Automated Model Building

Using the predicted phosphate positions, NucleoFind is able to build nucleic acid into electron density.

Command

Syntax:

nucleofind-build [OPTIONS]

Example Usage

Run NucleoFind-build with predicted map:

            nucleofind-build -mtzin hkl.mtz
                             -seqin sequence.fasta
                             -pdbin xyz.pdb
                             -pdbout output.pdb
                             -phosin phosphate.map
                             -colin-fo FP,SIGFP
                             -colin-fc FWT,PWHT
                             -colin-free FREE
                             -cycles 3
        

Options

Description of each option:

-mtzin

Path to MTZ file.

Required

-seqin

Path to sequence or FASTA file.

-pdbin

Path to input model.

-pdbout

Path to output model

Required

-phosin

Path to the predicted phosphate map

Required

-sugarin

Path to the predicted sugar map

-basein

Path to the predicted base map

-colin-fo

Column name for observed structure factors

Example: FP,SIGFP

-colin-fc

Column name for map coefficients

Example: FWT,PHWT

-colin-free

Column name for free reflections

Example: FREE

-xmlout

Path to XML summary

-cycles

Number of cycles to run

Default: 3

Last modified: 25 September 2024