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!
I've tried using the ruby script you recommended (flx_wrap.rb), but I always get errors because I don't quite understand how to specify the input in a way frealix understands.
First of all, and very simply, I don't understand how I'm supposed to specify micrograph names, and I don't understand what the structure of the other inputs (i.e. ctffind input, is it supposed to be all ctf files or a list of the ctf-files or what? same goes with boxes). When I use wildcards (i.e. *) frealix complains with this message:
**ERROR(filename_wild_find_qmarks): cannot find question mark in filename my_micrographs/14oct28a_*en-a.mrc
Fatal error in FILENAME_WILD_FIND_QMARKS
but then when I try using question marks, frealix tries to assume a naming convention for my micrograph which doesn't necessarily correspond to how the micrographs are named, so it complains that the micrographs don't exist.
i.e. here is the top of my frealix file:
FILM_SELECTION 1 # just for testing
TWIST_PER_SUBUNIT -27.688 #0.769 #degrees
RISE_PER_SUBUNIT 9.52 #4.7 #in Angstroms
FAL_WPS_IN_SCORE T # Whether the first and last segments of the filament should be included in the scoring function
and then the output:
**ERROR(mode_filament_startup): file does not exist: my_micrographs/14oct28a_00001sq_v01_0????hl_0????en-a.mrc
Fatal error in MODE_FILAMENT_STARTUP
am i supposed to follow some sort of naming convention for my input files?
is there a better way to convert frealign parameters into frealix input? sorry if i missed this information somewhere else.