Hydrogen atoms in RNA or DNA

[turtlecrk]

Generated models for RNA and DNA do not include hydrogen atoms, so they are less workable in ChimeraX.
Is there a way to include them?

[tomgoddard]

The ChimeraX addh command will add hydrogens to molecular structures.

[turtlecrk]

Sweet!

Still something that AlphaFold should fix for other uses. Maybe have an option if there's reason not to have them?

[tomgoddard]

Most experimental structures in the Protein Databank don't have hydrogens. Since the training of AlphaFold used those structures it is not surprising that they did not include hydrogens. Although ChimeraX and other software can add hydrogens there is some subtlety to it and the software may get it wrong in some cases. For example histidines can have different hydrogens depending on the local environment and biological pH. So I think it is sensible that AlphaFold does not add hydrogens because the training data usually does not have them and how to add them involves some guesswork.

[turtlecrk]

Thanks, that makes sense.