Pipes is the command-line implementation of PipesAndPlanks, which creates a VRML model of a protein showing helices as “pipes” (cylinders), strands as “planks” (rectangular boxes), and the remaining coil as thin connectors. Arrowheads can be included to indicate chain directionality. Pipes and planks are only generated for proteins; helix and strand assignments are taken from the input structure file or generated with ksdssp. See also: define, rainbow, ribbon, nucleotides, the Pipes and Planks tutorial
The pipes-and-planks model is assigned the same model number as the original molecule model, and the original model is hidden. The ~pipes command deletes the pipes-and-planks model and re-shows the original model. Models can also be hidden and shown using the Model Panel or the command modeldisplay.
Option keywords can be truncated to unique strings and their case does not matter. A vertical bar “|” designates mutually exclusive options, and default values are indicated with bold. Synonyms for true: True, 1. Synonyms for false: False, 0.
helixColor colorname
How to color helix pipes. The colorname can be none (default) to use the residue color (ribbon color) of the first residue in each helix; for example, if a protein chain had been rainbow-colored from N-terminus to C-terminus, each helix pipe would be shown with a different color in the rainbow range. Otherwise, the colorname can be any color name that specifies a single color.
strandColor colorname
How to color strand planks. The colorname can be none (default) to use the residue color (ribbon color) of the first residue in each strand, otherwise any color name that specifies a single color.
coilColor colorname
How to color representations of coil (non-helix non-strand biopolymer segments). The colorname can be none (default) to use the residue color (ribbon color) of the first residue in each coil segment, otherwise any color name that specifies a single color.
helixArrow true | false
Whether to place arrowheads on the C-terminal ends of helix pipes to indicate N→C directionality.
strandArrow true | false
Whether to place arrowheads on the C-terminal ends of strand planks to indicate N→C directionality.
helixFixedRadius true | false
Whether to use a constant radius for all pipes (default) or a variable radius based on the distances from the constituent α-carbons to the helix axis.
helixRadius radius
If fixed, the radius of helix pipes (default 1.25 Å).
helixSplit true | false
Whether to split a helix when the ratio of maximum to minimum distance from α-carbons to the axis exceeds the helix split ratio.
helixSplitRatio ratio
Ratio of maximum to minimum distance from α-carbons to the axis above which a helix will be split, if allowed (default 2.5).
strandFixedWidth true | false
Whether to use a constant width for all planks (default) or a variable width based on the distances from the constituent α-carbons to the strand axis.
strandWidth width
If fixed, the width of strand planks (default 2.5 Å).
strandFixedThickness true | false
Whether to use a constant thickness for all planks (default) or a variable thickness based on the distances from the constituent α-carbons to the strand axis.
strandThickness thickness
If fixed, the thickness of strand planks (default 1.0 Å).
strandSplit true | false
Whether to split a strand when the ratio of maximum to minimum distance from α-carbons to the axis exceeds the strand split ratio.
strandSplitRatio ratio
Ratio of maximum to minimum distance from α-carbons to the axis above which a strand will be split, if allowed (default 2.5).
displayCoils true | false
Whether to include coil representations in the pipes-and-planks model.
coilWidth width
Width of coil representations (default 0.25 Å).
coilThickness thickness
Thickness of coil representations (default 0.25 Å).
coilSubdivision N
The number of segments per residue used to represent coils (default 10).
helixEdgeColor colorname
How to color outlines on helix pipes. This and the following edge color (outline) options merely supplement silhouettes, and would typically be used together with silhouettes and in the same color, for example, all black as in the Pipes and Planks tutorial. The colorname can be none (default) for no outlines, otherwise any color name that specifies a single color.
strandEdgeColor colorname
How to color outlines on strand planks. The colorname can be none (default) for no outlines, otherwise any color name that specifies a single color.
coilEdgeColor colorname
How to color outlines on coil representations. The colorname can be none (default) for no outlines, otherwise any color name that specifies a single color.