Confusion running misalignment correction #15
Description
Hi!
So I have a small confusion with regards to running misalignment correction with relion. In the tutorial, it is described that using the Relion GUI, an additional arguments should be added to run the misalignment. However, a command line
“ mpirun -np 5 which relion_refine_mpi --o Refine3D/job001/run --auto_refine --split_random_halves --i job025_tutorial.star --ref HA_reference.mrc --firstiter_cc --ini_high 10 --dont_combine_weights_via_disc --preread_images --pool 30 --pad 2 --ctf --particle_diameter 170 --flatten_solvent --zero_mask --solvent_mask mask.mrc --solvent_correct_fsc --oversampling 1 --healpix_order 2 --auto_local_healpix_order 5 --offset_range 5 --offset_step 2 --sym C3 --low_resol_join_halves 40 --norm --scale --j 4 --gpu "" --external_reconstruct --keep_lowres --pipeline_control Refine3D/job001/”
was also given, specifying input particles, mask, references map, and even the output directory, which is not needed in Relion GUI since the program will automatically generate the directory. Does that mean you run the misalignment as a commandline on terminal not in the GUI? I thought all the commands would go to the “additional arguments” in the GUI. Please help me clarify. Thanks.