User:Eric Martz/How JSmol works: Difference between revisions

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Such molecular structure data files are called [[atomic coordinate files]]. JSmol is able to read more than 50 formats of such files. The most common are XYZ format for small organic compounds (usually <100 atoms), and [[PDB file|PDB or mmCIF formats]] for macromolecules.

Small molecule structures are available from [https://chemapps.stolaf.edu/jmol/docs/#load several large databases]. The international repository of macromolecular structures is the [[Protein Data Bank]]. The most reliable macromolecular structures are determined experimentally by [[X-ray crystallography]], [[Nuclear magnetic resonance]], or cryo-electron microscopy. Macromolecular models determined from [[Theoretical models|theory]] are much less reliable, and are excluded from the [[Protein Data Bank]].

==Chemical Bonds==

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Green links in Proteopedia use JavaScript to send scripts of commands to JSmol to change the rendering and coloring of the molecular scene, as well as the center of rotation, the degree of zooming, and many other options. In other web pages (e.g. Proteopedia's [[Scene Authoring Tools]], [[FirstGlance in Jmol]], or the simple.htm example mentioned above), buttons and forms use JavaScript to send command scripts to JSmol.

==See Also==

*[http://firstglance.jmol.org/fgij/whatis.htm What Is FirstGlance in Jmol?] Includes a brief description of how it works at the end.

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 Such molecular structure data files are called [[atomic coordinate files]]. JSmol is able to read more than 50 formats of such files. The most common are XYZ format for small organic compounds (usually <100 atoms), and [[PDB file|PDB or mmCIF formats]] for macromolecules.
+Small molecule structures are available from [https://chemapps.stolaf.edu/jmol/docs/#load several large databases]. The international repository of macromolecular structures is the  [[Protein Data Bank]]. The most reliable macromolecular structures are determined experimentally by [[X-ray crystallography]], [[Nuclear magnetic resonance]], or cryo-electron microscopy. Macromolecular models determined from [[Theoretical models|theory]] are much less reliable, and are excluded from the [[Protein Data Bank]].
 ==Chemical Bonds==
@@ Line 31: / Line 33: @@
 Green links in Proteopedia use JavaScript to send scripts of commands to JSmol to change the rendering and coloring of the molecular scene, as well as the center of rotation, the degree of zooming, and many other options. In other web pages (e.g. Proteopedia's [[Scene Authoring Tools]], [[FirstGlance in Jmol]], or the simple.htm example mentioned above), buttons and forms use JavaScript to send command scripts to JSmol.
+==See Also==
+*[http://firstglance.jmol.org/fgij/whatis.htm What Is FirstGlance in Jmol?] Includes a brief description of how it works at the end.