== Frealign ==
=== Overview ===
[[http://emlab.rose2.brandeis.edu/frealign|Frealign]] is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles,
originally developed at the MRC/LMB. It is now developed and maintained by the Grigorieff lab at Brandeis. 

The main Frealign documentation can be [[ http://emlab.rose2.brandeis.edu/sites/default/files/readme_frealign.txt|found here]].

=== Installation ===
'''Linux:'''

1)   [[http://emlab.rose2.brandeis.edu/frealign|Download Frealign here]]

2)   Move the Frealign tar file to your desired installation location

 . ex.   mv frealign_v8.09_######.tar.gz   /home/username/

3)   Untar Frealign: tar -xvf frealign_v8.09_######.tar.gz

4)   In your .bashrc, include the command:

 . export PATH=/home/username/frealign_v8.09/bin:$PATH

5) Frealign is ready to be run. From the command line:

 . frealign_v8.exe
6) '''''Note:''''' the frealign_v8.exe you downloaded is a 64 bit Linux executable. 
   If you are running a 32 bit Linux, you have to compile a 32 bit version of frealign by yourself.
   The compilation of frealign is pretty simple and straight forward. 
   First, make sure you have gfortran installed for your system, then: 
   {{{
   cd /home/username/frealign_v8.09/src
   make -f Makefile_linux
   }}}
   It will compile a new frealign_v8.exe and replace the old one.

'''OSX:'''
Since the Mac doesn't come with a Fortran compiler, we include a binary courtesy of Chuck Sindelar
in Dr. Grigorieff's lab.

1) [[attachment:frealign_mac_2256.tar|Download Frealign here]]

2) chmod a+x the frealign executable if it is not already execute permissed

3) move frealign to a folder in your path or add this to your .profile
      export PATH=/place_you_put_frealign:$PATH

     example:   export PATH=/Applications/frealign_mp_2256:$PATH

'''Windows:'''
Dr. Grigorieff has kindly made a windows executable available for download, since establishing a Fortran build environment
on Windows is not for the faint of heart.

1) [[attachment:frealign_2256.exe|Download the windows executable here]].

'''Bug fix version of e2runfrealign.py for EMAN2 workshop 2011'''
[[attachment:runfrealign.py|Download here]].