Julia Contreras-García: Software

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NCI web server: Online NCI tool for biosystems

Soon to be released! online tool especially designed for biosystems. No need to install anything! you will be provided with your NCI files from your pdb! Link

NCIPLOT : Visualization of non covalent interactions

This code enables graphical visualization of inter and intramolecular non-covalent interactions (i.e. hydrogen bonds, steric clashes and van der Waals) in systems ranging from small molecules to large biosystems.

NCI (Non-Covalent Interactions) is a visualization index based on the electron density and its derivatives. It enables identification of non-covalent interactions, based on the peaks that appear in the reduced density gradient (RDG) at low densities. RDG isosurfaces for these peaks enable the visualization of weak interactions. The isosurfaces correspond to both favorable and unfavorable interactions, as differentiated by the sign of the second density Hessian eigenvalue. The sign of this eigenvalue, times the density, is able to characterize both the strength and (un)favourable nature of the interactions and defines the isosurface colouring. See the reference below for a thorough explanation of the physics.

This program computes density and reduced density gradient (RDG) on a grid and provides Gaussian-format cube files and VMD scripts for the direct visualization of the results. It can be run using either SCF densities (wfn input files) or promolecular densities (xyz input files), which makes it applicable to large biosystems.

You can download NCIPLOT here

New addition:

Now you can create new cube files from a given one with just the interactions you want with just one simple script: range.csh !

You can download RANGE.csh here

Want to learn how to use NCIPlot through examples?

Download a guided tour through most common keywords here

CRITIC-JAIMELF : Topological analysis of ELF in the solid state

This programs is based on a novel computational procedure, general, automated and robust, for the analysis of local and global properties of the electron localization function (ELF) in crystalline solids.

The algorithm successfully faces the two main shortcomings of the ELF analysis in crystals:

  • the automated identification and characterization of the ELF induced topology in periodic systems, which is impeded by the great number and concentration of critical points in crystalline cells

  • the localization of the zero flux surfaces and subsequent integration of basins, whose difficulty is due to the diverse (in many occasions very flat or very steep) ELF profiles connecting the set of critical points.