Hydrogen in macromolecular models: Difference between revisions
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* 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. | ||
* Use the Vriend Lab's [ | * Use the Vriend Lab's [https://swift.cmbi.umcn.nl/servers/html/index.html WHATIF WWW Interface]. Hydrogens are added to both protein and nucleic acids '''and also to water'''. | ||
**Under Classes (at left) click "Hydrogen (bonds)". | **Under Classes (at left) click "Hydrogen (bonds)". | ||
**Select "Add protons to the structure". | **Select "Add protons to the structure". | ||
