nut is nutrition software to record what you eat and analyze your meals for nutrient composition. The database included is the latest USDA Nutrient Database for Standard Reference. This database contains values for vitamins, minerals, fats, calories, protein, carbohydrates, fiber, etc., and includes the essential polyunsaturated fats, Omega-3 and Omega-6. Nutrient levels are expressed as a percentage of the Daily Value, the familiar standard of food labeling in the United States, but also can be fully customized. Foods can be added from recipes or food labels, and nutrient intake can be graphed. The program is completely menu-driven and there are no commands to learn.
PLOTICUS is a command line utility for creating bar, line, pie, boxplot, scatterplot, sweep, heatmap, vector, timeline, Venn diagrams, and other types of charts and plots. ploticus is good for automated or just-in-time graph generation. It handles date, time, and categorical data nicely, and has some basic statistical capabilities. It can output to GIF, PNG, SVG, SWF, JPEG, PostScript, EPS, and X11. You can use convenient preset options or create complex scripts with rich and detailed color and style operations.
VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. VMD uses OpenGL and OpenGL Programmable Shading Language for high performance rendering of large structures.
The VP7 Way Kool Project is a GTK application which simulates a laboratory experiment with radioactive nuclei. The user can choose between many predefined radioactive sources or create new ones. The number of decayed nuclei and the activity of the source can be determined with a built-in counter. The beam can be attenuated with shields of paper, aluminium, and/or lead.
FlipDCD is a small utility for reversing the endianism of binary DCD trajectory files from Charmm and NAMD. This can be useful when running simulations on one architecture and visualizing or analyzing the results on another. FixDCD is a tiny utility to modify the header of an X-PLOR DCD file to make it readable by programs expecting Charmm DCD files, at the expense of a Timestep size value in the header.
Mol_Volume calculates the volume of a macromolecule by a method somewhat akin to the Monte Carlo method, namely, by measuring how many vertices of a dense regular grid happen to be within the probe radius of the molecule's atoms. The volume is then calculated as V = V_grid * N_near / N_total = N_near * V_per_node.
SODIUM places the required number of sodium ions around a (simulated) system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex). The ions are placed in the nodes of a cubic grid in which the electrostatic energy achieves the smallest values. The energy is re-computed after placement of each ion. A simple Coulombic formula is used for the energy. The coordinates of the placed ions are printed out in the PDB format for further usage. Trivial modifications to the program should allow the placement of any combination of multivalent ions of different charges.
Wat2ions is complementary to DelPhi, the renowned solver of the Poisson-Boltzmann equation. The electrostatic potential map pre-computed by DelPhi is used to replace a certain number of the water molecules of the bath, surrounding a solvated macromolecule, with ions. The potential on the oxygens of the water molecules is estimated using a 3D cubic spline interpolation of the pre-computed potential. The waters with the largest potential are replaced with chlorides, and the waters with the smallest potential, with sodii. No two ions are placed closer than a certain distance to each other. The coordinates of the macromolecule, the water bath (except the replaced waters), and the placed ions are output to a new PDB file.