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Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. [2] It is an open-source Java viewer for chemical structures in 3D [ 3 ] . The name originated from [ J ]ava (the programming language) + [mol]ecules, and also the mol file format .
This is a list of notable software systems that are used for visualizing macromolecules. ... Jmol: Free open-source: Java ... Includes single/multiple sequence viewer ...
To display molecules with Jmol, your browser needs to be Java enabled. Two examples of Jmol images in a wiki are here and here. These use Jmol to show medium sized molecules with buttons to control the rotation of the molecules. The right mouse button opens a Jmol menu while the left mouse button can be used to move the image.
Jmol extension is really useful --Pansanel 07:49, 11 April 2006 (UTC) Many molecular structures are difficult to handle in 2D sketch. A 3D visualization software is great for this job. For example, calixarene derivatives have a cone shape. Such molecule can really better understand with a 3D interactive tool.
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. [1]
The JME Molecule Editor is a molecule editor Java applet with which users make and edit drawings of molecules and reactions (including generating substructure queries), and can display molecules within an HTML page. [1]
Jmol is an open-source Java-based viewer for browsing molecular structures on the web; it includes a simplified "cartoon" version of ribbons. Other graphics programs such as DeepView (example: urease ) and MolMol (example: SH2 domain ) also produce ribbon images.
structure editable, show bond in helix sequence regions, 2D molecule viewer MUSCLE, MAFFT, ClustalW, ProbCons, FastAligner (region-align+auto-reference) arb-parsimony & -NJ, RAxML, PHYML, Phylip, FastTree2, MrBayes Edits huge alignments and trees. Supports NUCs + AA. Displays codons below DNA.