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Local Transformations |
Local transformations are rotations and translations of a selected set of atoms in the Workspace. In contrast to global transformations, which only change the viewing angle of the Workspace, local transformations change the coordinates of the selected atoms.
Like global transformations, local rotations and translations are done with the middle (rotation) and right (translation) mouse buttons. You can switch between local and global transformation mode with Ctrl+G (⌘G), or by choosing Edit → Transform → Pick to Transform. You can switch modes temporarily by holding down the Spacebar while you perform the rotation or translation. When you release the Spacebar, the previous mode is restored.
For a quick local transformation, you can select the atoms in the Workspace, then choose Transform from the Workspace shortcut menu, and perform the transformation. To exit the mode, press Ctrl+G (⌘G).
The tools for local transformations are available from the
Transform button menu on the
Edit toolbar.
This button menu has four groups of items:
Display Options: There are two options in this group, Display Interactions and Display Bond Lengths. The first displays interactions between the atoms being transformed and the rest of the atoms in the Workspace. The types of interactions that are displayed can be selected in the Non-bonded interactions – Criteria section of the Preferences panel. Display Bond Lengths marks bonds between the selected atoms and the other atoms with a dotted line and the length of the bond.
The display options are saved as preferences and are applied whenever you perform a local transformation.
Picking Choices: The five items in this section allow you to choose the object that you want to perform a local transformation on: Atoms, Residues, Chains, Molecules, or Entries. When you have selected one of these items, you can click on an atom in the Workspace to select the object. Each click replaces the previous selection. You can drag over multiple objects to select them.
Show Markers Option: With this option selected, the atoms selected for transformation are marked in the Workspace in yellow.
Advanced: This item opens the Advanced Transformations panel, which offers the full flexibility for performing local transformations.
A special kind of local transformation that includes minimization is provided
with the Sculpt button menu on the
Build toolbar.
With this tool, moving the selected atoms is followed by a short force-field
minimization that includes nearby atoms. Once you enter this mode, you can
select atoms and drag them to a new location (with the left mouse button). When
you release the mouse button, the minimization starts. The selected atoms are
restrained. Atoms in the same residues have no constraints placed on them; atoms
in complete residues that are within 5 Å of these residues are
restrained, and all other atoms are frozen. The minimization proceeds for a
fixed number of cycles or until there is no significant change. During the
minimization you can continue to work on the structure. The minimization stops
if you exit the mode, for example by choosing some other action that involves
picking atoms, or change the content of the Workspace. If you select some more
atoms and drag them while the minimization is proceeding, it stops and a new
minimization begins.
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