Frealix is a program for the refinement of helical filament reconstructions from cryo electron micrographs. It is primarily used to process images of amyloid fibrils, though it has also been tested on TMV and actin filaments.

References:

• Rohou, A, Grigorieff N. 2014. Frealix: model-based refinement of helical filament structures from electron micrographs J Struct Biol. 186:234–244.

• Frealix Main Site
• Frealix Tutorial

• Module Name: frealix (see the modules page for more information)
• Interactive use only
• Environment variables set
  • FREALIX_EXAMPLES
• Example files in $FREALIX_EXAMPLES

Frealix is a specific tool to be used along with other cryo-EM applications like EMAN2 and RELION

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load frealix
[user@cn3144 ~]$ frealix parameters.flx
                  ** Welcome to Frealix **

                      Version: 0.0.0          
                 SVN revision: 1201
                   Build date: Jan 02 2013
               Debug symbols?: No
 
             Control filename: test.flx
 
   User name (home directory): user (/home/user)
            Working directory: /lscratch/46116226
                 Command line: frealix test.flx
                    Host name: cn1995
           Host, machine type: ,
  OpenMP threading available?: Yes
 Max number of OpenMP threads: 56
         Number of processors: 56
  Nested threading available?: No
 
                  Date & time: 2018-01-03 01:03:31
 
Frealix will run its CALC_FSC mode
Frealix is running in its CALC_FSC mode
Mode description: Add description here
Run-time parameters:
                                 Key                                         Value Set by user? Description                                                     
                      INPUT_VOLUME_1                          2OM3_200_h_200_m.mrc            T Input volume 1                                                    
                      INPUT_VOLUME_2                         3drec_straight_hm.mrc            T Input volume 2               

...

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$