OVERVIEW OF THE OPEN SOURCE MOLECULAR VIEWERS

E. MALIKOVA

National Research Nuclear University "MEPhI", Moscow, Russia

Contents:

Introduction
1. PyMOL
- 1.1. Overview
- 1.2. Acceptable molecular file formats
- 1.3. PyMOL Main Features
- 1.4. Program integration, plugins and scripts
- 1.5. Gallery
2. Jmol
- 2.1. Overview
- 2.2. Acceptable molecular file formats
- 2.3. Jmol Main Features
- 2.4. JmolApplet integration
- 2.5. Gallery
3. OpenAstex
- 3.1. Overview
- 3.2. Acceptable molecular file formats
- 3.3. Main Features
- 3.4. Gallery
4. Molekel
- 4.1. Overview
- 4.2. Acceptable molecular file formats
- 4.3. Main Features
- 4.4. Gallery
5. MacMolPlt
- 5.1. Overview
- 5.2. Acceptable molecular file formats
- 5.3. Main Features
- 5.4. Integration
- 5.5. Gallery
6. Conclusions
7. References

Introduction

In this short communication we offer you a brief overview over some open source molecular viewers. Some of this molecular viewers can be used for analyses of the results of computer modelling of nanostructures, obtained with help of quantum chemistry packages ( for example, the General Atomic and Molecular Electronic Structure System (GAMESS) - free for use a general ab initio quantum chemistry package). Some are good for not only vieweing molecular structures, but also for giving live 3D Presentations and sharing interactive visualizations. Some support exporting geometry to such well-known formats of 3d computer graphics as VRML, OBJ, Pov-Ray and so on, so the results obtained can be imported and used in such programms of 3ds Max, Maya, Pov-ray for producing high quality films, video and graphic content.

All this viewers take advantages of open source programms, so their users have the right to modify, improve them and use them in any way in their professional work.

Below are described some open source molecular viewers. Their main features are presented, results of molecular structures visualization obtained with them are presented.

1. PyMOL

Overview

PyMOL [1] is a molecular visualization program provides functionality not only for viewing molecules, but also is capable of generating high resolution images for publishing or printing, making movies, can be used for giving live 3D Presentations and sharing interactive visualizations. PyMOL is a free cross-platform molecular graphics system made possible through recent advances in hardware, internet, and software development technology. PyMOL provides most of the capabilities and performance of traditional molecular graphics packages written in C or Fortran. However, its integrated Python interpreter endows it with features and expandability unmatched by any traditional package [2].

Here is what PyMOL's creator, Warren L. DeLano, Ph.D. wrote about it's advantages [3]:

"... In the long run, PyMOL aims to match the molecular graphics quality of Molscript/Raster3D, the molecular editing capabilities of MacroModel, the animations and performance of VMD, the electrostatic surfaces of Grasp, the macromolecular crystallography of O, the interactivity of Sculpt, and the programmability of M.O.E. (but using Python instead of SVL), all in one FREE & UNRESTRICTED OPEN-SOURCE package. If you haven't yet seen PyMOL in action recently, you will be surprised how far it has progressed toward this goal... "

PyMOL currently holds a large percentage of the high-quality images published in scholarly journals like Science and Nature (fig. 1) .

Fig.1

It should be remarked that a part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output. This makes this program a great tool for making journal covers or any press-related images . Some of the known PyMOL-created Journal Covers of 2009-2008 year are represented at fig.2.

Crystal structure of the catalytic domain of the mitotic checkpoint kinase Mps1 in complex with SP600125. Chu ML, Chavas LM, Douglas KT, Eyers PA, Tabernero L. J Biol Chem. 2008 Aug 1;283(31):21495-500. Epub 2008 May 14.	Allosteric motions in structures of yeast NAD-specific isocitrate dehydrogenase. J. Biol. Chem.	How a multicopper oxidase chooses its electron transfer partner. Acc. Chem. Res.	Crystal structure of the yeast nicotinamidase Pnc1p. Arch. Biochem. Biophys.	Philosophical Transactions of The Royal Society, B : Biological Sciences Jan, 2009
MD simulation of protein-protein binding Pymol generated Movie is avialable inside pdf or high quality AVI format	J. Chem. Inf. Model., 2008, 48 (10)	Protein Dynamics	Targeting DNA, BIOCHEMIE, July 1, 2008 Cover, Vol. 90.	Harnessing Helices, Chemical & Engineering News, June 2, 2008 Cover, Vol. 86, Issue 22

Fig.2

Programm’s official site:

http://www.pymol.org/

Acceptable molecular file formats

Some of PyMOL supported file formats are:

PDB - Protein Data Bank
CIF - Crystallographic Information File
CCP4 - The file format for electron densitym, a standard in X-ray crystallography and Cryo-electron microscopy where the result of the technique is a three-dimensional grid of voxels each with a value corresponding to density of electrons.
XYZ - Minnesota Supercomputer Institute XMol file
Gaussian CUBE
MOL/MOL2 - Elsevier MDL structure
MOE - Chemical computing Group M.O.E.
SDF - Elsevier MDL structure
GRD - Accelrys Insight II Grids

PyMOL Main Features

PyMol can be used for:

· Viewing 3D Molecular Structures

· Modeling and editing structures

· Editing Atoms

· Molecular sculpting

· Homology modeling

· Animating Molecules Dynamically

· Making high quality images and movies

o       Image Manipulation

o       Labels

o       Photoshop/GIMP

o       Stereo Figures

o       Publication-quality images

Program integration, plugins and scripts

PyMOL supports geometry export in following formats: VRML, IDTF, PovRay . So it can be used with such programms as 3ds Max and Pov-ray.

PyMOL can be integrated seamlessly with MS Powerpoint with help of Axpymol [4]- PyMOL ActiveX control.

PyMOL Plugins are user-developed modules that extend PyMOL's capabilities via the Tcl/Tk user interface. Among them are:

CAVER

CAVER [5] provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in protein structures. Study of these pathways is important in drug design and molecular enzymology. On the moment of writing this short communication CAVER wax available as online version or PyMOL plugin - CAVER Viewer that enables efficient visualization of calculated pathways and can be run online using Java Web Start technology.

GPSSpyMOL

GPSSpyMOL plugin for visualizing surfaces and voids using the CASTp algorithm [6].

Gallery

Below are represented some results of molecular structures visualization (static and animation) obtained with Pymol.

Static

Animation