Support forum for frealix, the helical refinement program.

Frealix seems to have trouble splitting the ali file, no error message


I'm learning how to use frealix for 3D reconstructions. I'm using 3 micrographs of synthetic amyloid fibrils. I selected 14 filaments (5 points per filament). When I run this command:

./flx_wrap.rb -r 1 -f 20 -s 20 -t 20 -n 1 --threads 2 -a waypoints.ali parameter_startup.flx

then a new folder for round 00 is created, the waypoints file is copied into it, and in the terminal it says:

I, [2017-08-23 12:44:01 #6814] INFO -- flx_wrap: Thanks for using Frealix! Let's get to work...

Filament selection

Questions about the filament selection and the saved box files.

In the tutorial (Ab(40) using Frealix) on line (, it said:

"With "Select" selected on the tools window, begin by picking an endpoint. This endpoint (as shown by the green arrow) should be located along the filament near its starting end, and should not be a crossover.
Following the filament, select the next crossover points in order.
After the last crossover has been selected, pick an endpoint near the end of the filament."

Questions about Frealix

Hi guys,

I want to try Frealix to hopefully get better resolution for one set of our filament

This website did post a tutorial, Ab(40) using Frealix, however, it is
outdated file. I am wondering whether I could obtain an updated tutorial about
Frealix. In addition, may I get an example input file to Frealix and the
scripts needed in Frealix?

Thank you very much!


polarity check

Hi Alexis,

this is probably a stupid question, but how does Frealix compare different filaments in order to check if they are in the same orientation? How does Frealix know if fibrils are polar or not, so how does the polarity check work?

Thank you very much and all the best,


frealix usage

Hi Alexis,

sorry if this is kind of a beginner's question, you've probably posted the directions on how to use frealix but for the life of me I can't figure out what I'm doing wrong.

Basically, I would like to try to refine frealign parameters (obtained for microtubules) using frealix. I already have pretty good estimates, but I'm wondering whether frealix may be able to refine the parameters further, it's worth a try I think!

failed sanity check in fmc_maximise


Frealix sometimes exits with a message like:

failed sanity check in fmc_maximise

Image PC Routine Line Source
frealix 00000000004EDBBA runtime_parameter 205 runtime_parameters.f90
frealix 0000000000B5381B fmcs_MP_fmc_maxim 298 fmcs.f90
frealix 0000000000DFA00F mode_filament_ref 1937 mode_filament_refine.f90
frealix 0000000000584597 modes_MP_mode_run 63 modes.f90

Par file in refinement mode

Hi Alexis,

What should I be using for the INPUT_PAR_FILENAME in refinement mode?

I'm currently getting the error Fatal error (ImageFile::ReadSlicesFromDisk): Last < first slice when I run frealix in filament_refine mode. I'm using the waypoints file generated by the previous run I did in startup mode as the par file, but am unsure what this file is supposed to contain.


test failures

Dear Niko,
I am interested in Frealix to refine the helical maps we obtained using Egelman's SPIDER package. During the test of the Frealix1.1.0 package, there were two failures.
Sun Sep 7 11:45:41 CDT 2014 : Unit tests... passed.
Sun Sep 7 11:48:19 CDT 2014 : helical symmetrisation test (new v pdb) ... passed.
Sun Sep 7 11:48:22 CDT 2014 : helical symmetrisation test (abeta; new v pdb) ... passed.
Sun Sep 7 11:48:24 CDT 2014 : helical symmetrisation test (new v old) ... passed.
Sun Sep 7 11:48:25 CDT 2014 : apply CTF test (Frealix v EMAN2) ... failed!