CNS: Introduction to Creating a Generate File
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.
chempilot
January 27th, 2010 at 12:29 PM #
thanks for all the info. i’ve been creating my first model and have found your site a lot of help. i have found a lot of books/web-sites, etc. on how x-ray diffraction works and the very basics of data reduction, modeling, but very little practical knowledge (i.e what is a good Rfree or Rwork, etc). i’ve been using Phenix simply because CCP4 seemed so convoluted and overwhelming. “change to this file format, then run it with x-program, then change back to this file format and run x-program, etc” geesh! no wonder a PhD takes 6years+. :O)
Sean
January 28th, 2010 at 1:51 PM #
Hi chempilot,
Welcome to P212121! I am glad to hear this site is proving helpful. All the best with your first model.