Refine single model to high resolution

After 3D classification, open the model.star file corresponding to the final iteration using Relion -> Display.

Select a homogenous class, right click the class, and then save the selected class as a star file.

This has been done already, and it is located:

Class3D/run1_ct13_it025_data_class1_and3.star

Now you can submit a Relion 3D auto-refine job with this class. In this example, the last iteration 3D class was provided as the reference and filtered to 40 Angstroms. The script is run_3DRefine.run:

#!/bin/bash

#$ -cwd
#$ -S /bin/bash
#$ -pe orte 256
#$ -q all.q
#$ -V
#$ -N run_3DRefine

mpirun relion_refine_mpi --o Refine3D/run1 --auto_refine --split_random_halves --i Class3D/run1_ct13_it025_data_class1_and3.star --particle_diameter 350 --angpix 1.77 --ref Class3D/run1_ct13_it025_class001.mrc --ini_high 50 --ctf --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale  --j 1 --memory_per_thread 4 --dont_combine_weights_via_disc 

My final resulting volumes can be found:

Refine3D/