Welcome to ResiDEM Documentation.

ResiDEM is a tool to analyze isomorphous difference density map and estimates residues having difference density feature associated with it.

This documentation provides the command line functionality of running ResiDEM in Linux and Mac OS environment. The code might still be used in Windows OS, but the code is not tested in Windows.

The Installation section contains the installation instructions of ResiDEM command line tool. Sample usage of basic command line definitions can be seen in Quick Start Guide. If you want to know about the algorithm or more About ResiDEM, you can check out our paper:

ResiDEM: Analytical Tool for Isomorphous Difference Electron Density Maps Utilizing Dynamic Residue Identification via Density Clustering

ResiDEM is a tool which is composed of a few command line utilities. A detailed description of the command line utilities are found here. The main function of the tool is to identify the residues associated with difference density in isomorphous difference density map. It also quantifies the difference density features(blob) in single and multiple time periods collected at different experimental time delays.

  • residem is a command line utility which takes three inputs for its calculations: Refined reference structure(pdb), structure factor amplitudes or intensity profile of reference and triggered states as mtz files. This command line utility computes the isomorphous difference density map and identifies the difference density blob associated to particular residues. It generates and saves the computed results which can be further used for network visualization and other analyses.

  • residem_svd_csv is a command line utility which takes a reference state pdb and other command line arguments. It
    generates plots associated with residues contributing to difference density blobs. It plots 1D,2D representation of normalized, quantified difference density which is further used for network representation.

  • residem_coot is a command line utility which requires two arguments: one that corresponds to reference state structure(pdb), and the other being the generated isomorphous difference density (DED) map in .ccp4 format.

A detailed version of command line arguments can be seen in command line section.