saving . . . saved the outsider oxygen molecules of protein does not take hydrogen molecule has been deleted. the outsider oxygen molecules of protein does not take hydrogen molecule has been hidden .
the outsider oxygen molecules of protein does not take hydrogen molecule
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<font size="3">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.</font><img align="none" alt="" src="https://photos.app.goo.gl/HGsxQTU6UCFUi1LJ7"><img align="none" alt="" src="https://photos.app.goo.gl/HGsxQTU6UCFUi1LJ7">

Jmol-Application Proteins-and-Macromolecules 05-06 min 30-40 sec 02-10-23, 1:18 p.m. riteshchowdhury

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



 
04-10-23, 12:23 p.m. snehalathak

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