6.13 Build a peptide

This tool allow to build a peptide from its primary structure defining the secondary structure type. To open it, you must select Edit -> Build -> Peptide in the main menu. The build procedure consists in two phases: 1) construction of the linear peptide; 2) change of the secondary structure.

Build a peptide

In the big editing box, it's possible to type the aminoacid sequence or copy & paste it from another application, using the single character convention. Alternatively, the input can be performed by the twenty buttons (one for each aminoacid) at the window bottom. The Structure type box allows to specify the secondary structure type: several pre-defined structure types are already present (Alpha helix, Left handed helix, 3.10 helix, Pi helix, Beta strand, Antiparallel beta strand and Parallel beta strand) but the user can create custom structures selecting Custom and changing the Phi, Psi and Omega torsion values:

Phi, Psi and Omega torsion angles

The checkboxes at the left of each torsion name allow to enable/disable which angles are changed to the characteristic secondary structure value, eventually keeping the values of the linear peptide generated in the first building phase.
By default, the tool build the backbone only without hydrogens, but checking Add the side chains and Add the hydrogens, the user can complete the peptide structure. Clicking the Build button, the structure is generated in the current workspace if it's empty or in a new one if it contains a molecule.
The Fix bond angles and the Consider selected atoms only checkboxes are intentionally inactive and they are operative changing the secondary structure of a 3D peptide.