Frealign

I have a problem extracting a class of particles after multi-refinement using Frealign. The multi-refinement gave three classes with about 15,000 particles in each class. But when I use merge_classes.exe to extract the thirst class of particles, I only got around 8,000 particles. Why is that?

This is the result when I run frealign_calc_stats.
1: N = 14852 Ave. OCC = 33.1751 Ave. LL = -17671.9 Ave. Score = 32.5013
2: N = 14293 Ave. OCC = 31.9257 Ave. LL = -17812.8 Ave. Score = 31.8804
3: N = 15624 Ave. OCC = 34.8992 Ave. LL = -17792 Ave. Score = 32.3776

Hi all,

I'm wondering what your preferences are (i.e. are there best practices) for generating initial Eulers. I've been using Frealign for years, but I've often wondered how much initial Eulers affect the final reconstruction. Do y'all boot off of an external program or use MODE 3 or 4?

Thanks,
Scott

Hi all,

I am experiencing a weird crash in the control script distributed with the most recent frealign version, where it submits the jobs (which run fine), waits a few minutes, then summarily crashes.

(I am running on an sge cluster)

What log files would help to diagnose the issue?

Axel

Hi, I consider trying frealign to continue to refine my 3d reconstuction after one run of relion 3d refine, I downloaded the conversion scripts and convert the data.star from last iteration to frealign par file, Now I am confusing what is the next step? which dataset I should use? where I put reference map, and which one ? what is the data format? star file or mrc file?
Please help me .
Thanks a lot,

We've been refining an icosohedral virus, and everything seems like it has been running normally, but the final map seems to have mirror symmetry along all symmetry axes... What could be causing this? The parameters we've been using are:

Control parameter file to run Frealign
======================================

This file must me kept in the project working directory from which the refinement scripts are launched.

Note: Please make sure that project and scratch directories (if specified) are accessible by all sub-processes that are run on cluster nodes.

Hello, I am new to frealign, I try to use frealing package with helical processing to refine my helical tube reconstruction. After I install Frealign v9 and downloaded helical processing part, I try to test all of scripts for helical processing, I found one file was missing in script: calc-ctftilt.amy, I don't know where it come from and how it was generated?
Please help me how to generate it.
Regards,

Hi all,

Thanks for your time and apologies if I'm just missing something simple!

I am moving over from using Relion to refine a structure with T symmetry. I'm aware that the convention for this symmetry group in Frealign is different to Relion and indeed reconstructions in Frealign are quite peculiar when imposing T symmetry, so I have something wrong. I can't figure out exactly what to do, presumably move my reference volume, but can you suggest what adjustment I should make to fit the conventions used by Frealign when coming from Relion?

Many thanks for your help!

Hello Team Frealign. I am running frealign v9.09 in search mode for a helical reconstruction, running on my mac using the bin_OSX executables. The job starts well (the new scripts are great for streamlining everything - thanks), outputting reasonable alignment parameters for many particles, but then will suddenly fail at specific particles withe a score of -100 followed by a seg fault (see the end of a log file below).

Hi,

Does the centers of particles in the output files use angstrom or pixel in frealign_v9? Thanks.

Xing

Hi everyone,

I was using frealign on our cluster this weekend and noticed that there is a small error in the submission lines for PBS clusters in "mult_search.com". Lines 217 and 219 both reference the mult_(h)refine_n.com scripts which terminates the search without producing any output. After changing both lines to the mult_(h)search_n.com scripts, everything works as expected. Maybe this change can be made in a future releases of frealign.

Best,
Thomas