11/R6 (or X11/R5).  Ximdisp requires a 24-bit TrueColor visual and around 
  1.2GB virtual address space to run. Machines with insufficient memory will 
  need to have increased swap space.

. Edit the first two executable lines in the file image2010/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/image2010

. 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/image2010/com/image.login

  and 

  source /disk7/public/image2010/com/image.cshrc

  respectively.

Note : if you are running on a 32-bit LINUX machine, files > 2GB cannot be read.


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

If you are running on a PC under LINUX with a G77 compiler, run
                   ../image2010/rebuild_image_g77
or for a GFORTRAN compiler :
                   ../image2010/rebuild_image_gfortran



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 ../image2010/com/image.login 
source ../image2010/com/image.cshrc

Run the command scripts in ../image2010/test  :

  a) allspace.com reads allspace.data    17 2    56.33655    15.96894
     to test allspace.exe, log file
     for comparison in allspace.log

  b) fftir.com sets up files for job2010.com which tests many programs. 
     Log files in fftir.log and job2010.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 
     ../image2010/test/hlxtest_scheme


You may need to use the command unlimit, fftrans now has a very large array. If 
this program fails with a segmentation fault, you can try increasing memory or
swap space but you may have to reduce the array parameter ARRMXSIZ. Try changing :

               PARAMETER (ARRMXSIZ=256000000)
to
               PARAMETER (ARRMXSIZ=37000000)

before re-compiling/linking.


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

Documentation on most of the programs is found as a plain text file in :
	../image2010/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


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 The package is LINUX compliant and machine architecture independent and 
provided that they were created on a matching-endian machine, the programs are 
also able to read old-style MRC Image format files (pre-2000). i.e. little-endian 
old-style maps can be read correctly on a little-endian but not on a big-endian 
computer. 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 format is 
described in more detail in :    image2010/doc/image.doc.



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Ximdisp problems :

Mac/OSX
-------
There are no borders to the menu and label windows. This is due to the window
manager and cannot be modified.

Ubuntu
------
It may be necessary to update your system :
sudo apt-get update
sudo apt-get install xfs
sudo aptitude install csh

Some versions of Ubuntu do not have the Athena widget version 7 and some other
software installed : 
System - Administration - Update Manager, Install updates.
   "          "           Synaptic Package Manager
                             X11/Xaw 
                             GL
                             M4

You will need to be running csh or tcsh as the software will not run under bash.
