Process X-ray Crystal Structures and Densities

Description

This is a utility floe which allows users to more easily run the Structural Biology Floes with densities from X-ray crystallography.

The floe has two modes: Reference Mode and Fit Mode.

In Reference Mode, given a reference dataset containing a design unit and a reference density file (in .cif or .mtz file format), the floe will map the density around the reference structure and save the density in .mrc file format.

In Fit Mode, given a reference dataset, a fit dataset, and a fit density file (in .cif or .mtz file format), the floe will find the transform that maps the fit design unit onto the reference, apply the same transform to the density, and save the mapped density as an .mrc file.

In both cases, the floe outputs a dataset containing the (transformed) design unit and the mapped density for inspection in the 3D & Analyze page.

Potential Input Sources SPRUCE - Protein Preparation

Related Floes Automated WEMD Simulation and Best Structure Search Guided by Target CryoEM Map

Limitations Currently, we only allow for mapping of one fit design unit density file at a time onto the reference design unit.

Promoted Parameters

Title in user interface (promoted name)

Reference Mode

Reference Density File (ref_density_file_input_param): Optional file containing the density associated with the reference structure (.cif or .mtz). If provided, the reference density will be mapped around the reference structure and outputted as a .mrc file. Note: If using a .cif file from the RCSB, ensure that it is the validation 2fo-fc file.

  • Type: file_in

Fit Mode

Fit Dataset (fit_dataset_input_param): Dataset containing DUs to be fit to the reference. It is recommended to use the output of SPRUCE protein preparation.

  • Type: data_source

Fit Density File (fit_density_file_input_param): Structure factor file containing the density to be mapped on to the reference structure (.cif or .mtz). Density will be mapped around the reference structure and outputted in the .mrc format, with a gap between the protein and box edges specified by the buffer parameter. Note: If using a .cif file from the RCSB, ensure that it is the validation 2fo-fc file.

  • Type: file_in