Prime User Manual - ISP

2. Click New Membrane (Auto-Place).
A membrane is placed, marked in the Workspace as described above.
3. Select Adjust membrane position.
Chapter 7: Prime–Refinement
4. Use the middle mouse button to rotate the membrane and the right mouse button to translate
the membrane.
5. Adjust the thickness by entering a value in the text box or using the arrow buttons to
adjust the thickness up or down by 0.1 Å at a time.
6. Deselect Adjust membrane position.
This is necessary to exit membrane adjustment and return to normal Workspace
operations.
If you want to add the membrane to the entries that are selected in the Project Table, click Save
to Selected Entries. The membrane is stored as a set of coordinates for each end of the white
line. The entries that you select should therefore contain proteins that occupy approximately
the same region of space as the protein used to define the membrane. Otherwise, you will have
to adjust the membrane location for these entries.
If you already have a membrane defined for another project entry, you can load it for the
current entry by selecting the entry that has the membrane and clicking Load from Selected
Entry.
If the protein has pockets that would be occupied by solvent (water), you can select these
regions to exclude from the implicit membrane using the tools in the Region to exclude from
membrane section. The solvent dielectric constant is then used for these excluded regions.
Excluded regions are defined by a set of spheres that are placed on atoms adjacent to the
region. The spheres can overlap, and should cover the entire excluded region. It does not matter
that they overlap the protein, because the protein dielectric is not affected. To define a region,
select Place exclusion sphere and pick atoms in the Workspace that are adjacent to the region.
For each pick a sphere is placed on the atom. You can remove the sphere by picking the atom
again. To adjust the sphere volume, use the Exclusion sphere radius slider. This slider only uses
integer values, because the exact size of the sphere isn’t critical: the spheres only has to cover
the excluded region.
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