Hydrogen in macromolecular models: Difference between revisions
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==Adding Hydrogens From Theory== | ==Adding Hydrogens From Theory== | ||
It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free | It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free programs listed below. Beware that the results are only as good as the molecular models themselves. Uncertainties in the positions of non-hydrogen atoms will, of course, produce inaccurate positions for hydrogen atoms. In fact, the quality of the molecular model can be judged in part from how well the hydrogens fit into the spaces between the non-hydrogen atoms. This degree of fit is quantitated in the ''overall clash score'' reported by the first method below, ''Molprobity''. | ||
* Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped. | * Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped. | ||
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* Use the free [[Jmol/Application|Jmol Application]]. Enter these commands in the white ''Jmol Script Console'' window: | * Use the free [[Jmol/Application|Jmol Application]]. Enter these commands in the white ''Jmol Script Console'' window: | ||
** set pdbAddHydrogens true | ** set pdbAddHydrogens true | ||
**[[ | **[[Jmol/Application#Loading_a_Molecule|Load the molecule]] (must be done AFTER the previous command). | ||
** select all (only the selected atoms will be written) | ** select all (only the selected atoms will be written) | ||
** write hadded.pdb ("hadded" can be your filename, but must end ".pdb") | ** write hadded.pdb ("hadded" can be your filename, but must end ".pdb") | ||
[[PDB files]] that you save from either of these methods, can, for example, be | [[PDB files]] that you save from either of these methods, can, for example, be dropped into [[FirstGlance in Jmol]] for visualization and analysis. | ||
===Test Results=== | ===Test Results=== | ||
