Workflows

Automated screening monitoring workflow designed to provide real-time feedback to the microscope during data acquisition. The pipeline processes movies on-the-fly, performing motion correction, maxshift analysis, CTF estimation and consensus validation, as well as micrograph quality assessment through AI-based categorization. The workflow also includes particle picking, automatic box size estimation, particle extraction, streaming 2D classification, and 2D class quality assessment. Results are ...

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 ...

Automated image processing from movies to 2D classification. Includes quality and curator micrgographs protocols as Dose analysis, maxshift, tilt analysis, categorize micrographs, ctf consensus, also include particle curator as Remove duplicates and Deep micrograph cleaner. It also include a support branch to calculate the Box Size and train a model to pick the particles. The list of plugins required are: pwem, xmipp3, motioncorr, miffi, cistem, emfacilities, sphire, gautomatch, relion, repic

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

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

2. Receptor preparation: uses bioPython to prepare the receptor structure, removing waters, adding hydrogens and removing unnecessary chains if asked. Also, uses PDBFixer to optimize the structure if selected.

3. Protein pocket search: uses 3 different software (P2Rank, AutoSite and FPocket) for predicting the receptor ...

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using Relion.

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.

Adapting to Tilted Samples

To process tilted experiments, use ”tilted” templates. These are modified workflows tailored to handle ...

Automated image processing from movies to 3D reconstruction. Includes CTF estimation, quality filters, box size estimation, picking model training, three 2D classification jobs (25k, 50k, and 100k particles), and 3D processing of the first 200k particles. Multiple 3D models are generated without symmetry, with automatic 2D and 3D class selection, using CryoSPARC.

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using Relion.

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 ...

Automated image processing from movies to 2D classes. Includes CTF estimation, quality filters, box size estimation, training a data-specific picking model, and three 2D classification jobs (25k, 50k, and 100k particles) using Relion.