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I am trying to get a pdb file that contains a single atom, it doesn't matter if it's Hydrogen or another atom. How can I obtain this? Are there any pdb files with just a single atom available to download? Or do I have to take an existing molecule and remove the atoms manually?

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  • $\begingroup$ How do you want to make a crystall of a single atom? $\endgroup$ – Chris Feb 2 '15 at 19:09
  • $\begingroup$ I have no idea why you would need sth like that, but you'd have to cut existing one $\endgroup$ – Mithoron Feb 2 '15 at 19:17
  • $\begingroup$ I'm currently working on a problem on molecular modeling and our software is having problems. I was told that a good way to debug this is to run the program using a pdf file with just a single atom $\endgroup$ – user4352158 Feb 2 '15 at 19:35
  • $\begingroup$ you'd have to cut existing one can you explain how? $\endgroup$ – user4352158 Feb 2 '15 at 19:35
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    $\begingroup$ @user4352158 In the PDB file you can remove every other entry except an atom. You can also view a single atom without altering the file itself(at least in swiss-pdb viewer) $\endgroup$ – WYSIWYG Feb 3 '15 at 5:32

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