Molecular modeling and visualization software: Difference between revisions
From Proteopedia
Jump to navigationJump to search
mNo edit summary |
Eric Martz (talk | contribs) |
||
| (15 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
==Visualization vs. Modeling== | ==Visualization vs. Modeling== | ||
Software for visualizing the three-dimensional structures of molecules, ''molecular visualization software'', can be distinguished from molecular modeling software. Strictly speaking, ''Visualization'' software displays a pre-existing molecular model without changing it, while ''modeling'' software can create the model, or modify it by adding or removing moieties, changing covalent bonds, bond angles, conformation, or non-covalent interactions. | Software for [[Introduction to molecular visualization|visualizing the three-dimensional structures of molecules]], ''molecular visualization software'', can be distinguished from molecular modeling software. Strictly speaking, ''Visualization'' software displays a pre-existing molecular model without changing it, while ''modeling'' software can create the model, or modify it by adding or removing moieties, changing covalent bonds, bond angles, conformation, or non-covalent interactions. | ||
==Free molecular visualization software== | ==Free molecular visualization software== | ||
| Line 8: | Line 8: | ||
*[[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). | |||
*[[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. | ||
| Line 19: | Line 24: | ||
* [http://istar.cse.cuhk.edu.hk/iview/ iView] - an interactive WebGL visualizer of protein-ligand complexes | * [http://istar.cse.cuhk.edu.hk/iview/ iView] - an interactive WebGL visualizer of protein-ligand complexes | ||
* [https://biasmv.github.io/pv/ PV - JavaScript Protein Viewer] | * [https://biasmv.github.io/pv/ PV - JavaScript Protein Viewer] | ||
==Free molecular modeling software== | ==Free molecular modeling software== | ||
| Line 33: | Line 37: | ||
*[http://dasher.wustl.edu/ffe/ TINKER] a free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers. | *[http://dasher.wustl.edu/ffe/ TINKER] a free molecular modeling package for molecular mechanics and dynamics, with some special features for biopolymers. | ||
*[http://www.biomolecular-modeling.com/Abalone/ Abalone] a program focused on molecular dynamics of biopolymers. | *[http://www.biomolecular-modeling.com/Abalone/ Abalone] a program focused on molecular dynamics of biopolymers. | ||
* [ | *[http://open.gpcr-modsim.org/ GPCR-ModSim] is a webserver for computational modeling and simulation of G-Protein Coupled Receptors (GPCRs). Models from sequence and also lets you place the models in a phospholipid bilayer and model them using Molecular Dynamics. | ||
==See Also== | ==See Also== | ||
* | *[[Introduction to molecular visualization]] | ||
*[[History of Macromolecular Visualization]] | |||
*[[Homology model]] | *[[Homology model]] | ||
*[[PyMOL]], an open-source molecular visualization program, extremely popular with crystallographers, that requires a subscription fee. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language. | *[[PyMOL]], an open-source molecular visualization program, extremely popular with crystallographers, that requires a subscription fee. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language. | ||
*[http://www.weizmann.ac.il/ | *[http://www.weizmann.ac.il/old_ISPC/eMovie.html eMovie] is a plugin for PyMOL that facilitates creation of [[Morphs#True_Movies|true movies]] using a storyboard approach. | ||
*[[Molecular sculpture]] | |||
*[[Web servers for convenient generation of publication-quality figures for molecular views]] | |||
