This project has moved

Go to https://github.com/BranniganLab/density_threshold_affinity for the latest versions of these scripts (and more)

densitymap

VMD and python tools for calculating and plotting 2D lipid density maps

Running: TCL

Start with the TCL folder. In the helpers directory you have three TCL scripts. BinTools has required functions for the overall script. Lipid_Saturation_Head sets up a series of macros to organize lipids by head group and saturation. asign_helices_2BG9_CG breaks down the protein's structure into the different chains and allows users to isolate specific alpha helicies. Not it will only work for 2BG9 structure. This version is a modification from Grace Brannigan's.

The file densitymap contains the TCL functions. It is suggested to build a run file to load coarse grained simulations and call the polarDensityBin function from there. To run:

source polarDensity.tcl polarDensityBin .

Please run for one lipid at a time. Side Note: This script uses qwrap by Jerome Henin (https://github.com/jhenin/qwrap). I have not been sucessful installing qwrap on a Mac.

Running: Python

polarDensity_helper contains the organization and plotting routines. This is the file you want to change paths in for your data files! Density_Analysis runs the analysis. Please note, in it's current stage it has been designed to work with a few very specific membranes.

To run:

Density(, ddg=False, lipids=[list of lipid resnames, saturations, or head groups], enrich=<True/False>) If enrichment is True, it will produce an a polar enrichemnt plot normalized to the bulk membrane. If False, it will produce a density plot. Please leave ddg=False, this was implemented later in Polar_Binning_DeltaG (https://github.com/BranniganLab/Polar_Binning_DeltaG).