## Friday, May 23, 2008

### 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.
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 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 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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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