Changing Atom and Residue Properties

secondary structure, assign, partial charge, SASA, isotope

Atoms and residues have properties of various kinds that are used in calculations or are generated by calculations. Some examples of these are residue names or types, isotope numbers, partial charges, pKa values, chemical shifts. Properties can be displayed as labels for the atoms. Some properties are displayed in the status bar when hovering over the atom.

To change atom or residue properties, first select the atoms or residues whose properties you want to change.

You can change any atom or residue property in the Change Atom Properties Panel. This panel provides tools for changing some of the common properties, but also has an option to choose an existing property from a list or add an entirely new property, and set the value of that property. The panel is available from the Other Editsbutton in the 3D Builder panel, or from the Additional Edits submenu on the selection shortcut menu.

Some of the more common atom properties can be changed more readily, from menus or special items.

  • Changing the isotope—click Other Edits in the 3D Builder panel and choose Change Isotope from the menu, or right-click the selection and choose Additional Edits → Change Isotope. A dialog box opens, in which you can enter the isotope number. This property is used to look up isotopic masses for use in various applications that need masses, such as moments of inertia and vibrational frequencies.

  • Assigning partial charges—choose Edit → Assign → Partial Charges. Partial charges are assigned from the default force field. This is done automatically if you display the dipole moment for a molecule (if it doesn't have one as an entry property).

  • Assigning secondary structure—choose Edit → Assign → Secondary Structure. The residues in the structure are assigned as part of a helix, sheet, or loop. The assignment identifies all inter-backbone hydrogen bonds, then searches for hydrogen-bonding patterns representing helices and strands. The assignment is used for the display of ribbons, the use of some color schemes, and for the Workspace sequence viewer. Secondary structure is used to align proteins in the Protein Structure Alignment Panel.

  • Assigning solvent-accessible surface areas—choose Edit → Assign → Solvent Accessible Surface Area. The solvent-accessible surface area (SASA) for each atom is evaluated and assigned to the atom property SASA. If the atom belongs to a residue, the solvent-accessible surface area for the residue is assigned to each atom in the residue as Residue SASA.

  • Assigning force-field atom types—choose Edit → Assign → Force Field Atom Types (OPLS2005) to assign the atom types for the OPLS2005 force field. Assigning atom types can change the element, formal charge, and number of attached hydrogens. These atom types are not used by the OPLS4 force field, which has its own much more extensive atom typing.