MembraneThickness

Membrane Thickness Tool

The tool performs two main calculations, namely:

• the per-frame bilayer thickness, and
• a 2-D thickness map, showing the local thickness

The two calculation types are presented as separated tabs in the tool's dialog (options shared by the two tools are at the top of the dialog).

1. Bilayer thickness

The (per-frame) thickness computation is based on the projected mass distributions for the selected atoms (usually "name P"). These projections should form two peaks; their distance is the membrane thickness, w(t).

1.1. Requirements

See [GeneralRequirements].

1.2. Input

1. Boundary layer atom selection: atom selection to define the membrane boundary layer. Default: “name P”.
2. From: initial frame number.
3. To: last frame number. To analyze until the last frame, type “last”.
4. Step: "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
5. Output file path: path to the output files that will be created. A file suitable for external analysis called filename.thickness will be created.

1.3. Output file format (tabulated)

filename.thickness

Frame ThicknessZ CenterZ
0  49.66 -48.02
1  49.63 -45.63
2  49.77 -44.52
3  49.56 -49.31
4  49.64 -44.74
5  49.42 -46.49
6  49.77 -50.88
7  50.00 -47.38
8  49.62 -49.88
9  49.72 -45.76

• Frame: frame number.
• ThicknessZ: Membrane thickness along the Z axis.
• CenterZ: Z location of the membrane center.

2. Thickness / deformation map

This function interpolates the z coordinates of selected atoms (usually "name P") into a regular orthogonal grid in the xy plane. Grid spacing is the user-selectable resolution. Thickness maps can be visualized in a contour plot (Plot average) or superimposed to the currently-loaded molecule as volumetric maps (Load avg. volumetric DX file).

The following definitions apply for the thickness map computation (.thicknessmap.dat file) :

• Zbottom Interpolated location of the selected atom in the bottom bilayer
• Zmid Location of the membrane midplane
• Ztop Interpolated location of the selected atom in the top bilayer
• ZMeasure Depends on the computation selected through the radio button:
  • "Total" --> (Ztop-Zbottom)
  • "Bottom" --> Zbottom
  • "Top" --> Ztop

Note that the Average thickness computation (2D display and .thicknessmap.dx file) is defined differently. Again, the value shown depends on the radio button selection, namely:

• "Total" --> Time-averaged bilayer thickness
• "Bottom" --> Time-averaged deformation map for the bottom leaflet
• "Top" --> Time-averaged deformation map for the top leaflet

Deformation is defined as the interpolated location of the head-groups after translating the chosen leaflet's center at Z=0. Therefore, deformation takes on both negative and positive values. Note that, irrespective of the leaflet, deformation is positive when it expands the membrane, and negative otherwise.

Limitations

• Averaging does not account for drift. If you system is drifting heavily (after accounting for the wrapping) averaged results will be incorrect. You may want to apply a suitable alignment before computing. (You will likely want to subtract a protein's center of mass.)
• The computation does not account for protein's excluded volume. The bilayer thickness will be interpolated everywhere. If you want to have an idea of the surface occupied by the protein, visualize it in the volumetric view.
• Only orthorhombic boxes are supported.

2.1. Requirements

• Only orthorhombic cells are supported.
• See [GeneralRequirements].

2.2. Input

1. Boundary layer atom selection: atom selection to define the membrane boundary layer. Default: “name P”.
2. From: initial frame number.
3. To: last frame number. To analyze until the last frame, type “last”.
4. Step: "step - 1" frames will be skipped at each iteration. One frame is analysed at each iteration.
5. Resolution: spacing of the interpolation grid, in Å
6. Type of analysis: total membrane thickness or top/bottom leaflet deformation can be selected.
7. Output file path: path to the output files that will be created. 2 files will be generated, a filename.thicknessmap.dat file suitable for external analysis, and a volumetric DX file called filename.thicknessmap.dx.

2.3. Output file format (tabulated)

filename.thicknessmap.dat

Frame GridX GridY  ZMeasure  Zbottom Zmid Ztop
0      74.45 -97.13  50.47  -73.49 -48.02 -23.02
0      74.45 -95.13  50.60  -73.54 -48.02 -22.94
0      74.45 -93.13  50.70  -73.59 -48.02 -22.89
0      74.45 -91.13  50.77  -73.63 -48.02 -22.86
0      74.45 -89.13  50.76  -73.68 -48.02 -22.92
0      74.45 -87.13  50.65  -73.72 -48.02 -23.07
0      74.45 -85.13  50.50  -73.75 -48.02 -23.25
0      74.45 -83.13  50.39  -73.77 -48.02 -23.37
0      74.45 -81.13  50.33  -73.77 -48.02 -23.44
0      74.45 -79.13  50.33  -73.78 -48.02 -23.45
0      74.45 -77.13  50.38  -73.80 -48.02 -23.42
0      74.45 -75.13  50.49  -73.84 -48.02 -23.35
0      74.45 -73.13  50.63  -73.89 -48.02 -23.26
[...]

• Frame: frame number.
• GridX: X coordinate of the grid point
• GridY: Y coordinate of the grid point
• ZMeasure: total thickness (Ztop - Zbottom) or leaflet thickness (Ztop or Zbottom), depending on the selected analysis type. See above.
• Zbottom: Z location of the bottom leaflet at the given grid point
• Zmid: Z location of the bilayer center at the given grid point
• Ztop: Z location of the top leaflet at the given grid point