Controls are tools that can manipulate the internal and absolute coordinates or other geometrical properties of the selected objects. Three controls are available: translate, rotate and resize. The latter, resize, can be applied to elements of pharmacophore models or to surfaces.
The translate control moves the selected object and changes its coordinates, thus the relative position of two (or more) objects (e.g.. two ligands in the same binding pocket) can be modified. To translate a molecule follow the steps below:
Select the structure in the selection panel: click on it with the left mouse button
click right button to get the popup menu
choose first item, Select, atoms of the selected structure become highlighted
now press the translate control button in the Toolbar:
drag the selected object: hold down the left mouse button plus press the Ctrl (control) key on the keyboard and move the mouse
Note, however, that this way the selected object can be translated in the plane of the screen only. In order to move it in other directions, that is, along the third axis towards the viewer's eyes or away from them, the Shift key has to be pressed too.
Note that rotation and translation of the scene is always possible, regardless of which monitor or control is being applied.
The next control button is the rotation control. With this the selected structure can be rotated without affecting any other object. For instance a ligand in a proteins binding pocket can be rotated while the protein remains in its original position. To rotate the selected object follow the steps of translation described above, except that in the 4th step press the rotate control button instead of the translate button:
Note, that the Ctrl (control) key on the keyboard has to be held down to rotate the selected object, otherwise the scene is rotated (thus no coordinates, relative positions of objects changes).
If both Ctrl (control) and Shift keys are pressed, the object rotates about the axis perpendicular to the plane of the canvas.
The resize control can be applied to increase/decrease the size of spheres and arrows used in pharmacophore model building.
This works similar to translation and rotation, though in this case the object to be selected is either a pharmacophore sphere or an arrow. Again, the Ctrl (control) key has to pressed to resize the selected object. Resize also has effect on surfaces. In this case the bounding box of a selected surface can be resized, and thus the surface will be clipped by 6 clipping planes determined by the sides of the bounding box.