Secondary structure: Difference between revisions
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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. | 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. | ||
If the above series of commands are applied when the structure of a human transferrin n-lobe mutant is displayed, you will see that in additional to the <font color=#FF0080>alpha helices</font> being displayed the <font color=#A00080>3<sub>10</sub> helices</font> are also shown. Different types of turns are shown in blue. | |||
== External Links == | == External Links == | ||
For more information: | For more information: | ||
* | * [http://chemapps.stolaf.edu/jmol/docs/#calculate Calculate structure] | ||
* | * [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure]. | ||
