Alternative to MinMover

[Anonymous]

Hello everyone,

I have checked the D070_Refinement.py* script provided by the Graylab, and I would like to make my own little refinement script based on it and the other guides and tutorials available.

I have, however, run into problems as the ‘MinMover’ method is not available under pyrosetta.rosetta.protocols.simple_moves which prevents me from using the approach outlined in D070_refinement.py to minimize the pose score.

Initially, I thought that it was a small mistake in the specific version I had download, but it is also not listed in the documentation, so I reckon it is a design choice. (see https://graylab.jhu.edu/PyRosetta.documentation/pyrosetta.rosetta.protocols.simple_moves.html)

Can someone recommend another mover for minimizing a pose score? I have had a look at the documentation, and there but with my limited experience, I could not find a suitable alternative. I have considering writing my own spaghetti code and including that in my routine, but that would not allow me to employ the very nice and transparent ‘SequenceMover()’ method to combine the different movers. Also, I reckon calling some C++ routine for minimization through PyRosetta is much faster than what it can conjure up in python.

Any suggestions would be very welcome – cheers!

Kind regards,

Martin

 

SPECS:

OS: MacOS 10.13.6

Python version: 3.6.3

Pyrosetta version: PyRosetta4.Release.python36.mac r183 2018.24

(In the feature I will probably install Pyrosetta on our linux cluster, but for now I am learning the ropes on my labtop – I don’t know if it important)

* see https://graylab.jhu.edu/pyrosetta/downloads/scripts/demo/D070_Refinement.py

[Anonymous]

We did a bit of reorganization of the simple_moves namespace, as it was getting crowded. (This was driven mostly by C++ level code organizational issues.)

The MinMover (and the PackRotamersMover) are now in the minimization_packing namespace: https://graylab.jhu.edu/PyRosetta.documentation/pyrosetta.rosetta.protocols.minimization_packing.html

The included search engine on the PyRosetta documentation page isn’t great but one trick to find such moved classes is to do a Google search with `site:site:graylab.jhu.edu/PyRosetta.documentation` added.  At least for me, when I do this with MinMover, this pulls up the minimization_packing documentation page as the first hit.

[Anonymous]

Hello rmoretti,

Thanks for both the heads up about the new location of MinMover and the googling tip – much appriciated

My code works now

kind regards,

Martin

[Author]

Posts