On Mon, Jul 28, 2014 at 9:19 AM, George Devaniranjan <devaniranjan@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.

-Nat