ELLLIP manual
ELLLIP
Written by M.V. Petoukhov.
Post all your questions about ELLLIP to the ATSAS Forum .
© ATSAS Team, 2019
The following describes the
method implemented in ELLLIP , details of the
dialog prompt as well as the required
input and the produced output files.
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.
ELLLIP can only be run in the dialog mode, no command line arguments are accepted.
ELLLIP interactive prompt:
Screen Text Description
Input PDB file, outer shell Lipid file name for the outer leaflet of the liposome
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 PDB file, inner shell Lipid file name for the inner leaflet of the liposome
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
There is no runtime output after the manual configuration
ELLLIP accepts two PDB files with the lipid structures for the outer and inner leaflets
ELLLIP writes out the PDB file with the liposome structure
>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