This section describes the relion tutorial jobs workflow: input parameters, explanation, expected results.
The RELION tutorial consists of 29 jobs of various types. To make our simplified tutorial more understandable, we consider each job as an independent step.
The visualization of the tutorial workflow represented below.
- Solid arrows show explicit data interconnectivity between steps. For example, the output data of the
CtfFind/ctffindis the input data of theExtract/LoG_based. - Bold solid and dashed arrows represents a transition between step chapters.
- Dashed arrows show implicit data interconnectivity between steps. For example, parameters calculated during the
AutoPick/optimize_paramsstep become input values for theAutoPick/template_basedstep. - The first and the last steps marked with the purple color.
Each step description subunit of this simplified RELION tutorial includes the following parts.
- Navigation block that looks like the example below
| Tutorial Unit | 1.2 Beam-induced motion correction |
|---|---|
| Previous Step | (1) Import/movies |
List of jobs that will become an input for the current step. ~ prefix means that relation is implicit. |
|
| Step Alias | (2) MotionCorr/own |
| The name for the current task (JobType/alias). It is recommended to set this alias to a completed job of the current step | |
| Next Step | (3) CtfFind/ctffind |
List of jobs that will use the output of the current step as input. ~ prefix means that relation is implicit. |
- Recommended parameters table. It looks like the one below. Note that the parameters are similar to the original RELION tutorial at ~95% and some of them differ.
| Field name | Field value |
|---|---|
| I/O | I/O (Name of tab in parameters input section of RELION GUI) |
| Input files (Name of parameter) | Movies/*.tiff (Value of parameter) |
| Node type | 2D micrograph movies [*.mrcs, *.tiff] |
- Explanation text for the step with pictures and screenshots.
Remember that each step represents a single job only. At some steps, you also need to run terminal applications and Chimera as well.
Some job types support parallel execution via message passing interface, or MPI. The table below describes the relation of each tutorial step to the MPI and how long a particular job running.
| N | Name | Uses MPI | Running time |
|---|---|---|---|
| 1 | Import/movies |
No | instantly |
| 2 | MotionCorr/own |
No | fast |
| 3 | CtfFind/ctffind |
Yes | fast |
| 4 | ManualPick/illustrate_only |
No | instantly |
| 5 | Select/5mics |
No | instantly |
| 6 | AutoPick/LoG_based |
Yes | fast |
| 7 | Extract/LoG_based |
Yes | fast |
| 8 | Class2D/LoG_based |
Yes | slow |
| 9 | Select/template4autopick |
No | instantly |
| 10 | AutoPick/optimize_params |
Yes | slow |
| 11 | AutoPick/template_based |
Yes | average |
| 12 | Extract/template_based |
Yes | average |
| 13 | Sort/after_autopick |
No | fast |
| 14 | Select/after_sort |
No | instantly |
| 15 | Class2D/after_sorting |
Yes | slow |
| 16 | Select/class2d_aftersort |
No | instantly |
| 17 | InitialModel/symC1 |
Yes | fast |
| 18 | Class3D/first_exhaustive |
Yes | slow |
| 19 | Select/class3d_first_exhaustive |
No | instantly |
| 20 | Extract/best3dclass_bigbox |
Yes | average |
| 21 | Refine/first3dref |
Yes | slow |
| 22 | MaskCreate/first3dref |
Yes | fast |
| 23 | PostProcess/first3dref |
No | fast |
| 24 | CtfRefine/ctfrefine |
Yes | fast |
| 25 | Polish/train |
No | slow |
| 26 | Polish/polish |
No | slow |
| 27 | Refine3D/polished |
Yes | slow |
| 28 | PostProcess/polished |
No | fast |
| 29 | LocalRes/polished |
No | fast |
Note that:
- The maximum useful number of MPI processes for all jobs that expect micrograph STAR files as input is the number of micrographs in a file, 1 MPI process per micrograph.
- MPI workflow in the "3D Refine" job type is
1 master+2 sets of slaves, so it is recommended to use an odd number of processes that greater than or equal to3.
All the preparations passed now, and we can proceed with the tutorial.
| ← 3 RELION Jobs | Top Page | 4.1 Prepare Input Data → |
|---|