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
Justin
February 8th, 2010 at 4:17 AM #
Instead of putting cns in background and using tail -f to see the log one could easily use tee
cns < refine.inp | tee refine.out
Sean
February 8th, 2010 at 3:19 PM #
Hi Justin,
Thanks! I will have to give that a try.
Jenn
February 9th, 2010 at 3:41 PM #
Sean, I’ve enjoyed your blog for a couple months now and just wanted to leave a general thank you for all the helpful posts!
Justin – what is the advantage of tee over the former? (Especially if you’re lazy and want to run a job in the background on your remote server while at home.)
Justin
February 9th, 2010 at 4:08 PM #
Well, in principal it does exactly the same for the user side. (man tee).
But I would always prefer running something in a screen session and detaching the remote screen session from you terminal, then sending a process in background and closing the ssh session. Screen is a very cool app, specially when you are often working on remote servers. Inside a screen, you can always leave your working env open.
Sean
February 10th, 2010 at 10:57 PM #
Hi Jenn,
Wow! Thanks for the comment and spending your time here over the last couple months.
I look forward to hearing more from you in the future