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Ramachandran Analysis (version 1.0.0+galaxy0)

DCD/XTC trajectory input:

PDB/GRO input:

Segment ID of the protein:

A valid segment ID selection for the current molecular system

Groupby analysis:

Optional, create a groupby of the selection using residue name or id

Residue Name:

Optional, choose a residue name to refine the selection, e.g. ALA

start Residue ID:

Optional, choose a residue ID to refine the selection, e.g. 5

end Residue ID:

Optional, choose a residue ID to refine the selection, e.g. 10

What it does

Creates a Ramachandran plot for proteins. All protein [φ,ψ] angles for a given segment ID are automatically selected for an entire trajectory and an averaged Ramachandran plot is returned. Optionally the selection can be refined by residue ID or residue name. Optionally the average Ramachandran plot can be deconvoluted and returned grouped by residue name or residue ID.

Input

Structure file (PDB)

Trajectory file (DCD).

Segment ID

Optionally: Group data by residue name or residue ID

Optionally: refine selection by residue ID range or residue name (e.g. ALA)

Note that a MDAnalysis 'segment' is a larger organizational unit, for example one protein or all the solvent molecules or simply the whole system.

Output

Image (as png) of the Ramachandran from MDanalyis with the allowed regions as a background.

Image (as png) of the Ramachandran plot as a distribution.

Data (H5 format). All phi, psi timeseries raw data in HDF5 format.

All plot images tabulated (in html). To view the HTML in Galaxy this tool must be added to the allowlist by a Galaxy Admin.