Reconstruct particle

The Reconstruct particle job generates a reference map from a particle set by averaging the particles using positions and orientations given in the input particles file. This reference map will then be used for further processing in 3D auto-refne, 3D classification, CTF refinement or Bayesian polishing.

Continuing the tutorial, we will now generate a first 3D reference map using the particles obtained by the previous Extract subtomos job at bin 6.

Running the job

Select the IO tab from the Reconstruct particle jobtype.

Input optimisation set::

Extract/job010/optimisation_set.star

OR: use direct entries::

No

Input particle set::

Input tomogram set::

Input trajectory set::

On the Average tab, make sure the following is set to reconstruct particles with a binning factor of 6:

Binning factor::

6

Box size (binned pix)::

192

Cropped box size (binned pix)::

96

Wiener SNR constant::

0

Symmetry::

C6

On the Running tab, set:

Number of MPI procs::

5

Number of threads::

12

Note that reconstructing from 2D tilt series relion_tomo_reconstruct_particle program has 3 thread arguments. The number of threads provided here sets both --j and --j_out arguments so, to avoid exceeding the available memory resources, the --mem argument should also be set using around 80-90% to keep a safety margin. In our system, we ran 1 MPI process per cluster node (64Gb) so we added:

Additional arguments::

--mem 50

Using the settings above, this job took less than 5 minutes on our system.

Analysing the results

You can look at the output map Reconstruct/job011/merged.mrc with a 3D viewer like UCSF chimera. When random halfsets are specified in the input particles file via the rlnRandomSubset field, the two halfmaps half1.mrc and half2.mrc are also generated.