the outsider oxygen molecules of protein does not take hydrogen molecule
whenever i try to fix hydrogen and minimize, hydrogen adds only in the backbone of protein structure. the oxygen molecules that present beside the protein does not get the hydrogen molecule. i tried it other pdb files, but there is same issue. is it a malfunction? give me suitable solution.
Jmol-Application Proteins-and-Macromolecules 05-06 min 30-40 sec
Answers:
Indeed this seems to be an issue. I have tried using script commands to add hydrogens but it is not working for oxygens.
You may write to Prof. Robert Hanson who is the principal developer of Jmol, I am sharing his email ID here. He may have some suggestion for resolving the problem.
hansonr@stolaf.edu
