Prime User Manual - ISP

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Chapter 7: Prime–Refinement
Prime 2.1 User Manual
Figure 7.1. The Prime Membrane Setup panel.
7.3 Setting Up an Implicit Membrane
The Prime implicit membrane model is intended for proteins embedded in a membrane. The
implicit membrane is a low-dielectric slab-shaped region, which is treated in the same way as
the high-dielectric implicit solvent region. Hydrophobic groups, which normally pay a solvation
penalty for creating their hydrophobic pocket in the high dielectric region, do not have to
pay that penalty while in the membrane slab. Conversely, hydrophilic groups lose any shortranged
solvation energy from the high dielectric region when moving into the low dielectric
region.
The implicit membrane model is intended for use with proteins that span the membrane. The
slab is trimmed for efficiency, so that any structure that is too small or too far away from the
membrane is likely to result in too much trimming and might not produce useful results.
The membrane is marked in the Workspace by a semitransparent cube with a white line that is
perpendicular to the surfaces of the membrane (which are planar). The membrane surfaces are
colored red, and the other faces of the cube (which are interior to the membrane) are colored
green. You can control whether the sides of the cube are displayed with the Show cube sides
option. The direction of the line shows the orientation of the membrane.You can adjust both the
thickness and the orientation of the membrane.
To set up an implicit membrane:
1. Click Set Up Membrane.
The Membrane Setup panel opens.