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This tool allows the user to easily generate contact maps and distance maps for protein molecules. Input may be given in one of two ways:
PDB ID: If an RCSB Protein Data Bank identifier is given, the tool will automatically retrieve the structure from www.pdb.org. A PDB id should be four characters long, and begin with a numeral. See www.pdb.org for more information.
File upload: The user may also upload their own .pdb file. A properly formed pdb file must be given, and may be obtained directly from www.pdb.org or as a result from a simulation tool. If a file is given which contains multiple models representing a trajectory, then the results will be shown as a sequence of plots.
If the selected structure contains multiple chains, the first chain is implicitly selected.
Other input parameters are available:
Distance map options:
- Title: An optional title may be given, which will be displayed on the distance map.
- Color: If enabled, the distance map will use a color (blue->red) scale. If disabled, the result will be grayscale.
- Contour lines: If enabled, contour lines will be displayed on the result.
- Interpolation: If enabled, the distance matrix will be interpolated, resulting in a smoother appearance. If disabled, each position in the distance matrix will be a discrete color value.
Contact map options:
- Title: An optional title may be given, which will be displayed on the contact map.
- Threshold: Threshold distance that determines how close two atoms must be to be deemed “in contact”
- Distance map: Presents the Cα-Cα distance between every pair of amino acids as a two dimensional matrix. A single image is produced if only one model is present, or a sequence of images if multiple models exist.
- Contact map: Similar to the distance map, except the data is a binary two dimensional matrix representing which amino acid pairs closer than a given threshold.
- Molecule viewer: Provides an interactive 3 dimensional view of the complete atomic coordinates for comparison with the distance and contact maps. A cartoon style representation can be useful for comparison. To select a molecule representation style, open the view settings panel by clicking on the wrench icon on the right hand side of the molecule viewer.