[phenixbb] real space refinement

Nathaniel Echols nechols at lbl.gov
Mon Jul 28 06:40:33 PDT 2014

On Mon, Jul 28, 2014 at 9:19 AM, George Devaniranjan <devaniranjan at gmail.com
> wrote:

> I know this is going to sound blasphemous in phenix (my apology
> particularly to Pavel) but is there other s/w that does similar things to
> phenix.real_space_refine ?
> I used that already (works very well) but was wondering if there was
> anything similar out there to do a comparison.

Not exactly the same, but several (non-graphical) methods for
refinement/rebuilding into low-resolution maps:

Dimaio, F., Tyka, M. D., Baker, M. L., Chiu, W., & Baker, D. (2009). J.
Mol. Biol. 392, 181–190.

Haddadian, E. J., Gong, H., Jha, A. K., Yang, X., Debartolo, J., Hinshaw,
J. R., Rice, P. A., Sosnick, T. R., & Freed, K. F. (2011). Biophysical
Journal. 101, 899–909.

Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, and
Klaus Schulten. Flexible fitting of atomic structures into electron
microscopy maps using molecular dynamics. Structure, 16:673-683, 2008.

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