Hydrogen bonds: Difference between revisions
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==Finding and Visualizing Hbonds== | ==Finding and Visualizing Hbonds== | ||
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 the chemical elements and interatomic distances. [[PyMOL]] likewise displays "polar contacts" using dashed bonds between the involved atoms, leaving assessment of hydrogen bonding to the user. | 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 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. | ||
Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|hydrogen atoms]], the possibility of an energetically significant hydrogen bond exists when donor and acceptor atoms are within about 3.5 Å of each other. However, before rigorously concluding that a hydrogen bond is present in a macromolecular crystal structure, viewers should first: | Since many [[PDB file|PDB files]] lack [[Hydrogen in macromolecular models|hydrogen atoms]], the possibility of an energetically significant hydrogen bond exists when donor and acceptor atoms are within about 3.5 Å of each other. However, before rigorously concluding that a hydrogen bond is present in a macromolecular crystal structure, viewers should first: | ||
* Consider the overall coordinate error implied by the resolution of the structure. | * Consider the overall coordinate error implied by the resolution of the structure. | ||
* Survey local temperature factor values to see if the involved | * Survey local temperature factor values to see if the involved model coordinates are well-determined. | ||
* Factor in corroborating evidence such as involvement in surrounding elements of secondary structure. | * Factor in corroborating evidence such as involvement in surrounding elements of secondary structure. | ||
* Inspect the electron density, if available, to confirm that the model coordinates are actually in density. | * Inspect the electron density, if available, to confirm that the model coordinates are actually in density. | ||
