| SecondaryStructure.DrawType | Draw type of all secondary structure components of the scene | Trace,   Tube,   PipeAndPlank,   RibbonLines,   Ribbon,   CartoonSquare,  * Cartoon | Cartoon | 
| SecondaryStructure.ColorType | Color type of all secondary structure components of the scene | "Constant", "Residue", "Chain", "Rainbow", "B-factor", "SecondaryStructure" | SecondaryStructure | 
| SecondaryStructure.Quality | Quality of all secondary structure components of the scene | "High", "Medium", "Low" | Medium | 
| SecondaryStructure.Color | The color used in constant color mode | java.awt.Color | #ffffff | 
| SecondaryStructure.HelixWidth | . | Float | 1.2 | 
| SecondaryStructure.HelixDepth | . | Float | 0.3 | 
| SecondaryStructure.HelixShift | . | Float | 2.5 | 
| SecondaryStructure.HelixArrow | . | true, false | true | 
| SecondaryStructure.HelixArrowWidth | . | Float | 3.8 | 
| SecondaryStructure.SheetWidth | . | Float | 1.2 | 
| SecondaryStructure.SheetDepth | . | Float | 0.4 | 
| SecondaryStructure.SheetArrow | . | true, false | true | 
| SecondaryStructure.SheetArrowWidth | . | Float | 3.8 | 
| SecondaryStructure.CoilWidth | . | Float | 0.3 | 
| SecondaryStructure.CoilDepth | . | Float | 0.3 | 
| SecondaryStructure.CoilUniform | . | true, false | true | 
| SecondaryStructure.Threads | . | Integer | 6 |