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<head>
<title>
MEM, MEMBRANE
</title>
</head>
<h1 align=center>
MEM, MEMBRANE
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
MEM, MEMBRANE - generate and manipulate the membrane associated with
the structure.
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
<table border=1 cellspacing=1 cellpading=0>
<td align="left">
<font color=#004400>
<b>
SHORT FORM
</b>
</font>
</td>
<td align="left">
<font color=#004400>
<b>
LONG FORM
</b>
</font>
</td>
<tr>
<td align="left">
MEM
<br>
MEM BET
<br>
MEM RAD value
<br>
MEM THI value
<br>
MEM TRA value
<br>
MEM OFF
</td>
<td align="left">
MEMBRANE
<br>
MEMBRANE BETA
<br>
MEMBRANE RADIUS value
<br>
MEMBRANE THICKNESS value
<br>
MEMBRANE TRANSPARENCY value
<br>
MEMBRANE OFF
</td>
</table>
<br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
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.
<br><br>
The experimental determination of the structure of fluid lipid bilayers in
<a href="http://blanco.biomol.uci.edu/Bilayer_Struc.html">
The Stephen White Laboratory at UC Irvine
</a>
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 Stephen White Laboratory!
<br><br>
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).
<br><br>
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.
<br><br>
If working with beta barrel protein (porin-like membrane proteins), the
keyword BETA may be used to improve membrane placement.
<br><br>
<font color=#880000>
<b>
KEYWORDS
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
KEYWORD
<br>
(SHORT)
</td>
<td align="left">
KEYWORD
<br>
(LONG)
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
OFF
</td>
<td align="left">
OFF
</td>
<td align="left">
Hide membrane.
</td>
<tr>
<td align="left">
BET
</td>
<td align="left">
BETA
</td>
<td align="left">
Attach membrane to beta barrel protein (porin).
</td>
<tr>
<td align="left">
THI
</td>
<td align="left">
THICKNESS
</td>
<td align="left">
Set the membrane thickness (in angstroms).
</td>
<tr>
<td align="left">
RAD
</td>
<td align="left">
RADIUS
</td>
<td align="left">
Set the radius of both planes (use angstroms).
</td>
<tr>
<td align="left">
THI
</td>
<td align="left">
THICKNESS
</td>
<td align="left">
Set the membrane thickness (in angstroms).
</td>
<tr>
<td align="left">
TRA
</td>
<td align="left">
TRANSPARENCY
</td>
<td align="left">
Set the transparency of both planes
<br>
(between 0 and 1).
</td>
</table>
<br>
<font color=#880000>
<b>
EXAMPLES
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
COMMAND
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
mem
</td>
<td align="left">
Initialize the membrane and make it visible.
</td>
<tr>
<td align="left">
mem rad 20
</td>
<td align="left">
Change the radius of both planes to 20 angstroms.
</td>
<tr>
<td align="left">
mem tra 0.3
</td>
<td align="left">
Change the transparency of both planes (new value: 0.3).
</td>
<tr>
<td align="left">
mem thi 20
<br>
mem beta
</td>
<td align="left">
Change membrane thickness and attach membrane to beta
<br>
barrel protein.
</td>
<tr>
<td align="left">
mem off
</td>
<td align="left">
Hide membrane.
</td>
</table>
<br>
<font color=#880000>
<b>
NOTES
<br>
</b>
</font>
(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.
<br><br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
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.
<br><br>
<hr size="3">
</html>
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