Kevin Cowtan, University of York, September 2011. Last updated September 2011.

Colophon Nautilus (from Greek ναυτίλος, 'sailor') is the common name of marine creatures of cephalopod family Nautilidae. (Wikipedia)


'Nautilus' is a program for automatic model building of nucleotide structures in electron density maps. It will trace a map with no model, extend an existing model, or add nucleotide chains to an existing non-nucleotide model.

The latest version of the software is available through the CCP4 update system.

How to run Nautilus

Copy the file 'nautilus_lib.pdb' to your current working directory, or alternatively specify the location of this file with the keyword '-pdbin-ref'.

Modify the following examples to match your data.

After parrot:
cnautilus -mtzin my.mtz -colin-fc "/*/*/parrot"

After dm:
cnautilus -mtzin my.mtz -colin-fo FP,SIGFP -colin-hl HLADM,HLBDM,HLCDM,HLDDM

After refmac:
cnautilus -mtzin my.mtz -colin-fc FWT,PHWT
cnautilus -mtzin my.mtz -colin-fc FWT,PHWT -pdbin my.pdb

If you have a complex, build the rest of the structure first as far as possible, and provide this as input to nautilus using -pdbin.

See the documentation linked above for a full list of keywords.

Latest News

v0.2 Fixed corruption of existing model residue types, fixed most clashes, much faster.
v0.1 Initial release.