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

--em

Enable EM mode

EM mode prevents phosphate position refinement

Last modified: 24 June 2025