Note - this program is normally run via the EMAN2 Project Manager.

This program will take various files, parameters, and meta data from a completed eman2 refinement and generate a card input file for FreAlign, a particle meta data file, a 3D map that is the refinement from eman2, and a 3D particle stack (along the z axis) that contains all of the boxed particles used in the refinement. It will create a directory called frealign_xx and put all of these files into the newly created directory.

The user must select a threed_filt_xx file as the input map for the frealign refinement.

The values for the low and high resolution data (reslow and reshigh respectively) to be included in the refinement are very important. These values represent what data in your particles are used for alignment. Setting the high value (note it is a low number, for example 15) denotes up to what value data is used. Too low of a number (for example 8) means that you are using up to 8 Angstrom data to align your particles, which in a lot of cases 8 Angstrom data is noise. Aligning your particles using noise is not a wise choice.

The resolution reconstruction value (rrec) indicates what value the reconstruction is calculated out too. Setting this value to a very high resolution (note, very low number) can lead to the final model being over filtered and incorporating a lot of noise. Too low resolution (note, high number) can cause your model to not be filtered enough, resulting in high resolution data and features being omitted.

For example: My data goes down to 8.5 Angstrom according to EMAN2. I choose 15 as reshigh, 150 as reslow, and 8 as rrec.

Helpful Links:


FreAlign Webpage

Program Options:



show program's version number and exit




show this help message and exit



(T/F)Apply extra real space symmetry averaging and masking to beautify final map prior to output



(T/F)Apply FOM filter to final reconstruction using function SQRT(2.0*FSC/(1.0+FSC))



(T/F)Calculate additional statistics in resolution table at end (QFACT, SSNR, CC, etc.). T Uses more than 50% more memory.



Resolution of reconstruction in angstroms. It is the resolution to which the reconstruction is calculated.



Resolution of the data included in the alignment. This is the low resolution value. ex:200



Resolution of the data included in the alignment. This is the high resolution value. ex:25



Phase Residual cutoff. Particles with a higher phase residual will not be included in the refinement. Useful to sort out bad particles you have labeled as having a high phase residual.

EMAN2/Programs/e2refinetofrealign (last edited 2013-07-09 20:44:50 by StephenMurray)