PipesAndPlanks creates and displays a VRML representation of protein secondary structure in which alpha helices are shown as "pipes" (cylinders) and beta strands are shown as "planks." Protein secondary structure is determined from HELIX and SHEET records in the input file, or if these are not present, using ksdssp. PipesAndPlanks does not work for nonprotein molecules such as nucleic acids.
There are several ways to start PipesAndPlanks, a tool in the Utilities category.
Starting PipesAndPlanks opens dialog box. The model of interest should be opened in Chimera and the corresponding file chosen from the listing near the top of the dialog box (click with the left mouse button on the black arrowhead). The helix and sheet colors can be changed by clicking the border of the respective color well and creating a new color with the Color Editor. The Helix Radius and Sheet Thickness parameters are in angstroms. If the radius or thickness is not Fixed, the specified value is ignored and the radius or thickness instead depends on the distances from the constituent alpha-carbons to the axis of the helix or strand. If the ratio of maximum to minimum distance from alpha-carbons to the axis exceeds the Split Threshold (and the corresponding Split option is set to true), the pipe or plank is broken into two pieces, each now having its own axis.
Clicking OK creates the display and dismisses the dialog box; clicking Apply creates the display without dismissing the dialog box. The pipes-and-planks representation is placed in the same model number as the corresponding molecule. It can be closed or hidden independently of the protein it represents with the Model Panel, or undisplayed/displayed (hidden/shown) with the command objdisplay.