Calculate structure: Difference between revisions
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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 is capable of determining and displaying these three types of structures with limitations as described in [[Secondary_structure#How Jmol Determines Secondary Structure | How Jmol Determines Secondary Structure ]]. The ''calculate structure''<ref name="calculate">A detailed description is at [http://chemapps.stolaf.edu/jmol/docs/#calculate].</ref> is a command which does a more fundamental identification of these secondary structures by re-calculating the secondary structure, and it identifies and displays the hbonds involved in these three types of secondary structures<ref name="calculate" />. | 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 is capable of determining and displaying these three types of structures with limitations as described in [[Secondary_structure#How Jmol Determines Secondary Structure | How Jmol Determines Secondary Structure ]]. The ''calculate structure''<ref name="calculate">A detailed description is at [http://chemapps.stolaf.edu/jmol/docs/#calculate].</ref> is a command which does a more fundamental identification of these secondary structures by re-calculating the secondary structure, and it identifies and displays the hbonds involved in these three types of secondary structures<ref name="calculate" />. | ||
On any Proteopedia page, click on the ''Jmol frank'', in the ''main menu'' click on ''Console'', in the bottom box of the console enter the commands: < | On any Proteopedia page, click on the ''Jmol frank'', in the ''main menu'' click on ''Console'', in the bottom box of the console enter the commands: <span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span> and then click ''Run''. | ||
The objectives of this article are: | The objectives of this article are: | ||
* Describe briefly how ''calculate structure'' identifies secondary structures, with a focus on turns, and relate its turn identification to β and γ-turns. | * Describe briefly how ''calculate structure'' identifies secondary structures, with a focus on turns, and relate its turn identification to β and γ-turns. | ||
