Ghemical User Documentation: Changing the perspective.

# 2.1.2 Changing the 3D-views

On the left toolbar there are 7 tools to change the way the current project is displayed. Ghemical stores each atom a point in the cartesian coordinate system. The first point is The X-axis is parallel to the bottom of the window, the Y-axis is parallel to the side of the window and the Z axis is pointing out of the screen. The molecule is from the perspective of a camera focused on all or part of the molecule.

- ## Zoom

  This moves the camera either further from or closer to the molecule, effectively zooming in or out of the molecule. To operate the zoom, click on the Zoom button on the toolbar. Left click on the view window and hold the mouse button down. Moving the mouse up will zoom out of the molecule and moving the mouse down will zoom out of the molecule. Releasing the mouse button stops the zooming process.

- ## Translate XY

  This tool moves the molecule in the XY plane. To operate it, click on the Translate XY button. Left click on the view window and hold the mouse button down. The molecule will be translated in the direction that the mouse is moved (up, down, left or right).

- ## Translate Z

  This will move the molecule along the Z-axis. To operate it, click on the Translate Z button. Left click on the view window and hold the mouse button down. Moving the mouse up or down will translate the molecule. This is similar to zooming the molecule, except in this case the molecule will be translated instead of the camera.

- ## Orbit XY

  This tool will rotate the molecule around the X or Y axis of the focus point of the camera. To use this tool, click on the Orbit XY button. Left click on the view window and hold the mouse button down. Moving the mouse button up or down will rotate the molecule around the X axis, moving the mouse button left or right will rotate the molecule around the Y axis. Releasing the mouse button ends the orbit operation.

- ## Orbit Z

  This tool will rotate the molecule around the X or Y axis of the focus point of the camera. To use this tool, click on the Orbit XY button. Left click on the view window and hold the mouse button down. Moving the mouse button up or down will rotate the molecule around the X axis, moving the mouse button left or right will rotate the molecule around the Y axis. Releasing the mouse button ends the orbit operation.

- ## Rotate XY

  This tool performs the same function as the Orbit XY tool except rotation is performed around the camera and not the focus point. It's operation is identical to the Orbit XY tool.

- ## Rotate Z

  This tool performs the same function as the Orbit Z tool except rotation is performed around the camera and not the focus point. It's operation is identical to the Orbit Z tool.

## Moving only some atoms

It is possible to move only the selected atoms. To do this, select the atoms you want to move with the Select tool from the left toolbar and click on the tool that you want to use (Translate XY, Orbit XY...). Now hold down the shift button perform the translation, rotation or orbit. Only the selected atoms will be affected by the operation.

## Viewing only some atoms

For some molecules (especially macromolecules), it is preferable to only view a portion of the molecule. The Clipping tool allows the user to do this. Clipping is controlled by selecting the Clipping icon from the toolbar and then left clicking on the View screen. Clipping is adjusted by moving the mouse up or down while holding down the left mouse button. The amount of clipping is determined by a scale between 1.00 and 0.01. When clipping is at 1.00, the whole molecule is displayed. All values lower than that show only the frontmost section of the molecule determined by the scale factor (ie, when clipping is 0.50, only the frontmost half of the molecule is shown). This scale factor is increased by moving the mouse up and decreased by moving the mouse down. In the console window, the scale factor is displayed after every adjustment to it, as well as size of the displayed section in nanometers.

    clipping = 0.99 = 6.03407 nm.
    clipping = 0.865 = 5.27219 nm.
    clipping = 0.7675 = 4.67793 nm.
    clipping = 0.5875 = 3.58082 nm.
    clipping = 0.3825 = 2.33135 nm.
    clipping = 0.2575 = 1.56947 nm.
    clipping = 0.235 = 1.43233 nm.
    clipping = 0.23 = 1.40185 nm.

In this example, a ball and stick model of the enzyme CYP3A4 is clipped so that only the frontmost portion is displayed.

#### Non-clipped CYP3A4.

#### Clipped CYP3A4.

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