Command Line Usage

Once the models for NucleoFind are installed, NucleoFind is ready to run. Use this command line syntax to predict nucleic acid positions from density.

Command

Syntax:

nucleofind [OPTIONS]

Example Usage

Simple Syntax:

nucleofind -m nano -i reflections.mtz -o predicted.map

Advanced Syntax:

            nucleofind -m core -i reflections.mtz -o predicted.map -r 2.5 -amplitude F -phase phi
        

Options

Description of each option:

-i, -input

Path to input file.

Formats accepted: MTZ, CCP4, MRC and zipped equivalents

Required

-o, -output

Path to output folder which will contain NucleoFind predicted phosphate, sugar, and base maps.

e.g. -o nucleofind-predictions

Required

-m

Name of NucleoFind model

Available Models:

nano (25M parameters)
core (105M parameters)
ultra (415M parameters)

Optional if only one model is installed, otherwise required.

-r, -resolution

Resolution cutoff off to use with reflection data

E.g. a value of 2.5 uses only the 2.5 Angstrom and greater reflctions in the map calculation

-n, -nthreads

Number of threads to use

Default: Max available

-f, -amplitude

Column name of structure factor amplitudes.

Default: FWT

-phi, -phase

Column name of structure factor phases.

Default: PHWT

-no-symmetry

Predict over the entire unit cell instead of the asymmetric unit

Default: True

Advanced

-gpu

Use GPU acceleration. (Linux only)

Advanced

-debug

Enable debug logging.

-silent

Disable progress bar.

-h, --help

Displays help.

-v, --version

Displays version and exits.

Last modified: 02 January 2025