PLA, PLANE

When a PDB file is read, a new structure is stored into program memory. A single plane is associated with this structure. By default, the plane is unvisible and movement controls are affecting both the structure and the associated plane. The command PLANE may be used to make the plane visible, to set the plane transparency or radius, or to hide the plane.

Plane is represented by an ellipse. One side of this ellipse will be colored blue and other side will be colored orange-red. Blue side is treated as top (upper) side, while orange-red side is treated as bottom side. Far side of the plane is dark.

The transparency value should be between 0 and 1. If transparency is equal to zero the plane is opaque. Default plane transparency is 0.4 (hard-coded). The initial (default) plane radius is based on the spacial extent of the structure. The image below shows two semi-transparent planes: the left plane is seen from above, while the right plane is seen from below. Transparency is equal to 0.3 for both planes.



Plane may be used for different purposes:
(1) To represent the cellular membrane. This is interesting for visualization of membrane proteins (like in the image above).
(2) To distinguish protein domains. Many soluble proteins fold into two domains. Plane may be used to outline the border between these domains.
(3) Atoms may be selected according to their position with respect to plane. The command SEL ABO (SELECT ABOVE) selects atoms which are above the plane. The command SEL BEL (SELECT BELOW) selects atoms which are below the plane. The image below shows what may be achieved when applying different drawing styles to atoms on different sides of the plane.

(1) By default, the plane moves with the structure. If movement controls affect only the plane, be sure to make it visible. Otherwise, you may push the plane far away from the object to which this plane belongs.

(2) In garlic source code, each plane is defined by the plane center (three coordinates) and by the normal vector (three-component vector).

(3) At present, garlic associates only one plane with each structure. If for some reason you need two planes (for example, to simulate the cellular membrane), use the following trick:
(3.1) Prepare the structure and its associated plane (the first plane).
(3.2) Load another structure (something small, like a single residue) and hide it.
(3.3) Make the plane (which is associated with this small structure) visible.
(3.4) Change radius and transparency for the second plane.
(3.5) Set the position and orientation of this plane.
If you learn this trick, you will be able to prepare images like this one: