A collection of image processing templates designed to support data collection and automated processing for Single Particle Analysis (SPA) in cryo-electron microscopy. The workflows range from simple pipelines—including movie alignment, CTF estimation, and quality assessment—to fully automated 2D and 3D processing. Please select the workflow that best suits your needs.

A set of generic and automatic workflows designed to: 

• Run on-the-fly and unattended.

• Maintain robust stability for a wide range of samples.

• Covers steps from movies to CTF estimation (for the moment).

• Monitor the acquisition process and provide user feedback.

• Comprise three proposed workflows, each with an additional layer of complexity.

This workflows contains a pipeline in Scipion that performs the following steps:

1.1) Import small molecules: introduces a set of small molecular structures in the pipeline as prospective ligands

1.2) Import atomic structure: introduces a protein atomic structure in the pipeline as receptor.

2.1) Ligand preparation: uses RDKit to prepare the small molecules optimizing their 3D structure.

2.2) Receptor preparation: uses bioPython to prepare the receptor structure, removing waters, adding hydrogens ...

This workflow performs a basic Virtual Drug Screening Pipeline. THe workflows uses the following protocols: 1.a) Import receptor: Imports the atomic structure with PDB code 4ERF. 1.b) Import small molecules: Imports a set of 4 molecules from local files. 2.a) Receptor preparation: selects A chain and cleans the structure from waters and heteroatoms 2.b) RDKit Molecules preparation: adds hydrogens and prepares the molecules for docking 3.a) Find pockets: uses P2Rank to predict the most promising ...

The ultimate-level complexity workflow is one among a collection of workflows designed to address tasks up to CTF estimation. In addition to the functionalities provided by layer 0 and 1 workflows, this workflow aims to enhance the quality of both acquisition images and processing.

Quality control protocols

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Combination of methods

• CTF consensus
• New methods to compare ctf estimations
• CTF xmipp criteria (richer parameters i.e. ice detection)

Advantages: 

• Control of ...

The second-level complexity workflow is one among a collection of workflows designed to address tasks up to CTF estimation. In addition to the functionalities provided by the layer 0 workflow, this workflow aims to enhance the quality of acquisition images using quality protocols.

Quality control protocols

• Movie max shift: automatic reject those movies whose frames move more than a given threshold. 

• Tilt analysis: quality score based in the Power Spectrum Density (astigmatism and ...

The simplest workflow among a collection of workflows intended to solve tasks up to CTF estimation.