Fukui functions shows the level of reactivity of different places in a complex molecule. They can be easily plotted with GabEdit software but it has a pure functions of chemical drawing. PyMol is a powerful drawing instrument and here we show how to plot Fukui function with PyMOL after two calculation steps with FireFly (PC-GAMESS).

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With QM software like GAMESS/Firefly it is possible to obtain much information about a molecule in text format. There exist some «envelope» software like Gabedit or WxMacMolPlt that could help you to visualize this information. Here we provide some instructions that will allow you to make your own visualization using powerful abilities of PyMol. Below […]

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This PyMol script is capable of generating a set of a molecule’s conformations, which can be further used to calculate their potential energy or any other properties. The script enables one to vary several internal degrees of freedom (DOFs) synchronously as well as scanning over a multidimensional grid in a space of DOFs. To use […]

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Some distributives (gentoo, openSuse, etc.) contains default Pymol  without vmd molfile plugins. By the way these plugins are essential because give an ability to open trj, xtc, cube and other different useful file formats. Here is step-by-step instruction to compile pymol-1.4.x on openSuse 12.1 but I suppose it might work on other distributives as well.

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This script allows one to visualize normal modes, calculated with GROMACS package, using PyMol. In particular the script loads Hessian matrix from an .mtx file produced by Gromacs, solves for it’s eigenvectors and eigenvalues and prints them out, and finally produce several frames corresponding to selected vibrational mode. See related media in the end of […]

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The script generates nanotubes of arbitrary structure. See related media in the end of the page. To use it, save script to some file, then load into PyMol with the command: PyMol> run /path/to/script.py then issue the command: PyMol> ntgen obj_name, n, m, l This will produce an object «obj_name», containing SWNT characterized by two […]

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The script is intended to be used from PyMol molecular visualization system and allows one to generate &QM_KIND, &LINK and &CELL parts of CP2K input easily. Given a molecular object name and QM part selection name (which can be defined using either approach available in PyMol) it generates output file with corresponding input groups. To […]

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