Calculate structure

An important part of protein structure is the secondary structure which is made up of [[Helices in Proteins|helices]], [[Sheets in Proteins|sheets]] and [[Turns in Proteins|turns]] and Jmol as described in [[Secondary_structure#How Jmol Determines Secondary Structure | Secondary structure]] is capable of determining and displaying these three types of structures. The '''Calculate structure'''<ref>A detailed description is at [http://chemapps.stolaf.edu/jmol/docs/#calculate].</ref> command which re-calculates the secondary structure does a more complete job of identifying and displaying the secodnary structures, is available in Jmol ver. 12, but is not available in Jmol 11.8 which is used in Proteopedia as of June 2011. Any one page of Proteopedia can be run in the signed ver. 12 by appending "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page and reloading the page. The user must give permission for the signed version of Jmol to open, and when it does it has a red frank, whereas in the unsigned version it is grey. Click on the ''Jmol frank'', in the ''main menu'' which opens click on ''Console'', in the bottom box enter the commands: select protein; calculate structure; cartoon; color structure and then click ''Run''.