CNS: Introduction to Creating a Generate File

26 January 2010

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
cns generate CNS: Introduction to Creating a Generate File
A new window will open
3) Change ‘convert chainid to segid if chainid is left blank’ to True
cns protein CNS: Introduction to Creating a Generate File
Scroll down a ways to ‘general parameters’
4) Change: set bfactor flag to True AND set occupancy flag to True
cns generate parameters CNS: Introduction to Creating a Generate File
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.

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     | Posted by Sean | Categories: Crystallographic Data Processing | Tagged: , , , , , |