I would like to ask if there is a function that causes "tethering" or
"atom fixing" during optimization in modeller (i.e. is there a function
that forces the molecule to remain close to it's original PDB during
optimization?)
If so, is there a way to turn it off?
Of course - that is what Modeller does. It builds models by restraining
them to look like the templates, so the model will remain close to the
original PDB (at least in regions of high sequence identity) by
construction. You could "turn it off" by not building homology-derived
restraints, but then obviously homology modeling wouldn't work.
If you want to force specific parts of the system not to move (or not to
move much) then you have several options:
1. Override automodel.select_atoms() and deselect the atoms you want to
remain fixed (they then will not move at all).
2. Use features.x_coordinate in a restraint to restrain an atom on the
x axis (see also y_coordinate and z_coordinate).
3. Add a rigid body to the system.
4. Restrain one or more moving atoms with distance restraints to a
fixed atom.
Ben Webb, Modeller Caretaker
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