elija-feigl / dnaFit

collection of scripts related to the fitting of pseudoatomic models into cryo-EM maps of DNA-Origami

| Usage | Dependencies | Installation | References

dnaFit: cascading mrDNA-driven flexible fitting

A Python3 package that contains a collection of scripts related to the fitting of pseudoatomic models into cryo-EM maps of DNA-Origami structures.

Usage

Usage: dnaFit [OPTIONS] COMMAND [ARGS]...

  Cascaded mrDNA-driven MD flexible fitting script module:

  dnaFit commands:
      main pipeline:
      1. mrdna:   mrDNA structure prediction with custom settings for cadnano file.
                  (includes creation of prep folder for fitting)
      2. vmd_info:    print info for rigid body docking with VMD
      3. fit:     shrink wrap fitting if of rigid body docked mrDNA prediction
                  includes mask, pdb2cif, and link

Options:
  -v, --version  Show __version__ and exit.
  -h, --help     Show this message and exit.

Commands:
  center-on-map  Recenter atomic model center-of-mass on mrc cryo map...
  fit            Cascaded mrDNA-driven MD flexible fitting (shrink wrap...
  link           Links structural information of the CADNANO design file...
  mask           Mask mrc map to fitted atomic model.
  mrdna          MrDNA simulation of CADNANO design file with custom...
  pdb2cif        Generate atomic model in mmCIF format from namd PDB...
  prep           Prepare mrDNA results for fitting "dnaFit fit".
  vmd-info       Print VMD command for rotation of pdb around center of...

Dependencies

• see setup.cfg

without mrDNA:

• Operating system independent
• NAMD molecular dynamics
• VMD visual molecular dynamics

with mrDNA:

• Linux operating system
• g++ >= 4.8
• mrDNA Multi-Resolution DNA simulations
• CUDA toolkit >= 6
• ARBD simulation engine
• NAMD molecular dynamics
• VMD visual molecular dynamics

Installation

  pip install git+https://github.com/elija-feigl/DNA_Fit#egg=dnaFit

or

  git clone https://github.com/elija-feigl/DNA_Fit
  cd dnaFit
  pip install .

The simulation frameworks mrDNA + ARBD, NAMD + VMD have to be installed separately.

References

When using dnaFit Python Package in published work, please cite the following paper:

Kube, M., Kohler, F., Feigl, E. et al. Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution. Nat Commun 11, 6229 (2020). https://doi.org/10.1038/s41467-020-20020-7