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, but it is not available in Jmol 11.8 which is used in Proteopedia as of June 2011. It is available in Jmol ver. 12. ''Calculate hbonds structure'' is also available in ver. 12, 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, but it is not available in Jmol 11.8 which is used in Proteopedia as of June 2011. It is available in Jmol ver. 12. ''Calculate hbonds structure'' is also available in ver. 12, and it identifies and displays the hbonds involved in these three types of secondary structures<ref name="calculate" />.

Any 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'' click on ''Console'', in the bottom box of the console enter the commands: <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center> and then click ''Run''.

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, but it is not available in Jmol 11.8 which is used in Proteopedia as of June 2011. It is available in Jmol ver. 12. ''Calculate hbonds structure'' is also available in ver. 12, 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, but it is not available in Jmol 11.8 which is used in Proteopedia as of June 2011. It is available in Jmol ver. 12. ''Calculate hbonds structure'' is also available in ver. 12, and it identifies and displays the hbonds involved in these three types of secondary structures<ref name="calculate" />.
 <blockquote>
 Any 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'' click on ''Console'', in the bottom box of the console enter the commands: <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center> and then click ''Run''.