On 7/30/13 9:30 AM, David Johnson wrote: > I would like to make a handful of mutations that are not necessarily in > sequential order in the primary structure.

Did you look at http://salilab.org/modeller/wiki/Mutate%20model ? That only performs a single mutation, but it would be straightforward to modify the script to call mutate() multiple times.

> I would like to preserve the > backbone of the model and to keep fixed all side-chains except those of > the mutations and possibly nearby residues, which are to be moved ONLY > if necessary to void steric clashes.

If you deselect an atom, it won't move at all. If you select it, it will move if doing so reduces the scoring function. So it sounds like what you want here is to select the mutated residue and some nearby ones.

> Selecting all but the mutated atoms and setting > env.edat.nonbonded_sel_atoms = 2

This will only consider nonbonded terms between the mutated atoms (i.e. they won't see the rest of the protein). You probably want 1 here, not 2.

> a.library_schedule = autosched.slow

This will perform more steps of CG optimization than the default. It's probably unnecessary in your case.

> a.md_level = None OR a.md_level = refine.very_fast

The first turns off simulated annealing entirely; the second just does fewer steps of MD than the default. Again, the default is probably fine for you here.

> a.repeate_optimization = 3

Like it says, this repeats the entire optimization 3 times. Probably not necessary.

Ben Webb, Modeller Caretaker