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
CNS (Crystallography and NMR systems) is able to generate a composite omit map. In getting started, one must first create a generate file.
1) Input then scroll down to Refinement, composite_omit_map.inp and Edit
2) Three ‘amy’ files need to be placed with your appropriate files
The space group, unit cell and angles also need to be updated (I find this slightly annoying since the information is contained in the files you are submitting)
3) Bulk solvent correction needs to be set to False
4) I suggest putting the map grid at 0.25, raising the starting temp to 1500 and 50 K steps. I have come across those that adjust the random number generator, but haven’t noticed a huge difference.
Save an updated file
In your terminal:
type: cns < composite_omit_map.inp > composite_omit_map.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 composite_omit_map.out
This will allow to see the progress of the processing in your terminal
Doing this has allowed me to quickly see if my inputs have generate an error
CNS (Crystallography and NMR systems) is able to perform simulated annealing as well as generate a composite omit map, which is nice compliment to the CCP4 suite of programs (Phenix has similar features). In getting started, one must first create a generate file which is what the post will be covering via their website.
1) In your terminal type: cns_web (note: admin may have set up this command different)
Web browser should launch and select input files at middle left
2) Scroll down to generate.inp and click edit
A new window will open
3) Change ‘convert chainid to segid if chainid is left blank’ to True
Scroll down a ways to ‘general parameters’
4) Change: set bfactor flag to True AND set occupancy flag to True
Save and Exit
In your terminal
type: cns < generate.inp > generate.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 generate.out
This will allow to see the progress of the processing in your terminal
Doing this has allowed me to quickly see if my inputs have generate an error
Note: Depending on your needs using generate_easy.inp may be sufficient
Additional information can be found in the tutorial section of the CNS website.