xPyder is a PyMOL plugin to analyze and visualize on the 3D structure dynamical cross-correlation matrices (DCCM), linear mutual information (LMI), communication propensities (CP), intra- and inter-molecular interactions (e.g. PSN), and more, to produce highly customizable publication-quality images. xPyder identifies networks (using concepts from graph theory, such as hubs and shortest path searching), compares matrices and focuses the analysis on relevant information by allowing extensive data filtering. xPyder includes a user-expandable plugin system that takes advantage of structural and dynamical information, contributing to bridge the gap between dynamical and mechanical properties at the molecular level.
The xPyder binary installers for Linux (32 or 64 bit), Windows and OS X
can be downloaded here. Please consult the user
manual and install the required software and libraries before
installing xPyder. While the installers should work fine on most
platforms, a plain compressed archive is also available to perform manual
installation in case it was necessary.
The user manual is available here:
Here are several useful scripts and utilities designed to easy the obtainment of xPyder-compatible input files.
We present here the test case of the psychrophilic alpha-amylase from Pseudoalteromonas haloplanktis (AHA)
and its mesophilic homolog pancreatic porcine amylase (PPA). Here you can
download a dynamical cross correlation matrix (DCCM), which describes the
correlated motions between alpha carbons of the proteins, both for AHA and
PPA. A pdssp file, which describes the persistence degree of secondary
structure in the MD simulation, and a dssp output file are also available.
The data were calculated on full-atom molecular dynamics simulations. The
crystal structure of AHA (1AQH) is also available to plot the correlations
encoded by the matrices, as long as the dssp output file for 1AQH.