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 detailed identification (For this detail go to [[Helices in Proteins|helices]], [[Sheets in Proteins|sheets]] and [[Turns in Proteins|turns]].) ~~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 has always been 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 has been more recently developed and does a more detailed identification of these secondary structures. (For this detail go to [[Helices in Proteins|helices]], [[Sheets in Proteins|sheets]] and [[Turns in Proteins|turns]].) Calculate structure by itself only identifies the secondary structural components. Additional commands are required to display the secondary structures and the hbonds. In order to display this detailed information on any Proteopedia page which does not display it, 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''.

In order to display this detailed information on any Proteopedia page which does not display, 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:

* 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 identification of β and γ-turns.

* Summarize the observations obtained from using ''calculate structure '' to identify turns in two proteins.

* Show details of the above identifications.

Myohemoerythrin is shown in the applet below. (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>)

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 detailed identification (For this detail go to [[Helices in Proteins|helices]], [[Sheets in Proteins|sheets]] and [[Turns in Proteins|turns]].) 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 has always been 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 has been more recently developed and does a more detailed identification of these secondary structures. (For this detail go to [[Helices in Proteins|helices]], [[Sheets in Proteins|sheets]] and [[Turns in Proteins|turns]].) Calculate structure by itself only identifies the secondary structural components.  Additional commands are required to display the secondary structures and the hbonds.  In order to display this detailed information on any Proteopedia page which does not display it, 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''.
-In order to display this detailed information on any Proteopedia page which does not display, 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:
-* 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 identification of β and γ-turns.
 * Summarize the observations obtained from using ''calculate structure '' to identify turns in two proteins.
-* Show details of the above identifications.
 Myohemoerythrin is shown in the applet below. (<scene name='Calculate_structure/Erythrin/2'>Restore initial scene</scene>)