Visualize

Visualization and exploration tool for MD trajectories using Bokeh and PyMOL

Prerequisites

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.

Installation

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 pymol

How-To

1 . 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.csv

Command 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]

Citation

Jérôme Eberhardt. (2017, February 2). jeeberhardt/visualize. Zenodo. http://doi.org/10.5281/zenodo.268039

License

MIT

jeeberhardt / visualize