MEM, MEMBRANE

NAME
MEM, MEMBRANE - generate and manipulate the membrane associated with the structure.

SYNOPSIS

SHORT FORM	LONG FORM
MEM MEM BET MEM RAD value MEM THI value MEM TRA value MEM OFF	MEMBRANE MEMBRANE BETA MEMBRANE RADIUS value MEMBRANE THICKNESS value MEMBRANE TRANSPARENCY value MEMBRANE OFF

DESCRIPTION
The command MEM (MEMBRANE) may be used to associate the membrane with a protein structure. By default, no membrane is associated with the structure when it is loaded into memory. The membrane is initialized after the first execution of the command membrane. The membrane is useful when analysing some membrane protein, but it does not make much sense when working with a soluble protein.

The experimental determination of the structure of fluid lipid bilayers in The Stephen White Laboratory at UC Irvine has revealed a significant thermal motion of lipid molecules. This means that there is no clear edge of the biological membrane. However, the model used in garlic is just the opposite: the membrane is represented by two parralel planes, with clear external edges. The membrane thickness is also precisely defined. The idea was to give at least a bad model of the membrane, to allow selection of the transmembrane region. Please be sure to read those beatifull pages from Steven White Laboratory!

The planes used to simulate the membrane are represented as elliptical surfaces. The inner sides are colored orange-red, while the outer sides of the membrane are colored blue. The transparency of these planes may be adjusted, but not individually. The allowed range of transparency from 0 to 1. If the transparency is equal to zero both planes will be opaque. Default transparency is 0.4 (hard-coded).

In addition to the transparency, the membrane thickness and the radius of both planes may be adjusted (keywords THICKNESS and RADIUS, short forms THI and RAD). Default radius will be 50% larger than the membrane thickness. Default membrane thickness is 30 angstroms. It is not possible to change default membrane thickness through .garlicrc file. If you want to change it, modify the hard-coded value in the source file defines.h and recompile the program.

If working with beta barrel protein (porin-like membrane proteins), the keyword BETA may be used to improve membrane placement.

KEYWORDS

KEYWORD (SHORT)	KEYWORD (LONG)	DESCRIPTION
OFF	OFF	Hide membrane.
BET	BETA	Attach membrane to beta barrel protein (porin).
THI	THICKNESS	Set the membrane thickness (in angstroms).
RAD	RADIUS	Set the radius of both planes (use angstroms).
THI	THICKNESS	Set the membrane thickness (in angstroms).
TRA	TRANSPARENCY	Set the transparency of both planes (between 0 and 1).

EXAMPLES

COMMAND	DESCRIPTION
mem	Initialize the membrane and make it visible.
mem rad 20	Change the radius of both planes to 20 angstroms.
mem tra 0.3	Change the transparency of both planes (new value: 0.3).
mem thi 20 mem beta	Change membrane thickness and attach membrane to beta barrel protein.
mem off	Hide membrane.

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

RELATED COMMANDS
LOAD is used to load the structure (PDB file). MOVE is used to define which object should be moved. POSITION is used to place the chosen object (structure, plane, membrane or all) to arbitrary position.