Secondary structure: Difference between revisions
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[[PDB files]] usually contain HELIX, SHEET, and sometimes contain TURN records, in their headers. These represent the authors' determinations, and when present, [[Jmol]] obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix. | [[PDB files]] usually contain HELIX, SHEET, and sometimes contain TURN records, in their headers. These represent the authors' determinations, and when present, [[Jmol]] obeys them (see [[Help:Color Keys#Secondary Structure|secondary structure colors]]). Secondary structure assignments are somewhat arbitrary. Proteins are not rigid (unlike PDB files!), and phi/psi angles may change from instant to instant. For example, there may be an alpha helix with a small kink in the middle. Objective software may determine that this represents two alpha helices, while the authors may specify it as a single helix. | ||
When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria (see | When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria (see . | ||
Optionally, using Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]], you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. ''This does not work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the [[Jmol/Application]] (version 12).'' You can run a Proteopedia page in Jmol 12.0 and observe the effect of this command by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and re-opening the page. You must permit the signed version of Jmol | Optionally, using Jmol [[Scene_authoring_tools#Using_Jmol.27s_Command_Language|command language]], you can re-determine secondary structure objectively, overriding the authors' specifications in the PDB file. ''This does not work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the [[Jmol/Application]] (version 12).'' You can run a Proteopedia page in Jmol 12.0 and observe the effect of this command by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and re-opening the page. You must permit the signed version of Jmol to open in order to use ver. 12. Open the Jmole console (Right click the Jmol frank and select Console.), enter into the lower box the commands: select protein; calculate structure; cartoon; color structure and then click run. | ||
== External Links == | == External Links == | ||
For more information | For more information: | ||
* Calculate structure see [http://chemapps.stolaf.edu/jmol/docs/#calculate calculate structure] | |||
* Secondary structure see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | |||
