.. _sec_wrappingup: Wrapping up =========== Cleaning up your directories ---------------------------- In order to save disk space, |RELION| has an option to clean up job directories. There are two modes of cleaning: 'gentle' cleaning will only delete intermediate files from the job directory being cleaned; 'harsh' cleaning also deletes files that may be necessary to launch a new job that needs input from the job being cleaned. For example, harsh cleaning will remove averaged micrographs from a :jobtype:`MotionCorr` job, or extracted particles stacks from a :jobtype:`Particle extraction` job, while gentle cleaning will remove all files from itermediate iterations of :jobtype:`2D classification`, :jobtype:`3D classification` or :jobtype:`3D auto-refine` jobs. You can clean individual jobs from the :button:`Job actions` button; or you can clean all jobs from the 'Jobs' pull-down menu at the top of the GUI. We used the 'Gently clean all jobs' option from that menu before making a tarball of the project directory that we distributed as our precalculated results. You might want to gently clean your project directory before you put your data in long-term storage. Asking questions and citing us ------------------------------ That's it! Hopefully you enjoyed this tutorial and found it useful. If you have any questions about |RELION|, please first check the FAQ on the |RELION| Wiki and the CCPEM mailing list. If that doesn't help, use the CCPEM list for asking your question. .. attention: Please, please, please, do not send a direct email to Sjors, as he can no longer respond to all of those. If |RELION| turns out to be useful in your research, please do cite `our papers `_ and tell your colleagues about it. Further reading --------------- The theory behind the refinement procedure in |RELION| is described in detail in: - S.H.W. Scheres (2012) "|RELION|: Implementation of a Bayesian approach to cryo-EM structure determination" **J. Struc. Biol.**, 180, 519-530. - S.H.W. Scheres (2012) "A Bayesian view on cryo-EM structure determination" **J. Mol. Biol.**, 415, 406-418. A comprehensive overview of how to use |RELION| for all types of classifications is described in: - S.H.W. Scheres (2016) "Processing of structurally heterogeneous cryo-EM data in |RELION|" **Meth. Enzym.**, 579, 125-157. This tutorial does not cover multi-body refinement, which is useful to describe continuous motions in relatively large complexes. You can find a manuscript with specific instructions on how to perform multi-body refinement on the `RELION Wiki `_