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Advanced Transformations Panel |
The Advanced Transformations panel allows you to change the focus of molecular transformation from global to local, select the atoms to transform, and define the center for rotation.
You can also perform a local transformation by selecting the atoms to transform first, then choosing Transform from the Workspace shortcut menu.
To open the Advanced Transformations panel, you can:
Choose Edit → Transform → Advanced in the main window.
Choose Advanced from the Transform button menu on the Edit toolbar.
You can specify both the atoms to be locally transformed and the centers around which the atoms will be transformed with the standard picking controls.
If you do not wish to manually define a local center, you may allow Maestro to define one for you. To do so, leave the ASL text box in the Center For Transformation section of the panel blank. Note that the global center of rotation is unaffected by the selection of a local center.
The standard picking controls are available in this section to define the atoms for transformation.
The standard picking controls are used to define a center of rotation for local transformations. If you specify atoms to be used as a local center of rotation, Maestro uses the centroid of that atom set for the center.
If you do not specify a center, Maestro defines the local center as the centroid of the atom group specified in the Atoms For Transformation section. Maestro updates the center of rotation whenever the Atoms For Transformation ASL expression is reevaluated. Reevaluation occurs any time you press the ENTER key while the cursor is in the ASL text box, when additional picks add ASL text to the Atoms For Transformation text box, when you move the cursor outside the text input box, or when the structure changes.
In Maestro, "global" refers to operations or properties that affect all atoms in the Workspace, and "local" refers to operations or properties that affect a selected group of Workspace atoms. You can switch between local and global transformation by choosing the appropriate option in this section of the panel, or by using Ctrl+G (⌘G) to enter and exit local transformation mode.
The program remains in this mode until you specify a different mode through interaction with the Maestro interface or by using another key combination. You can also 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.
When performing a local transformation on a set of atoms that include atoms with alternate positions, transform the coordinates for both alternatives. Deselect this option to transform the displayed location and not the alternate.
Atom Specification (ASL) expressions that include within or
beyond may cause
unexpected behavior because, in these cases, the membership of the local set of
atoms may change under certain circumstances. For example, if you use the
within operator in an expression and then locally translate the
group of atoms that it defines, when those atoms pass within the
"within" distance of non-local atoms, the non-local atoms will be
added to the local group. The additional atoms will then begin to translate too,
as if the local atom group were attracting them like a magnet. Similarly, use of
the beyond operator may cause atoms to drop out of the local group
as the group is moved toward the rest of the Workspace structure.
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