[cctbxbb] pdb shake - dihedral angles

Nathaniel Echols nechols at lbl.gov
Wed Feb 20 06:22:50 PST 2013

On Wed, Feb 20, 2013 at 3:51 AM, Dmytro Guzenko
<Dmytro.Guzenko at pharm.kuleuven.be> wrote:
> I wonder what would it take to write an equivalent to pdb_shake script from
> iotbx/examples with randomization of the backbone dihedral angles phi and
> psi, instead of all coordinates perturbation? I want to be able to randomize
> models in a more “realistic” way.
> Are there data structures/procedures that can be useful for this in cctbx,
> or should I extract the coordinates and take it from there?

I think this is non-trivial because of the lever-arm effect - you
would need to figure out a way to change phi/psi without propagating
down the rest of the chain.  What we do have is the ability to run
short molecular dynamics, which is what we usually use for this.  The
big disadvantage right now is that the geometry restraints aren't even
close to physically realistic, just good enough for X-ray refinement,
so the protein will tend to fly apart over time.  I believe you can
run it like this:

phenix.pdbtools model.pdb simple_dynamics=True discard_psi_phi=False

The final argument is optional but probably a good idea - we leave out
those restraints for validation purposes, but in this case it is
better to keep them within realistic limits.

The source code for this is in mmtbx/pdbtools.py.  You need to have
the geometry restraints available somewhere; obviously these are
distributed with Phenix, but I'm pretty sure you could also use an
external installation of the CCP4 monomer library - never tried this
myself though.  Another issue is that this will change all torsion
angles, not just the backbone; to prevent this, I think you'd need to
modify the dihedral angle restraint proxies for non-phi/psi angles
internally to have very high weights.  (We don't have any ready-made
code to do this but mmtbx/command_line/interpolate.py shows an example
of modifying the dihedral proxies in place.)


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