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ELLLIP manual

ELLLIP

Written by M.V. Petoukhov.
Post all your questions about ELLLIP to the ATSAS Forum.

© ATSAS Team, 2019

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 from lipid models as two decoupled building blocks for inner and outer leaflet. Two quasi-uniform angular grids with arbitrary user-specified number of axes for outer and inner liposomal membrane leaflets are generated. Then the two lipids are aligned with these axes and they are positioned at the inner and outer surfaces of the user-defined ellipsoid with semiaxes A, B, C. Finally, the program allows for randomizing the positions of the lipids whereby their centres are additionally displaced along the appropriate direction to account for the possible non-ideality and disorder of the bilayer.

Running ELLLIP

Interactive Configuration

ELLLIP can only be run in the dialog mode, no command line arguments are accepted.

ELLLIP interactive prompt:

Screen TextDescription
Input PDB file, outer shell Lipid file name for the outer leaflet of the liposome
A-semiaxis, outer shellSemiaxis along X in Angstroems
B-semiaxis, outer shellSemiaxis along Y in Angstroems
C-semiaxis, outer shellSemiaxis along Z in Angstroems
Randomization amplitudeDisorder amplitude of the liposome shell
Number of grid points, outer shellTotal number of lipids in the outer shell
Input PDB file, inner shell Lipid file name for the inner leaflet of the liposome
Half-width of the shellHalf distance between the head groups of inner and outer lipids
A-semiaxis, inner shellSemiaxis along X in Angstroems
B-semiaxis, inner shellSemiaxis along Y in Angstroems
C-semiaxis, inner shellSemiaxis along Z in Angstroems
Number of grid points, inner shellTotal number of lipids in the inner shell
Output PDB fileResulting file with the liposome

Runtime Output

There is no runtime output after the manual configuration

ELLLIP Input Files

ELLLIP accepts two PDB files with the lipid structures for the outer and inner leaflets

ELLLIP Output Files

ELLLIP writes out the PDB file with the liposome structure

Example

>elllip.exe
***  Makes an elipsoidal liposome from the structure   ***                                                              
***  of two monomers                                   ***                                                              
***  Written by M.Petoukhov  ---   Version 1.0         ***                                                              
***     Last revised  ---  10/06/19 15:00              ***                                                                                                                                                                                     
Input PDB file, outer shell ............ <         .pdb >: p2r2                                                         
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 ................ <         .000 >: 8                                                            
Number of grid points, outer shell ..... <        67548 >:                                                              
Input PDB file, inner shell ............ <         .pdb >: p2r1                                                         
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 PDB file ........................ <         .pdb >: tt

  Last modified: October 29, 2019

© BioSAXS group 2019