Note

cryo_fit2 is under active development.

Consider to use cryo_fit1 instead.

Author

Pavel Afonine, Doo Nam Kim (doonam.kim@gmail.com)

When cryo_fit1 and cryo_fit2 are useful?

See the When cryo_fit1 and cryo_fit2 are useful? in FAQ

When cryo_fit2 is useful?

See the When cryo_fit2 is useful? in FAQ

When cryo_fit2 is more useful than cryo_fit1?

See the When cryo_fit2 is more useful than cryo_fit1? in FAQ

Theory

• This program uses phenix.dynamics.
• Simulated annealing is carried out by default to minimize the object function T ( = T_target_map*map_weight + T_geom*wc ).

• map_weight is cryo-EM map weight and wc is a geometry keeping weight.

How to install

See the installation notes for cryo_fit2

How to Run Cryo_fit2

See the tutorial notes for cryo_fit2

FAQ

See the cryo_fit2 FAQ

Limitation

• Cryo_fit2 does not use electrostatic interaction. Therefore, it does not fully capture all physical forces.
  • See phenix.dynamics for detail.
  • Cryo_fit version 1 also omits electrostatic interaction so that molecular dynamics simulation runs faster.