I would disagree with your assertion that they use pymol to "insert" the
protein into the membrane. They use the program they wrote, g_membed, to
insert the protein. They used pymol to overlap them for the beginning of
the simulation. That is, they use pymol to place the atoms of the protein
on top
there is an article''g membed: Efficient insertion of a membrane protein
into an equilibrated lipid bilayer with minimal perturbation.'' which use
pymol to insert protein into bilayer membrane. How can they do it?--
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