Hydrogen bonds: Difference between revisions
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==Finding and Visualizing Hbonds== | ==Finding and Visualizing Hbonds== | ||
Since many [[PDB files]] lack hydrogen atoms, the presence of an energetically significant hydrogen bond can be inferred when a probable donor and acceptor are within 3.5 Å of each other. | Few, if any, free molecular visualization programs show hbonds as rods or sticks between atoms. This is because determining the positions of hbonds with high confidence requires expert and detailed examination of the donor-acceptor chemistry and geometry. Instead, some molecular visualization programs display potential donor-acceptor pairs, deeming them "putatively" hbonded. [[Protein Explorer]] and [[FirstGlance in Jmol]] have ''Contacts'' dialogs that show putatively hbonded donors and acceptors based simply on element and distance. | ||
Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|hydrogen atoms]], the presence of an energetically significant hydrogen bond can be inferred when a probable donor and acceptor are within 3.5 Å of each other. [[FirstGlance in Jmol]]'s Contacts display defines "likely noncovalently bonded" oxygens and nitrogens (shown as balls) as those within 3.5 Å of other oxygens or nitrogens. | |||
''An interactive example in Jmol is needed here.'' | |||
==Content Attribution== | ==Content Attribution== | ||