Biowulf High Performance Computing at the NIH

Sidesplitter reduces over-fitting in both idealised and experimental settings, while maintaining independence between the two sides of a split refinement. It can improve the final resolution in refinements of structures prone to severe over-fitting, such as membrane proteins in detergent micelles.

Important Notes

Sidesplitter can also be used in tandom with RELION v3.1:

# Usage:
# path/to/
# To use from RELION 3.1, set the RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE environment variable to point to this script,
# set SIDESPLITTER to point to the sidesplitter binary (or make sure sidesplitter can be found via PATH), and run
# relion_refine with the --external_reconstruct argument. For example:
#     export SIDESPLITTER=/path/to/sidesplitter
# then run RELION auto-refine from the GUI and put "--external_reconstruct" in the additional arguments box. To run on
# a cluster, depending on your configuration you might need to put the environment variable definitions into your
# submission script.

# Troubleshooting
# If you have problems running SIDESPLITTER using this script, the first thing to check is that external reconstruction
# from RELION is working correctly. Try running a normal refinement job, using the "--external_reconstruct" argument
# but without setting the RELION_EXTERNAL_RECONSTRUCT_EXECUTABLE environment variable. If this fails, the problem is
# likely to be with your RELION installation - perhaps it is the wrong version, or different installations are
# conflicting with each other. If normal external reconstruction is successful, the problem is likely to be with the
# SIDESPLITTER installation, or a bug in this script.

# How this script works:
# If the target file name contains "_half", this script assumes two copies of itself will be running (for the two half
# data sets). The two copies will coordinate with each other by creating, checking for and deleting a directory called
# "sidesplitter_running". Both scripts will run relion_external_reconstruct for their given half data set. The first
# script will wait for both reconstructions to finish, then call SIDESPLITTER to process both half maps. The second
# script will wait for the first to finish running SIDESPLITTER and then exit (because if either of the scripts exits
# before the processing is finished, RELION moves on and tries to continue its own processing before the filtered
# volumes are ready).
# If the target file name does not contain "_half", this script assumes there is only a single copy of itself running.
# In this case it call relion_external_reconstruct, waits for the reconstruction to finish and then exits.
# This handles the final iteration when the two half sets are combined, at which point RELION calls the external
# reconstruction program just once to reconstruct the final combined volume.
# Note that this script is not particularly robust. If one of the commands fails, it's possible you might need to
# manually tidy up the job directory and remove the "sidesplitter_running" directory to avoid problems in the next run.

For use with the GUI as detailed above, before launching the GUI

module load RELION sidesplitter

Then within the Running tab for a refinement run:

Additional arguments
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load sidesplitter

[user@cn3144 ~]$ OMP_NUM_THREADS=$SLURM_CPUS_ON_NODE sidesplitter --v1 half_map1.mrc --v2 half_map2.mrc --mask mask.mrc

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

set -e
module load sidesplitter
OMP_NUM_THREADS=$SLURM_CPUS_ON_NODE sidesplitter --v1 half_map1.mrc --v2 half_map2.mrc --mask mask.mrc

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]