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 of the atoms of the membrane.
For this, they likely: 1) Open protein and equilibrated membrane in pymol 2) From the menu: Choose Mouse-> 3 button editing 3) Shift+Middle click to move the protein on top of the membrane 4) Shift+Left click to rotate the protein into the desired orientation. 5) save the protein in its new location Then, they run the program they wrote, which uses grimaces to insert the protein into the membrane at roughly the position and orientation where they have dragged it. If you don't have any experimental evidence for how the protein sits in the membrane, http://opm.phar.umich.edu/server.php can give you a start. On Sat, Nov 14, 2015 at 11:35 AM, samira poulakchi <sa...@modares.ac.ir> wrote: > 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? > > > ------------------------------------------------------------------------------ > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >
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