Dear Modeller users,
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?
Thank you in advance, Abdullah Ahmed _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969
On 4/1/10 7:28 AM, abdullah ahmed wrote: > 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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abdullah ahmed -
Modeller Caretaker