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

--remove_clashing_protein

Enable clashing protein removal

If protein is built into nucleic acid density, NucleoFind will remove it. It is unlikely NucleoFind will remove correct amino acids, but it is possible.

Last modified: 28 November 2025