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FreAlign is a software suite for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles. [[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.
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You can download FreAlign here: http://emlab.rose2.brandeis.edu/frealign

And view the FreAlign documentation here: http://emlab.rose2.brandeis.edu/sites/default/files/readme_frealign.txt		 The main Frealign documentation can be [[ http://emlab.rose2.brandeis.edu/sites/default/files/readme_frealign.txt|found here]].
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Linux: '''Linux:'''
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1) Download FreAlign from the above link. 1) [[http://emlab.rose2.brandeis.edu/frealign|Download Frealign here]]
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2) Move the FreAlign tar file to your desired installation location 2) Move the Frealign tar file to your desired installation location
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3) Unzip FreAlign: tar -xvf frealign_v8.09_######.tar.gz 3) Untar Frealign: tar -xvf frealign_v8.09_######.tar.gz
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5) FreAlign is ready to be run. From the command line: 5) Frealign is ready to be run. From the command line:
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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.
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OSX: '''OSX:'''
Since the Mac doesn't come with a Fortran compiler, we include a binary courtesy of Chuck Sindelar
in Dr. Grigorieff's lab.
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1) Download FreAlign from the above link. 1) [[attachment:frealign_mac_2256.tar|Download Frealign here]]
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2) Move the FreAlign tar file to your desired installation location 2) chmod a+x the frealign executable if it is not already execute permissed
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 . ex. mv frealign_v8.09_######.tar.gz /home/username/ 3) move frealign to a folder in your path or add this to your .profile
      export PATH=/place_you_put_frealign:$PATH
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3) Unzip FreAlign: tar -xvf frealign_v8.09_######.tar.gz      example: export PATH=/Applications/frealign_mp_2256:$PATH
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4) Ensure you have the fortran compiler installed. '''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.
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5) Change to the source directory in your frealign installation directory: 1) [[attachment:frealign_2256.exe|Download the windows executable here]].
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 . cd /home/username/frealign_v8.09/src

6) Use the appropriate Makefile. Assuming you are using the Intel 64-bit x86:

 . make -f Makefile_OSX_86-64_intel		 '''Bug fix version of e2runfrealign.py for EMAN2 workshop 2011'''
[[attachment:runfrealign.py|Download here]].

Frealign

Overview

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.

Installation

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: 
       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) 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.

Ws2011/Frealign (last edited 2011-03-16 18:31:32 by gtang)