Hydrogen bonds: Difference between revisions

Before the availability of Jmol ver. 12, free molecular visualization programs displayed potential donor-acceptor pairs, deeming them "putatively" hbonded because determining the positions of hbonds with high confidence required expert and detailed examination of the donor-acceptor chemistry and geometry. [[Protein Explorer]] and [[FirstGlance in Jmol]] (see applet below) have ''Contacts'' dialogs that show putatively hbonded donors and acceptors based simply on the chemical elements and interatomic distances. [[PyMOL]] likewise displays "polar contacts" using dashed bonds between the involved atoms, leaving further assessment of hydrogen bonding to the user. One of the new features of Jmol 12.0 is a command, '''calculate hbonds structure''', which determines and displays the hbonds in helices, sheets and turns.<ref>The hbonds which are displayed by this command are among the hydrogen bonds identified but not displayed by recalculating the secondary structure using Jmol's implementation of DSSP.</ref> Until Proteopedia is upgraded with Jmol 12.0 the above command can be used in a Proteopedia page by using a signed copy of ver. 12.0.  This is accomplished by adding "?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar" to the url of the page being used and then reloading the page. You will have to approve the use of the signed version of Jmol, and after the applet has loaded if the Jmol frank is red instead of grey the signed version has loaded.  Click on the ''Jmol frank'', in the ''main menu'' which opens click on ''Console'', in the bottom box enter the commands: select protein; calculate hbonds structure; and then click ''Run''. Try using the above method to display the hbonds in the helices, sheets and turns in the protein shown on the right.