On Mon, Jul 23, 2012 at 9:50 AM, Scott Foy <[email protected]> wrote: > We are computationally averaging several homologous protein structures into a > single structure. This of course will lead to a single protein structure that > possesses poor biophysical characteristics of bond lengths, bond angles, > steric hindrance, etc. Therefore, we will need a refinement program that is > very rapid and that will restore optimal protein parameters upon input of a > single PDB coordinate file. We are considering several programs such as > Phenix and CNS and would appreciate any comments or opinions as to > recommendations, advantages, and disadvantage for these, or other, programs. > We will need to refine thousands of PDB files so speed is a significant > consideration.
Can you clarify whether you intended to refine against experimental data, or just clean up the model geometry? -Nat
