CNS: Simulated Annealing
CNS (Crystallography and NMR systems) is able to perform simulated annealing to get started, one must first create a generate file.
1) Input then scroll down to Refinement, refine.inp and Edit
2) amy.pdb needs to be replaced with your pdb file
3) The space group, unit cell, angles and amy.cv need to be updated
4) Adjust the resolution to your desired range. The overall B-factor correction should be set to isotropic unless you are dealing with very high resolution data (~1 Angstrom). Set Bulk solvent correction needs to be set to False
5) Change annealing schedule to slowcool
Note: Not shown, but I usually set the map grid to 0.25 for better viewing
Save an updated file
In your terminal:
type: cns < refine.inp > refine.out &
Note: if you renamed your generate files then use them as your .inp
The ‘&’ symbol allows your cursor to be free
type: tail -f refine.out
This will allow to see the progress of the processing in your terminal
This allows you to quickly see if the inputs have generate an error