Secondary structure: Difference between revisions

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When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria (see [http://chemapps.stolaf.edu/jmol/docs/#calculate calculate structure].

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. 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 toopen 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 ==

For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].

Secondary structure: Difference between revisions

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@@ Line 18: / Line 18: @@
 When the PDB file lacks HELIX and SHEET records, Jmol will determine secondary structure using objective criteria (see [http://chemapps.stolaf.edu/jmol/docs/#calculate calculate structure].
-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. 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 toopen 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 ==
 For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].