Selecting Rotamers and Torsions

Another way of adjusting the conformational state of a structure is to select from a set of rotamers of rotatable groups. For protein side chains, the set consists of the commonly observed rotamers. For non-protein rotatable groups, they are generated by performing a rapid torsion scan of a single dihedral with a given increment, and sorting by energy. This means that the molecule must be a properly prepared structure, with bond orders assigned and all hydrogens present, which you can do in the LigPrep Panel.

Protein Side-Chain Rotamers

For a single residue, the rotamer selection can be made from the Workspace.

1. Select an atom in a residue or a single residue in the Workspace.

2. Right-click on the selection and choose Select Rotamer.

   The Select Rotamer banner is displayed.

   

3. You can then perform the following actions with the buttons:

   • Use the arrow buttons to step through the rotamers.
   • Click the star button to select the best (most common) rotamer.
   • Click the reset button to return to the original rotamer.
   • Click the information button to open the Rotamers Dialog Box.

   Information on the rotamers is displayed as a tooltip over the information button.

4. Click OK to confirm the change or Cancel to discard the change and return to the original structure.

If you select multiple residues, the Rotamers Dialog Box opens instead. In this dialog box you can select rotamers for all the selected residues. You can also open this dialog box by choosing Edit → Rotamers.

Small-Molecule Torsions

As for the protein residues, you can select rotamers for a single selected torsion in the Workspace.

1. Select two atoms or a bond in the Workspace.

2. Right-click on one of the atoms in the selection and choose Scan Torsions.

   The torsional scan is run, and then the Rapid Torsion Scan Panel opens with the results.

When opened with Edit → Rapid Torsion Scan, the Rapid Torsion Scan Panel allows you to adjust a single dihedral for a small molecule ("ligand"), and allows control over the scan parameters.

Alternate Positions

Some X-ray structures have alternate positions for atoms that can adopt different conformations in the crystal. These positions are stored with the structure when it is imported (or generated with PrimeX—see Partial Occupancy Refinement). To switch between the alternate positions, select the atoms, then right-click on one of the atoms and choose Additional Edits → Switch Alternate Positions, or choose Other Edits → Switch Alternate Positions in the 3D Builder panel.