What are PMV, ADT and Vision?Up to table of contents
This FAQ applies to: Any version.
PMV is the Python Molecule Viewer, which allows one to view molecules and rotate them in 3D. Molecules can be colored and rendered in various ways, including as secondary structure ribbons or as molecular surfaces. PMV has a sophisticated selection mechanism based on its four level hierarchical data structure: Molecules are at the top and contain Chains, which contain Residues, which consist of Atoms. PMV is written in Python, an interpreted, object-oriented language that is easy to learn. While the the user accesses PMV commands via the menus of its Graphical User Interface, PMV records these operations in a file called 'mvAll.log.py'. This log file is a pure Python script which can be edited and/or sourced at a later time, to re-do these earlier operations. PMV also offers an extremely useful 'Undo' command for most operations.
also known as AutoDockTools, consists of 5 specialized modules for PMV, so learning about PMV helps to understand
what is possible with ADT. Take a look at both the ADT Tutorial
Tutorial. ADT is an easy-to-use graphical front-end to the
automated docking software packages AutoDock and AutoGrid. ADT provides menus to:
- set up a ligand (the 'moving' molecule to be docked) and write out a PDBQ file;
- set up a macromolecule (the 'fixed' molecule being docked to) and output a PDBQS file with solvation parameters;
- assign Kollman United Atom charged to a protein or peptide, or DNA or RNA;
- compute Gasteiger PEOE partial charges for small molecules or cofactors;
- add polar hydrogens, or 'merge' non-polar hydrogens;
- set up a grid box for atomic affinity grid maps and electrostatic potential maps around the target macromolecule;
- set various docking parameters;
- write GPF and DPF files (grid parameter and docking parameter files);
- launch AutoDock and AutoGrid calculations;
- read in DLG files (docking log files) and visualize AutoDock results;
- visualize grid maps by isocontouring them in 3D(using isocountouring library developed in Chandrajit Bajaj's group at UT Austin - part of UTpackages - http://ccvweb.csres.utexas.edu/software ); and also
- cluster and re-cluster docking results in various ways.
VISION, or the Visual Programming Environment, is
an advanced environment in which Python-based object-oriented components can
dragged-and-dropped and 'wired' together to create new applications. It
consists of various libraries of 'nodes', each node performing some
well-defined computational task. Molecules can be read in, for example,
using one of the 'MolKit' library's nodes.