Overview

Unlike Cryo_fit1 that uses gromacs, CryoFit2 runs within phenix suite. Therefore, it doesn't require gromacs installation and is faster to execute. It suits the need not only traditional "static" fitting but also "dynamic" fitting.

Theory

This program uses phenix dynamics algorithm written by Pavel.

Simulated annealing is carried out by default to effectively minimize the objection function T (=T_target_map * wx + T_geom * wc ). wx and wc are weights.

Traditional “static” fitting (A) versus “dynamic” fitting (B)

Cryo_fit 1 & 2 are recommended when the initial structure is different from map

How to Run Cryo_fit2

See the tutorial notes for cryo_fit2

Limitation

If wx is too small like 5, it may break starting secondary structure. When wx is 100, it kept starting helix structure. If wx is too big, angle change for each step maybe too big (~30 degree), so pdb validation later (like molprobity) may raise a red flag.

We will add real_space_refine style wx, wc auto-optimization module soon.

Author

Doo Nam Kim, Pavel Afonine