phenix.dynamics: simple model perturbation

This program performs very crude molecular dynamics on a model, usually for the purpose of removing any bias in R-free due to previous refinement against a different test set. It is not suitable for generating physically realistic trajectories, due to the lack of attractive forces such as electrostatics, and lengthy runs will result in the model falling apart. However, it is very effective for de-biasing while maintaining approximately correct geometry, and is also very fast (unlike simulated annealing in phenix.refine).

The inputs for the program are very similar to those for phenix.geometry_minimization; the only required files are a model and any necessary restraints (CIF) files for non-standard ligands. By default the dynamics is run at approximately room temperature; higher temperatures will result in faster movement. Note however that unlike simulated annealing, the model will tend to unfold rapidly at high temperatures.

Alternatives and complementary programs

  • Simulated annealing has some advantages due to the ability to simultaneously de-bias and optimize the model against the data, which prevents the structure from unfolding at high temperatures. The main disadvantage is the much longer runtime.
  • phenix.pdbtools can be used to reset B-factors, or shake coordiantes without geometry restraints. The latter is redundant if dynamics is run, but setting the B-factors to suitably low starting values (approximately 10 for most resolutions) will help remove bias.
  • Both of the above steps can also be run at the start of phenix.refine; click the "Modify start model" button in the GUI to access options.
  • To perturb structures for use as molecular replacement models, there is a separate program providing an interface to the normal modes method in Phaser (also available in the GUI under "Model tools"). This does a better job conserving local structure.

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