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 hydrogen bonds in helices, sheets and turns.<ref>These hydrogen bonds are among the hydrogen bonds identified but not displayed by recalculating the secondary structure using Jmol's implementation of DSSP.</ref> Until Jmol is upgraded in Proteopedia the above command can be used by adding '?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar' to the url of the page being used and then reload 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.  Right click the frank, select Console, enter the above command in the lower concole box and click Run.