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 found here.

Linux:

1) 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: 
 <code>
 cd /home/username/frealign_v8.09/src
 make -f Makefile_linux
 </code>
 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) 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) Download the windows executable here.

Bug fix version of e2runfrealign.py for EMAN2 workshop 2011 Download here.