Re: [modeller_usage] Make non-adjacent mutations, preserve backbone and avoid clashes
To: David Johnson <>
Subject: Re: [modeller_usage] Make non-adjacent mutations, preserve backbone and avoid clashes
From: Modeller Caretaker <>
Date: Tue, 30 Jul 2013 10:12:37 -0700
Cc:
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.