Molecular modeling and visualization software: Difference between revisions
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*[[Jmol]], an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia, and in the free educational software [[Molecular Workbench]]. Effective use of Jmol requires learning a command scripting language. | *[[Jmol]], an open-source java-based program available in stand-alone or applet forms. The applet is used in Proteopedia, and in the free educational software [[Molecular Workbench]]. Effective use of Jmol requires learning a command scripting language. | ||
*[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol|More ...]] | *[[FirstGlance in Jmol]], an open-source user-interface to [[Jmol]] utilized for a decade in the ''3D View'' links in papers in the journal [http://www.nature.com/nature Nature] that report new macromolecular structures. Proteopedia's automatically seeded pages (pages titled with a [[PDB code]]) have links for further exploration of the structure in'' FirstGlance in Jmol''. Although ''FirstGlance in Jmol'' by no means exploits all the power in Jmol, it does show the main structural features of a macromolecule '''without learning any command scripting language'''. [[FirstGlance in Jmol|More ...]] | ||
*[[ | *[[ChimeraX]] (free for non-commercial use only). | ||
*[https://molstar.org/ Mol*] (MolStar) is offered as a visualization option by the [[wwPDB]]. | *[[iCn3D]], a powerful menu and command driven package from the [https://www.ncbi.nlm.nih.gov/ US National Center for Biotechnology Information]. | ||
*[https://molstar.org/ Mol*] (MolStar) is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL], and it can handle very large numbers of atoms. | |||
*[https://nglviewer.org/ NGL Viewer] is offered as a visualization option by the [[wwPDB]]. Its rendering is fast and smooth because it uses [https://developer.mozilla.org/en-US/docs/Web/API/WebGL_API WebGL]. | |||
*[https://www.samson-connect.net/ Samson], a powerful visualization and modeling package that is menu-driven. Free for basic use. See demos at [[Sculpting protein conformations]] and the step-by-step demo at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | |||
*[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]]. | *[[Kinemages, Mage and KiNG]] (KiNG = Kinemage, Next Generation) are designed to present the author's viewpoint of a molecular structure. They excel in specialized areas, but are not optimal for general purpose visualization. KiNG can be used in Proteopedia; an example may be seen at [[Hemoglobin#Hemoglobin_subunit_binding_O2]]. | ||
*[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language. | *[[RasMol]], an open-source stand-alone program released in 1993, and still popular. Effective use of RasMol requires learning a command scripting language. | ||
