Business Information

The section "Business Information" continues to publish information about latest hard/soft-ware developments in computer graphics and geometry applications.
V.Pilyugin

---

OpenSource Molecular Viewers

 

Contents:

PyMOL Jmol OpenAstex Coot

 

PyMOL

Overview

PyMOL is an open-source molecular visualization program functioning on a variety of computer platforms (Windows, Mac, Linux/UNIX, etc). The software is indeed is an open-source and is released under the BSDL OSI-approved license. PyMOL is capable of generating high resolution images for publishing or printing, making movies and much more. PyMOL is robust, fast and extensible. The PyMOLWiki comes with many scripts to extend the features in PyMOL.

PyMOL currently holds a large percentage of the high-quality images published in scholarly journals like Science and Nature. PyMOL images frequently grace the covers of high impact journals.

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

o       PovRay

·        Exporting Geometry: VRML, IDTF

Plugins and scripts

PyMOL can be integrated seamlessly with MS Powerpoint. For this is used Axpymol - PyMOL ActiveX control.

There are a lot of scripts and plugins ready for use for this product. Among them are such as

 -  CAVER - provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Study of these pathways is important in drug design and molecular enzymology to understand binding of inhibitors to the receptors, substrate binding and product egress from the enzyme active sites. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER allows analysis of any molecular structure including proteins, nucleic acids, inorganic materials, etc.

CAVER Viewer enables efficient visualization of calculated pathways and can be run online using Java Web Start technology.

-   APBS, the Adaptive Poisson-Boltzmann Solver, is a freely available macromolecular electrostatics calculation program released under the GPL. It is a cost-effective but uncompromised alternative to GRASP, and it can be used within pymol. Pymol can display the results of the calculations as an electrostatic potential molecular surface.

PyMol currently supports the APBS plugin written by Michael Lerner. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units K_bT / e_c) in the molecular display window (as with the image to the right).

Some of PyMol integrations

1. Nuccyl -- Nuccyl is a great PyMol extension
2. CASTp -- Binding and Active site prediction
3. CCTBX -- Computational Crystallography Toolbox

Gallery

Part of PyMOL's popularity comes from the fact that it is very flexible and it offers arbitrarily high-resolution images as output; this make it a great tool for making journal covers or any press-related images.

Here are some of the known PyMOL-created Journal Covers. There are surely more out there. If you have a cover you'd like to add, feel free.

Targeting DNA, BIOCHEMIE, July 1, 2008 Cover, Vol. 90.	Harnessing Helices, Chemical & Engineering News, June 2, 2008 Cover, Vol. 86, Issue 22.	Fusarium head blight (FHB), JBC, January 18, 2008 Cover, Vol. 283, Issue 3.	Pumping Irons, Nature, Dec. 13th, 2007.	[1], Dec 2007.
Science, Nov. 23rd, 2007.	Sensing Calciums[2], Nov 20th, 2007.	Aminoacyl-tRNA synthetases from human mitochondria[3], Nov. 13th, 2007.	Science, Oct. 19th, 2007.	Sensing Acid, Nature, Sept. 20th, 2007.
Form Finds Function?, Nature, Aug. 16thm 2007.	Nature Neuroscience Vol. 10 No. 8 Aug. 2007	Paused transcription complexes, Molecular Cell, August 3 2007 Cover, Vol. 27, Issue 3.	Vitamin D, ABB, April 14 2007 Cover, Vol. 460, Issue 2.	Auxin Action Revealed, Nature, April 5, 2007.
Glucose-1-phosphate uridylyltransferase, Protein Science, March 3, 2007 Cover, Volume 16 Issue 3.	How Ribosomes Work, Chemical & Engineering News, Feb. 19th, 2007.	HIV's Hidden Weakness, Nature, Feb. 15th, 2007.	Sen1 Control of RNA Pol II Termination, Molecular Cell, December 8, 2006 Cover, Volume 24 Issue 5.	Transposon Loops, Molecular Microbiology, December 1, 2006 Cover, Volume 62 Issue 6.
Glycosylation Engineering, Chemical & Engineering News, Sept. 4th, 2006.	Chromatin Code Decoded, Nature, Aug. 17th, 2006.	Halogenases, Chemical & Engineering News, May 22nd, 2006.	Poly (2S-proline), Protein Science, January 1, 2006 Cover, Volume 15, Issue 1.	Ribonuclease A, JMB, November 18, 2005 Cover, Volume 354, Issue 1.
The B to Z of DNA, Nature, Oct. 20th, 2005.	GalNAc kinase, JBC, September 23, 2005 Cover, Volume 280, Issue 38.	Neurotransmission, Nature, Sept. 8th, 2005.	Science, July 22nd, 2005.	JMB, June 24, 2005 Cover, Volume 349, Issue 5.
Probing Prions, Nature, June 9th, 2005.	Science, April 29th, 2005.	Science, Sept., 10th, 2004.	Science, Jan. 23rd, 2004.	Chem. Biol.
Accounts of Chemical Research

More

More information about Pymol can be found at it’s official site:

http://www.pymol.org/

 

Jmol: an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules

Overview

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.

• The JmolApplet is a web browser applet that can be integrated into web pages.
• The Jmol application is a standalone Java application that runs on the desktop.
• The JmolViewer is a development tool kit that can be integrated into other Java applications.

Features

• Free, open-source software licensed under the GNU Lesser General Public License
• Applet, Application, and Systems Integration Component
• The JmolApplet is a web browser applet that can be integrated into web pages. It is ideal for development of web-based courseware and web-accessible chemical databases. The JmolApplet provides an upgrade path for users of the Chime plug-in.
• The Jmol application is a standalone Java application that runs on the desktop.
• The JmolViewer can be integrated as a component into other Java applications.
• Multi-language
• Translated into multiple languages: Catalan (ca), Czech (cs), Danish (da), Dutch (nl), Estonian (et), French (fr), German (de), Hungarian (hu), Italian (it), Korean (ko), Norwegian Bokmal (nb), Polish (pl), Portuguese (pt), Portuguese - Brazil (pt_BR), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) (in addition to the native English, en-US).
• Automatically adopts the language of the user's operating system, if it is among the translations available. You can change to another language if desired.
• For up-to-date details or instructions for adding your language, see the Wiki.
• Cross-platform
• Windows
• Mac OS X
• Linux / Unix
• Supports all major web browsers
• Internet Explorer (Win32)
• Mozilla and Firefox (Win32, OSX, Linux, Unix)
• Safari (Mac OS X)
• Opera 7.5.4 (Win32 only)
• Konqueror (Linux)
• IceWeasel (Linux)
• ...
• High-performance 3D rendering with no hardware requirements
• File formats :
• CIF/mmCIF - Crystallographic Information File and Macromolecular Crystallographic Information File, the standards from the International Union of Crystallography
• CML - Chemical Markup Language
• CSF - Fujitsu CAChe chemical structure, now Fujitsu Sygress
• CTFile - Elsevier MDL chemical table
• GAMESS - General Atomic and Molecular Electronic Structure System output, Gordon Research Group, Iowa State University
• Gaussian 94/98/03 output - Gaussian, Inc.
• Ghemical
• HIN - HyperChem from Hypercube, Inc.
• Jaguar - Schrodinger, LLC
• MM1GP - Ghemical molecular mechanics
• MOL - Elsevier MDL structure
• MOLPRO - Molpro output
• MOPAC - MOPAC 93/97/2002 output (public domain)
  - MOPAC 2007 (v.7.101) graphf output (.mgf files) (public domain)
• NWCHEM - NWChem output, Pacific Northwest National Laboratory
• odydata - Odyssey data, WaveFunction, Inc.
• PDB - Protein Data Bank, Research Collaboratory for Structural Bioinformatics
• QOUT - Q-Chem, Inc.
• SDF - Elsevier MDL structure
• SHELX - Structural Chemistry Department, University of Göttingen ( Germany )
• SMOL - Spartan data, Wavefunction, Inc.
• spinput - Spartan data, Wavefunction, Inc.
• xodydata - Odyssey XML data, WaveFunction, Inc.
• XYZ - Minnesota Supercomputer Institute XMol file
• XYZ+vib - XYZ format files with added vibrational vector information
• XYZ-FAH - Folding@home XYZ file

* Files which are compressed with gzip will automatically be decompressed

• Animations
• Vibrations
• Basic support for unit cell and symmetry operations
• Schematic shapes for secondary structures in biomolecules
• Measurements
• distance
• angle
• torsion angle
• Support for RasMol/Chime scripting language
• JavaScript support library
• Exports to .jpg, .png, .ppm, .pdf, and PovRay

Gallery

Small molecules

Acetic acid using CPK colors and spacefilled atoms.	A shaded rendering of caffeine, with some measurements shown (distance, angle, dihedral).
Display of bounding box and axes of coordinates space. Note the transparency of the yellow halo around selected atoms.

Macromolecules

.
A few residues with backbone in blue and vdw dots surface		Hemoglobin with backbone trace colored by chain and spacefilled hemes.

 

More

More information about Jmol can be found at it’s official site:

http://jmol.sourceforge.net/

OpenAstexViewer 3.0 - Software for molecular visualisation.

Overview

OpenAstexViewer is a Java molecular graphics program that assists in structure based drug design. It can be used as an Applet in a web page or as a desktop application. The software should run on most operating systems and in most internet browsers. OpenAstexViewer has been used most extensively in Internet Explorer v5+ running on Microsoft Windows. The software is known to run as an Applet within the Safari browser on Mac OS X.

• AstexViewer™ was originally developed by Mike Hartshorn at Astex Therapeutics between 1999 and 2007.
• The software was shaped by the input of many people from the structural biology and computational chemistry groups at Astex Therapeutics.
• Version 1 was made available via the Astex Therapeutics web site and published in JCAMD from 2002.
• Version 2 was made available via the website from 2004.
• OpenAstexViewer was made available with support from Astex Therapeutics, GlaxoSmithKline and dotmatics Limited.

OpenAstexViewer is distributed in Open Source form under the terms of the LGPL license. Briefly, this means that you may distribute OpenAstexViewer as part of other applications. You must display a copyright notice that indicates that OpenAstexViewer is included in your application.

Features

OpenAstexViewer 3.0 is a major upgrade of the software first described in the original publication (M.J.Hartshorn, JCAMD, 16, 871 (2002)). New functionality includes

• Sphere, cylinder and stick display styles for molecules.
• Versatile labelling and distance monitors.
• Shaded molecular surfaces, with transparency and property mapping.
• Protein schematics and secondary structure assignment.
• High quality image production to arbitrary resolution, with antialiasing and shadows.

 

Image gallery

More

More information about OpenAstexViewer 3.0 can be found at it’s official site:

http://openastexviewer.net/web/

 

 

 

Coot - Crystallographic Object-Oriented Toolkit

Overview

Coot is for model building, model completion and validation.

Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots and so on. Coot has some features that resemble those of Frodo, O, Quanta and XtalView's XFit. It is a completely independent system of course. Coot doesn't do many aspects of structure represention

Some Features

• Acceptable file formats are: PDB, mmCIF, MTZ files, .phs and others.
• Making maps from MTZ and .phs files
• Reads conventional CCP4 maps and CNS maps
• It is sctiptable and hundreds of functions are made available to the user via SWIG and can be scripted in either Python or scheme.

Gallery

More

More information about Coot can be found at it’s official site:

http://www.ysbl.york.ac.uk/~emsley/coot/

Publication is based on sites:

http://www.ysbl.york.ac.uk/~emsley/coot/

http://openastexviewer.net/web/

http://www.pymol.org/

http://jmol.sourceforge.net/

Prepared by editor J. Malikova (Russia).