Workflows

Image processing from movies to micrographs, including CTF estimation and quality filters for image curation.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle high drift and lower resolution commonly observed in tilted samples. Key adjustments include:

• Motion Correction Filters: Max per-frame shift = 30; Global drift = 120.

• CTF Consensus Filters: Adapted to 6.5 Å and 8.5 Å resolution cutoffs.

• **Defocus ...

Image processing pipeline from movies to micrographs, including CTF estimation and quality filters for image curation.

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 the most basic Virtual Drug Screening Pipeline to import a set of small molecules and dock them to an imported protein structure.

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.

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

…

Combination of methods

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

Advantages: 

• Control of ...