Pro-origami:
Generate a protein structure cartoon

DDOMAIN will used the DDOMAIN program to decompose the protein into domains. Cath CDF will use a Cath DomAll File (CDF) to decompose the protein into domains according to CATH domain definition. Note that the DDOMAIN option will decompose any protein into domains according to the DDOMAIN algorithm, however the Cath CDF option will only define domains for those proteins listed in the currently used DomAll file, and proteins not present in that file will be defined as consisting of a single domain by default.

The include 3_10 helices and include pi helices options will include 3_10 and pi helices, respectively, in the cartoon. If not selected, only alpha helices are included.

The use HELIX and SHEET cards option will use the HELIX and SHEET records from the PDB file to define the helices and sheets in the protein secondary structure. If these records are not present or cannot be used due to apparently bad definitions, then the DSSP or STRIDE (depending on the selected progam) definitions will be used instead.

The use distance matrix option will try to place helices close to SSEs that they are in contact with rather than the heuristic placment which tries to align them neatly on the same axis as strands.

The prevent helices from being placed between neighboring sheets option will, when heuristic helix placement is in use, prevent helices from being drawn between sheets that are close to each other, moving them instead so that they do not cause the sheets to be drawn further apart.

The multidomain cartoon option will place all domains on the one cartoon, instead of ge nerating multiple cartoons, one for each domain.

The interdomain connectors option, when using multidomain cartoons, will draw connectors between domains rather than leaving pseudo-terminus as used for single domain cartoons.

This option will cause neighbouring helices to be grouped into a rectangular cluster within the diagram and for this cluster to be highlighted in a particular color.

These options simply determine the labels that appear on SSEs in the diagram.

These options simply determine the color schemes used for SSEs in the diagram.

Given it may be impossible for connectors not to overlap or cross, these coloring options give the ability to highlight these situations and therefore allow readers of the diagrams to better distinquish connectors from each other.

Diagrams will be prodcued with orthogonal connector routes (only vertical and horizontal line segments). Rounded corners results in a smooth curves rather than sharp bends at corners.

Adjusting the connector routing penalty can sometimes improve the quality of diagrams with many crossings. Note, this penalty will noticably slow down generation of some diagrams.

The nudge distance is the amount of pixels that Dunnart will try to separate connector segments that share the same path, effectively nudging them apart.

The connector line width is the pixel width for connectors in the SVG of the prodcued diagram. Thicker connectors might be beneficial in a very large diagram since they will allow easier selection of connector in a zoomed-out diagram.