6.13 Build a peptide
This tool allows to build a peptide from its primary structure, defining the secondary structure type. To show 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.
In the big editing box, it's possible to type the aminoacid sequence or copy & paste it from another application, using the single character codes. 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:
The checkboxes at the left of each torsion name allow to enable/disable which
angles are changed to the typical secondary structure value, eventually
keeping the values of the linear peptide generated in the first building phase.
By default, the tool builds the backbone without hydrogens only, but checking Add the side chains and Add the hydrogens, the user can complete the peptide structure. Clicking Build, the structure is generated in the current workspace if it's empty or in a new one if it contains a molecule.
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.