CCP4 Program Suite
Author: Kevin Cowtan

# NAUTILUS (CCP4: Supported Program)

## NAME

nautilus - Statistical protein chain tracing

## SYNOPSIS

cnautilus -mtzin filename -pdbin filename -pdbout filename -colin-fo colpath -colin-hl colpath -colin-phifom colpath -colin-fc colpath -colin-free colpath -cycles number of cycles -hits number of seeds to find -resolution resolution -verbose verbosity -pdbin-ref filename -stdin
[Keyworded input]

## DESCRIPTION

'nautilus' performs automated building of RNA/DNA from electron density.

'nautilus' does not currently perform refinement - you will need to refine and recycle for further model building yourself. Neither does it assign sequence - the model is built as ploy-U.

## HOW TO RUN NAUTILUS

## INPUT/OUTPUT FILES

-mtzin
  Input 'work' MTZ file. This contains the data for the unknown, work structure. The required columns are F, sigF, and a set of HL coefficients or PHI/FOM from phase improvement, or alternatively map coefficients F/PHI if the phase improvement program provides them.
-pdbin
  [Optional] Input PDB file containing an initial model to be extended. Chains containing at least one non-nucleotide will be left untouched.
-pdbout
  [Optional] Output MTZ file. This will contain the new HL coefficients and map coefficients.
-pdbin-ref
  [Optional] Input PDB file containing a library of nucleotide geometry. Place the file nautilus_lib.pdb (from PDB 1HR2) in the current direcoty or give its location with this keyword.

## KEYWORDED INPUT

See Note on keyword input.

> ### -colin-fo colpath

> Observed F and sigma for work structure. See Note on column paths.

> ### -colin-hl colpath

> Hendrickson-Lattman coefficients for work structure. See Note on column paths.

> ### -colin-phifom colpath

> Phi/Fom as an alternative to Hendrickson-Lattman coefficients for work structure. See Note on column paths.

> ### -colin-fc colpath

> Observed map coefficients F and phi for work structure. If map coefficients are supplied, they are used to calculate a map directly, all the other input columns are then unneeded. See Note on column paths.

> ### -colin-free colpath

> Free R flag. See Note on column paths.

> ### -resolution resolution/A

> [Optional] Resolution limit for the calculation. All data is truncated.

> ### -cycles number of cycles

> [Optional] Number of cycles of model building to run. After a few cycles a refinement step is needed to allow further progress. Default=3.

> ### -cycles number of seeds

> [Optional] Number of chain seed positions to find as starting points for building. Half of these will be sugar-like features and half will be phosphate-like features.

> ### -verbose verbosity

#### Note on column paths:

When using the command line, MTZ columns are described as groups using a slash separated format including the crystal and dataset name. If your data was generated by another column-group using program, you can just specify the name of the group, for example '/native/peak/Fobs'. You can wildcard the crystal and dataset if the file does not contain any duplicate labels, e.g. '/*/*/Fobs'. You can also access individual non-grouped columns from existing files by giving a comma-separated list of names, e.g. 'FP,SIGFP'.

#### Note on keyword input:

Keywords may appear on the command line, or by specifying the '-stdin' flag, on standard input. In the latter case, one keyword is given per line and the '-' is optional, and the rest of the line is the argument of that keyword if required, so quoting is not used in this case.

## Reading the Ouput:

The output consists primarily of lists of the lengths of each chain at each step of the calculation. It provides little of use in tweaking how the program runs (indeed there is almost nothing to tweak), but I would be very grateful if you could send me your logfile so I can get some idea of whether the program works. Feel free to redact filenames and the cell parameters.

## Problems:

## AUTHOR

Kevin Cowtan, York.

## SEE ALSO