Phenix (Python-based Hierarchical ENvironment for Integrated Xtallography) has been developed for the determination of macromolecular crystallographic structures. Phenix is a leader in automating the structure determination process.
I am going to start playing around with Phenix, but first wanted bring together helpful resources about the program suite:
Are you using Phenix? Why or why not?
What resources have you found especially helpful? Do you have any tips or tricks for getting started?
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.