Selects the color-scheme. Can be either GPCRDB or monotonous. Fill color for the background of a residue Groups color-related options Groups shape-related options Define a new color. Defined colors can be referenced by name throughout the input file. Groups the main sections that determine how the diagram will appear. Groups options that can affect how the diagram is rendered. Determines how individual residues will be rendered. Attributes determine when and what type of shape is used to render a residue. When can be either linked or nothing. "linked" selects residues that are hyperlinked. "other" select all the other residues. Three shapes are supported: rectangular, circular, and octagonal When to use the shape. Values can be linked (when residue is linked), or nothing (when residue is not linked). Must be "circular", "rectangular", or "octagonal"', Groups elipses related options Excludes elipses from a range of residues. Allows elipses to be included in a range of residues. Describes the graphical arrangement of secondary structure units on the 2D page. Defines the graphical subunits of the diagram. Use the bundle to layout integral membrane proteins. Specify the number of transmembrane (TM) segment to display, and the bundle will automatically calculate the layout of the diagram. Attributes of the bundle include the direction the N-term will take (up or down). Ids must also be generated for each subunit the tm-bundle contains, so that subunits can be referenced by the secondary -structure section of the diagram. The N and C-term X and Y attributes relate to the spacer values that can be used when drawing the diagram. Direction is a vector(x,y) which indicates the orientation of a subunit (helix or loop) within the plane. Select options for an image output of the diagram. Output an image map document. Currently not supported. (maps are embedded in the XML produced.) Describes hyperlinks attached to various components of the diagram. Links a subunit to a URL. The subunit is referenced by id. The url attribute provides the URL. For non-SVG outputs, only subunits of type edu.mssm.crover.domain2d.ProteinSegmentDomain can be linked to a URL. the SVG export supports this feature for any type of subunit. Name of the protein Groups options related to the diagram output. Generates an XML document that describes one diagram. This document will contain information suitable to generate HTML pages that embed the diagram images. When provided, the template attribute names an XSL stylesheet that will be set in the document. Describes the protein to be rendered. Input file for construction of one diagram. Links a residue to a URL. This feature is supported for all types of export (GIF,JPG, SVG, etc). Residue position numbering starts at 1. Residues of the protein Color one residue on the sequence. Residue position numbering starts at 1. Define the shape of one residue on the sequence. Residue position numbering starts at 1. Defines the secondary structure for this protein. The start-residue-numbering is used when the protein sequence that is being represented is only a partial sequence of the whole protein. Describes a disulfide bridge. A yellow line is drawn on the diagram between the to and from residues. Defines the limits of of segment of secondary structure. Segments should span non overlapping parts of the sequence. The separation between the first residue of the subunit and the last, on the page. Each subunit is located on the page according to the location and spacer of the subunit that preceeds it. The location of the first subunit is determined so that the complete diagram is visible. At the time of writing, the following types of subunits are available (all types should be entered starting with edu.mssm.crover.domain2d): FreeLoop, ExtremityDomain (for N-terms), CtermDomain, HelicalDomain, BetaStrandDomain, ProteinSegmentDomain Defines the bound of the parameter search that scales loops when not enough residues can fit in the path. Increase the max attribute to allow loops to grow larger before ellipses are inserted in the sequence. Rendering is appear incorrect if this parameter does not allow the loop to be enlarged, and ellipsis have been restricted the sequence of this subunit. Use only when subunit type is FreeLoop, Nterm or Cterm. Provides control points for the shape of the loop (Bezier control points). Control points are defined in a 2D space centered on the position of the first residue of the subunit. Thus, the first control point must have position (0,0). The last control point should be placed such that it matches the spacer of the subunit. The other control points can be placed to control the shape of the path along which residues of the subunit will be laid out. A control point. x and y coordinates are doubles.