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 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 | 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 an objective identification of these secondary structures. ''Calculate structure'' by itself only identifies the different secondary structures and does not result in the display of a structure. Additional commands are required to color and render the secondary structures differentially and to display the hydrogen bonds (hbonds). The development of the scenes in this article included the use of the script ''select protein; calculate structure; cartoon; color structure''. Since the post-green link processing of the ''calculate hbonds structure'' command is malfunctioning, it was not used when making the scenes. In order to display hbonds in any scene which does not show them, click on the ''Jmol frank'', in the ''main menu'' click on ''Console'', in the bottom box of the console enter the command ''calculate hbonds structure'' and then click ''Run''. This same technique, with the exception of entering <span style='background-color:yellow;'>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</span> into the lower console box, can be used to do an objective identification of the secondary structures on any Proteopedia page in which it has not been done. | ||
The objectives of this article are: | The objectives of this article are: | ||
