PrimeX Basics: Structure Adjustments

There are several places in Maestro from which you can perform structure adjustments:

• the 3D Builder panel, which you open by clicking the Build button on the toolbar or choosing Edit → 3D Builder. With the Move tool you can rotate dihedrals, lengths, and angles, and rotate peptide planes and carbonyl planes on the protein backbone. The Other Edits menu allows you to invert the chirality of atoms, convert peptides from cis to trans, find torsions, and switch alternate positions.

• the Move Atoms banner, which you display by choosing Inin the Maestro main window, choose Edit → Move Atoms, choosing Move Atoms from the selection shortcut menu, or pressing Ctrl+G (⌘G). In addition to rotating or translating the selected atoms with the usual rotate and translate mouse actions, you can perform quick adjustments of dihedrals, lengths, or angles, as well as peptide plane and carbonyl plane rotations on the protein backbone.

• the shortcut menu for an atom selection in the Workspace, which you open by right-clicking on a selected atom or bond. As well as displaying the Move Atoms banner, you can invert the chiralities of the selected atoms or switch alternate positions , by choosing from the Additional Edits submenu.

• the Rotamers Dialog Box, which you open by choosing Edit → Rotamers, allows you to select a side-chain rotamer from among the common rotamers for each residue, or choose the rotamer that best fits the density of the displayed map.