Visualization and exploration tool for MD trajectories using Bokeh and PyMOL
You need, at a minimum (requirements):
- Python 2.7 (only for the moment)
- NumPy
- Bokeh (=0.12.10)
- MDAnalysis
- xmlrpclib
- PyMOL
And screen unix command.
I highly recommand you to install the Anaconda distribution (https://www.continuum.io/downloads) if you want a clean python environnment with nearly all the prerequisites already installed (NumPy, Bokeh).
For the rest, you just have to do this.
pip install xmlrpclib
conda config --append channels conda-forge
conda install mdanalysis
conda install -c schrodinger pymol1 . First, you need to start Bokeh and PyMOL.
python run_servers.py #(Yep, that's all)2 . Now, it's time to explore your MD trajectory!
python visualize.py -t topology.psf -d traj.dcd -c coordinates_2d.csvCommand line options
- -t/--top: topology file (psf, pdb)
- -d/--dcd: single trajectory or list of trajectories (dcd, xtc)
- -c/--configuration: 2D coordinates obtained using your favorite dimensional reduction method (like SPE ?)
- -b/--bin: size of the histogram's bin (default: 0.025)
- --max-frame: maximum number of randomly picked frames (default: 25)
- --min-bin: minimal number of frames needed to show the bin (default: 0)
- --cartoon: Turn on cartoon representation in PyMOL (default: False)
Coordinates file format
It's a simple csv file with 2, 3 or 4 columns:
- 2 columns: [X,Y]
- 3 columns: [frame_idx,X,Y]
- 4 columns: [frame_idx,X,Y,energy]
- Jérôme Eberhardt. (2017, February 2). jeeberhardt/visualize. Zenodo. http://doi.org/10.5281/zenodo.268039
MIT