| Usage | Dependencies | Installation | References
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: 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...
- see setup.cfg
- Linux operating system
- g++ >= 4.8
- mrDNA Multi-Resolution DNA simulations
- CUDA toolkit >= 6
- ARBD simulation engine
- NAMD molecular dynamics
- VMD visual molecular dynamics
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.
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