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 electron density.

Command

Syntax:

nucleofind [OPTIONS]

Example Usage

Simple Syntax:

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

Advanced Syntax:

            nucleofind -m phosphate -i reflections.mtz -o predicted.map -r 2.5 -intensity F -phase phi -no-symmetry
        

Options

Description of each option:

-i, -input

Path to input file.

Formats accepted: MTZ or CCP4 map

Required

-o, -output

Path to output .map file

e.g. -o prediction.map

If multiple models are specified, the suffix _model.map will be added to the outputs.

e.g. -m phosphate,sugar -o prediction outputs two files prediction_phosphate.map and prediction_sugar.map

Required

-m

Name of nucleic acid characteristic to predict

e.g. -m phosphate

e.g. -m phosphate,sugar

e.g. -m all

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

-intensity

Column name of structure factors weights.

Default: FWT

-phase

Column name of phase weights.

Default: PHWT

-no-symmetry

Predict over the entire unit cell instead of the asymmetric unit

Advanced

-raw

Use raw predicted values to form the output map.

Advanced

-variance

Use point-wise variance values to form the output map.

Advanced

-gpu

Use GPU acceleration. (Linux only)

Advanced

-model_path

Path to ONNX model for use with a custom model.

Advanced

-debug

Enable debug logging.

-silent

Disable progress bar.

-h, --help

Displays help.

-v, --version

Displays version and exits.

Last modified: 25 September 2024