XCrySDen 

May 31, 2005

The version 1.4 is released. XCrySDen has been ported to MAC OSX (thanks to Mike Ford) and Windows. The former needs X11, while the latter the CYGWIN environment.

• multi-band display of Fermi surfaces in one widget (read more)
• visualization of vector-fields with arrows (read more)
• added support for PWscf v2.1 and later (read more)
• added support for CRYSTAL03
• more configurable options for the display of force arrows (color, thickness, aspect) (read more)
• the color of the "Coordinate system" is configurable (read more)
• automatic labeling of k-points for k-path selection (thanks to Peter Blaha) (read more)
• Stereo display mode (thanks to Gerardo Ballabio)
• Anaglyph display mode, i.e. fake stereo, requires red-blue glasses (thanks to Eric Verfaillie)
• improved EPS printing (also PDF printing) thanks to new gl2ps-1.2.4. The vectorial EPS printing of Lighting-On display mode is finally good enough.
• comments added to the XSF format; comment-lines start with the "#" ( read more)
• dummy "X" (atomic number 0) atoms do not have bonds anymore
• updated Documentation

vida

VIDA:

VIDA is a graphical interface designed to visualize, manage and manipulate large sets of molecular information. It is capable of handling 100,000s of molecules simultaneously. It supports all standard visualization paradigms, including 2D depiction, both hardware and software stereo, surface selection and manipulation, and many other unique facilities.

VIDA is based on OpenEye's OEChem toolkit and as such handles chemistry properly as well as reading and writing a wide range of formats. The primary features include:

• A simple and intuitive interface
• Robust and powerful list manager
• Chemically-oriented, fully functional spreadsheet
• Automatic browsing facilities (slide show)
• List operations
• Substructure searching
• Integrated Python interpreter
• Interactive surface selection/sub-setting, real-time contours
• Concurrent interaction between data in spreadsheet and 2D/3D displays
• Multi-level undo
• Easily save and restore a session
• Single-click visualization of docking, shape overlay, and electrostatic overlay results
• Supported on Windows, Linux, Mac OSX, and IRIX systems

Like all OpenEye software, VIDA is available free of charge for non-commercial use.

Sting

What is STING Millennium

STING Millennium is a web based suite of programs that starts with visualizing molecular structure and then leads a user through a series of operations resulting in a comprehensive structure analysis:

amino acid sequence and structure positions,with emphasis on bi-directional coupling of sequence and 3D information
pattern search, neighbors identification,
H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

In addition, a user can obtain:

sequence to structure relationships,
analysis of a quality of the structure,
nature and volume of atomic contacts of intra and inter chain type,
analysis of amino acid relative conservation at specified position among homologous proteins, and
Accessible Surface Area
relationship of relative conservation to the intra-chain contacts
functional parameters deciphered etc..

ChemAxon's Reactor

ChemAxon's Reactor.
http://www.chemaxon.com/jchem/examples/reactor/jsp/index.jsp

ramaplot

http://boscoh.com/ramaplot/

MacOSX Universal binary

The Ramachandran Plot Explorer is designed to make it easy to examine the conformation of a polypeptide - through the interactive Ramachandran plot (φ-ψ angles) and χ-angle tool. Simply click on a residue, then drag the marker on the Ramachandran plot.

To see how conformational changes might affect the energetics, I've included real-time calculation of H-bonds, weak H-bonds and steric clashes. This makes it easy to see why (i) certain regions of the Ramachandran plot (what is this?) are forbidden, and (ii) certain sidechain chi angles are favoured, (iii) the core is packed so tightly.

You can also edit (cut/paste/insert) protein sequences and mutate residues, with a simple click of the mouse.

I've worked hard to make an intuitive interface with lots of visual cues and feedback, and I've included what, I think, is a necessary set of navigating tools (sequence-bar, z-slab-bar, snake-measure tool). The program uses native widgets (standard file open/save dialogs!) and you can resize the window to your heart's content.

There is a 3-point-clamp function, that (i) explores discrete solutions of a loop with fixed anchors and 3 hinge-residues, and (ii) allows the exploration of the phi/psi angles of residues inside the clamp without disturbing the rest of the protein.

Limited to a single chain.

qute mol

QuteMol is an open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects. QuteMol visualization techniques are aimed at improving clarity and an easier understanding of the 3D shape and structure of large molecules or complex proteins.

• Real Time Ambient Occlusion
• Depth Aware Silhouette Enhancement
• Ball and Sticks, Space-Fill and Liquorice visualization modes
• High resolution antialiased snapshots for creating publication quality renderings
• Automatic generation of animated gifs of rotating molecules for web pages animations
• Real-time rendering of large molecules and protein (>100k atoms)
• Standard PDB input
• Quick installers for Win and Mac OS X (intel) (new!)
• Support as a plugins of the NanoEngineer-1 the modeling and simulation program for nano-composites (new!)

pymol macOSX

NOTE: A 3-button wheel or mighty mouse is required to use PyMOL on the Macintosh. Be sure to reconfigure your mighty-mouse to use the secondary button (right-click) and button 3 (middle-click). Tiger (OS X 10.4) is required, although some users have reported success with the final release of Panther (10.3.9).

Option 1: MacPyMOL. MacPyMOL is an Aqua-based PyMOL with a more Mac-like user interface. In addition to supporting native OpenGL rendering, its unique features include Copy-and-Paste of images and direct output of QuickTime movies.

1. Download and uncompress macpymol-0_99rc6.tar.gz. A Universal Binary
2. Install by copying MacPyMOL into your Applications folder (or any suitable location).
3. Launch PyMOL by double-clicking on the MacPyMOL icon.

Option 2: PyMOLX11Hybrid. MacPyMOL now includes a hybrid X11 mode. Assuming that X11 is already installed, simply duplicate and rename the application bundle to "PyMOLX11Hybrid" and then launch (requires Tiger).

<!--Option 3: MacPyMOL for Panther. This is a backwards-compatible release for PowerPC machines running the prior release of Mac OS X.

1. Download and uncompress macpymol-0_99rc1-panther.tar.gz.
2. Install by copying MacPyMOL into your Applications folder (or any suitable location).
3. Launch PyMOL by double-clicking on the MacPyMOL icon.

-->Option 3: PyMOL for Mac OS X / X11. This is the Mac equivalent of the standard Linux, IRIX, and Solaris builds of cross-platform PyMOL. It accesses OpenGL and Tcl/Tk entirely through X11 and is thus completely compatible with the standard version. Requires Mac OS X Tiger with X11 installed.

1. Download the version appropriate for your system:
   
   pymol-0_99rc6-bin-macosx-ppc-x11.tgz
   pymol-0_99rc6-bin-macosx-x86-x11.tgz
2. Extract the archive
   

   tar -zxf pymol-0_99rc6-bin-macosx-ppc-x11.tgz

   
   to create a "pymol" directory
3. Run the setup script from within the new directory
   

   cd pymol
   ./setup.sh

   
   to create the "./pymol" launch script.
4. Then test-launch PyMOL as
   

   ./pymol

   
   
5. Optional: copy or link "./pymol" to an appropriate location in your path.
   

   ln -s $PWD/pymol $HOME/bin/pymol

   
   
6. Optional: to avoid having to click twice when moving the mouse between windows, issue
   

   defaults write com.apple.x11 wm_click_through -bool true

   
   and then restart the X-server.

chemical drawing software and 3D visu software

MolMol has been cited by over 500 scientific journal articles (search for "molmol" at highwire.stanford.edu). It ranks among the most popular free visualization programs, including RasMol (>700) and KineMages (>450).

http://www.ac-orleans-tours.fr/svt/mol3d/molusc/pcindex.htm

http://dragon.klte.hu/~gundat/rajzprogramok/dprog.html

http://howard.nebrwesleyan.edu/classes/cs295/shoemaker/chem/index.php

http://www.geocities.com/Athens/Thebes/5118/viewdraw.htm

http://www.geocities.com/Athens/Thebes/5118/obc/isis.htm

http://kinemage.biochem.duke.edu/website/kinhome.htm

http://www.pirx.com/iMol/

iMol is a free molecular viewer for Mac OS X operating system. iMol can load molecules using several file formats: PDB, XYZ, MOL2, HIN, CAR, ALC, BIO. The molecules can be saved as PDB, XYZ or BIO files (the BIO file stores all rendering settings, i.e. colors, lighting, orientation of molecules). iMol can easily handle both small and large molecules, it can load multiple molecules, move and rotate them independently.

iMol can load multimodel PDB files and display them as an animation (e.g. molecular dynamics trajectory). iMol supports QuickTime movie format for rendering the animations. The movies are efficiently compressed for web applications.

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http://www.interprobe.co.uk/inter/interprobe.html

Jmol: (English, Spanish, Dutch )

Cross-indexing terms:   java applet;   applet;   chime-compatible applet.

Jmol is an open source molecular viewer written in Java. It comes in two forms. There is a Jmol applet which, like Chime, displays the molecule within a web browser. Unlike Chime, you don't have to install a plugin -- Jmol arrives automatically with the web page and displays the molecule. Jmol's second form is a stand-alone application (like RasMol).Because Jmol is written in Java, Jmol runs on a wide variety of operating systems (Windows, Mac OSX, linux, among others) and in all popular browsers (Internet Explorer, Netscape 4/6/7, Mozilla, Safari, etc.). Jmol supports the RasMol/Chime scripting language. The Jmol applet provides a migration path for Chime-based web applications. Jmol includes a perl script which will automatically convert many Chime web pages. The source code and java binaries are available from http://jmol.sourceforge.net and are covered under the GNU Publice Licenses.

Author: Project, Jmol Submitted by: the author. (Entry 50). Submitted on Dec 14, 2003.

JMolEditor:

Cross-indexing terms:   java applet;   computational chemistry;   molecular builder;   molecular editor;   gaussian;   gamess, mopac, amber;   vasp;   gromacs;   isosurfaces;   molecular orbitals;   electron densities;   electrostatic potential;   java3d;   picture generation;   BMP;   JPEG;   PNG;   PovRay.

JMolEditor supports submission of Gaussian jobs to remote computer using the ssh2 protocol. It can monitor submitted jobs and retrieve output files after job completion.

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MAGE: MAGE (available for Windows, Mac, Unix, Linux, and now Java) is the freeware which first brought powerful macromolecular visualization to personal computers (in 1992). Over a thousand excellent tutorials on molecular structures are available in the form of kinemages (presentations that run in MAGE). MAGE has a number of unique and powerful capabilities not available in RasMol nor Chime. (Here is a brief comparision of MAGE vs. RasMol.) There is now a capable Java version of Mage which runs on the Web with no plug-ins. The above page (by Martz) comparing Mage and Rasmol is nicely done in general. However, Mage has ribbons, backbone, ball&stick, etc. representations; kinemages are not scripts but are heirarchical, commented, 3D display lists; and making a simple kinemage is extremely easy, and its exploration is just as open-ended as in RasMol - it's only if you want to make a custom-crafted presentation that it gets "technical". Also, an important use of Mage now is to show all-atom contacts made by Probe

Molecular Workbench: Molecular Workbench is free, content-oriented molecular modeling software for use in education. Unlike the static ball-and-stick models, the Molecular Workbench software computes and visualizes the motion of ensembles of atoms in real time, in both 2D and 3D.

MolViewX: MolviewX is a freeware Macintosh application for OSX that can read several types of coordinate files and display ribbon, CPK, stick, ball&stick, and surface figures. The interface is completely interactive (i.e. no comand line input). There are countless options that control the display colors and characteristics. The output includes object-oriented PICT, QuickDraw 3D 3DMF files, and VRML files. In addition, there are several analysis tools such as neighbors, distance lines, hydropathy plots, Edmunson wheel plots, B value plots (and color coded stick models), distance plots. In addition, the user can open 2 different structures and even perform 3D alignments on them. Also, subsets of the structure can be stored as MOL files and be read in later.

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http://www.openrasmol.org/

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POLYVIEW

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PyMOL Molecular Graphics System

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http://www.parallelgraphics.com/products/cortonamacosx

Cortona VRML Client for Mac OS X Complete Web3D viewer for Mac OS X!Cortona VRML Client for Mac OS X is a fast and highly interactive Web3D viewer that is ideal for viewing both simple 3D models and complex interactive solutions on the Web. This is a plug-in for Internet Explorer, iCab, Mozilla, OmniWeb and Opera browsers. Cortona for Mac OS X offers:

navigation paradigms (such as walking or flying) that enable the user to move the viewer through a virtual world

a mechanism that allows the user to interact with a virtual world through a sensor in the scene

a hardware renderer based on OpenGL

structure moleculaire

http://www.ncbi.nlm.nih.gov/Structure/index.shtml

pdb file --molecular

http://hmdb.ca/scripts/show_card.cgi?METABOCARD=HMDB01895