Calculate structure
From Proteopedia
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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 | + | 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 with limitations as described in [[Secondary_structure#How Jmol Determines Secondary Structure | How Jmol Determines Secondary Structure ]] Jmol is capable of determining and displaying these three types of structures. The ''calculate structure''<ref name="calculate">A detailed description is at [http://chemapps.stolaf.edu/jmol/docs/#calculate].</ref> command which re-calculates the secondary structure does a more fundamental identification of these secondary structures but is not available in Jmol 11.8 which is used in Proteopedia as of June 2011 but 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> | <blockquote> | ||
| - | 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''. | + | 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: <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center> and then click ''Run''. |
</blockquote> | </blockquote> | ||
| - | + | The objective of this article is to describe briefly what structures are identified by ''calculate structure'' and how it is done and also to compare its results with other ways of identifying and classifying these structures. | |
== Basis of Secondary Structure Determination == | == Basis of Secondary Structure Determination == | ||
<StructureSection load='2mhr.pdb' size='500' side='right' caption='' scene='Globular_Proteins/Anti_helix_erythrin2/1'> | <StructureSection load='2mhr.pdb' size='500' side='right' caption='' scene='Globular_Proteins/Anti_helix_erythrin2/1'> | ||
Revision as of 19:48, 1 July 2011
An important part of protein structure is the secondary structure which is made up of helices, sheets and turns, and with limitations as described in How Jmol Determines Secondary Structure Jmol is capable of determining and displaying these three types of structures. The calculate structure[1] command which re-calculates the secondary structure does a more fundamental identification of these secondary structures but is not available in Jmol 11.8 which is used in Proteopedia as of June 2011 but 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[1].
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; calculate hbonds structure and then click Run.
The objective of this article is to describe briefly what structures are identified by calculate structure and how it is done and also to compare its results with other ways of identifying and classifying these structures.
Basis of Secondary Structure Determination
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References
- ↑ 1.0 1.1 A detailed description is at [1].
- ↑ 2.0 2.1 W. Kabsch & C. Sanders, Biopolymers, 22, 2577-2636, 1983.
