Diff for "Ws2011/Frealign"

Differences between revisions 2 and 6 (spanning 4 versions)

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 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

OSX:

1) Download FreAlign from the above link.

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

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

3) Unzip FreAlign: tar -xvf frealign_v8.09_######.tar.gz

4) You will need a fortran compiler installed on your Mac.

5) Change to the source directory in your frealign installation directory:

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

Windows: Dr. Grigorieff has kindly made a windows executable available for download, since establishing a Fortran build environment on Windows is

-  ⇤ ← Revision 2 as of 2011-03-07 21:09:09 → 
  Size: 747
  Editor: StephenMurray
  Comment: Updating For Workshop
+   ← Revision 6 as of 2011-03-08 13:41:42 → ⇥
  Size: 1630
  Editor: SteveLudtke
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
-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.
-Line 5:
+Line 6:
-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]].
-Line 12:
+Line 11:
-)   Download FreAlign from the above link.
+)   [[http://emlab.rose2.brandeis.edu/frealign|Download FreAlign here]]
 Line 14:
-           ex.   mv frealign_v8.09_######.tar.gz   /home/username/
3)   Unzip FreAlign: tar -xvf frealign_v8.09_######.tar.gz
+ . ex.   mv frealign_v8.09_######.tar.gz   /home/username/

3)   Untar FreAlign: tar -xvf frealign_v8.09_######.tar.gz
-Line 17:
+Line 20:
-                  export PATH=/home/username/frealign_v8.09/bin:$PATH
+ . export PATH=/home/username/frealign_v8.09/bin:$PATH

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

 . frealign_v8.exe

OSX:

1) Download FreAlign from the above link.

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

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

3) Unzip FreAlign: tar -xvf frealign_v8.09_######.tar.gz

4) You will need a fortran compiler installed on your Mac.

5) Change to the source directory in your frealign installation directory:

 . 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


Windows:
Dr. Grigorieff has kindly made a windows executable available for download, since establishing a Fortran build environment
on Windows is