Secondary structure: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eran Hodis, Karl Oberholser, Eric Martz, Wayne Decatur, Karsten Theis, Joel L. Sussman

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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 appear to work in Jmol 11.8 employed in Proteopedia in June, 2011. It works in the [[Jmol/Application]] (version 12).'' Here are the commands to do that:
+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.
-*select protein
-*calculate structure
-*cartoon
-*color structure
 == External Links ==
 For more information, see [http://en.wikipedia.org/wiki/Secondary_structure Wikipedia's page on secondary structure].