Manual

The following describes the method implemented in ELLLIP, details of the dialog prompt as well as the required input and the produced output files.

Introduction

The program ELLLIP builds quasi-atomistic models of liposomes with elliptical shapes using lipid models as two decoupled building blocks for the inner and outer leaflets. It generates two quasi-uniform angular grids with a user-specified number of axes for both the outer and inner liposomal membrane leaflets. The lipids are then aligned with these axes and positioned on the inner and outer surfaces of a user-defined ellipsoid with semiaxes A, B, and C. Finally, the program allows for randomizing the positions of the lipids, displacing their centers along the appropriate direction to account for possible non-ideality and disorder of the bilayer.

Running ELLLIP

Usage:

$ elllip [OPTIONS]

OPTIONS known by ELLLIP are described in next section.

Command-Line Arguments and Options

ELLLIP does not accept any command line arguments. Instead the configuration is done interactively.

ELLLIP recognizes the following command-line options. Mandatory arguments to long options are mandatory for short options too.

Short Option Long Option Description
  --model-format <FMT> Format of the output models, one of: cif, pdb (default: cif)
-h --help Print a summary of arguments, options, and exit.
-v --version Print version information and exit.

Interactive Configuration

ELLLIP can only be configured in the dialog mode. ELLLIP interactive prompt:

Screen Text Description
Input model for outer shell Lipid file name for the outer leaflet of the liposome in .pdb or .cif format.
A-semiaxis, outer shell Semiaxis along X in Angstroems
B-semiaxis, outer shell Semiaxis along Y in Angstroems
C-semiaxis, outer shell Semiaxis along Z in Angstroems
Randomization amplitude Disorder amplitude of the liposome shell
Number of grid points, outer shell Total number of lipids in the outer shell
Input model for inner shell Lipid file name for the inner leaflet of the liposome in .pdb or .cif format.
Half-width of the shell Half distance between the head groups of inner and outer lipids
A-semiaxis, inner shell Semiaxis along X in Angstroems
B-semiaxis, inner shell Semiaxis along Y in Angstroems
C-semiaxis, inner shell Semiaxis along Z in Angstroems
Number of grid points, inner shell Total number of lipids in the inner shell
Output PDB file Resulting file with the liposome in .pdb or .cif format.

Runtime Output

There is no runtime output after the interactive configuration.

ELLLIP Input Files

ELLLIP accepts up to two files with atomic coordinates in .pdb or .cif format, with the lipid structures for the outer and inner leaflets. In the case of a micelle, one input file is sufficient.

ELLLIP Output Files

ELLLIP writesthe atomic coordinates with the liposome structure in .pdb or .cif format to the given file name. The actual format used depends on its extension.

Examples

Generating a liposome

$ elllip

  ***  Makes an elipsoidal liposome from the structure   *** 
  ***  of two monomers                                   *** 

 Input model for outer shell ............ <         .cif >: p2r2.pdb
 Number of atoms, single molecule ....................... : 138
 Geometrical center, single molecule X0 =   42.908 Y0 =   -0.202 Z0 =    4.053
 A-semiaxis, outer shell ................ <        50.00 >: 620
 B-semiaxis, outer shell ................ <        620.0 >: 590
 C-semiaxis, outer shell ................ <        590.0 >: 550
 Randomization amplitude ................ <        0.000 >: 
 Number of grid points, outer shell ..... <        67548 >: 
 Input model for inner shell (empty for micelle) <         .cif >: p2r1.pdb
 Number of atoms, single molecule ....................... : 138
 Geometrical center, single molecule X0 =   25.703 Y0 =    0.203 Z0 =   -4.053
 Half-width of the shell ................ <        22.18 >: 
 A-semiaxis, inner shell ................ <        575.6 >: 
 B-semiaxis, inner shell ................ <        545.6 >: 
 C-semiaxis, inner shell ................ <        505.6 >: 
 Number of grid points, inner shell ..... <        62435 >: 
 Output file ............................ <         .cif >: liposome.pdb

Generating a micelle

$ elllip

  ***  Makes an elipsoidal liposome from the structure   *** 
  ***  of two monomers                                   *** 

 Input model for outer shell ............ <         .cif >: p2r2.pdb
 Number of atoms, single molecule ....................... : 138
 Geometrical center, single molecule X0 =   42.908 Y0 =   -0.202 Z0 =    4.053
 A-semiaxis, outer shell ................ <        50.00 >: 100
 B-semiaxis, outer shell ................ <        100.0 >: 200
 C-semiaxis, outer shell ................ <        200.0 >: 50
 Randomization amplitude ................ <        0.000 >: 10
 Number of grid points, outer shell ..... <         2483 >: 
 Input model for inner shell (empty for micelle) <         .cif >: 
 Output file ............................ <         .cif >: micelle.pdb