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Modelling missing hydrogens from X-ray crystallography

  1. Aug 30, 2006 #1
    I had recently stumbled upon a computer program that can automatically add missing hydrogen atoms to protein structures from files from the protein data bank. (due to the hydrogen atom having only 1 electron, hence making its electron density too low to be detected by X-ray crystallography methods) I am curious on the physics used by the program to calculate and detect and add the hydrogen atom to those long chained molecules and would be more than delighted if someone could recommend me a book or web resources or even describe the theories here so that I can at least have a clear direction on which field/area to read up on to fully understand what is going on. :)
  2. jcsd
  3. Aug 30, 2006 #2
    The computer program should provide reference to how the program does what is does. That would be the first place to look.
  4. Aug 30, 2006 #3


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    Info about what software you are actually using would help as well.
  5. Sep 12, 2006 #4
    If the program you are using is VMD, or something like it, then it is simply putting a hydrogen at the equilibrium bond distance and with an angle based upon the force field (CHARM, Amber, OPLS, etc).

    You obviously would not consider this to be accurate if you're talking about a proton involved in a reaction center, etc. but for the bulk protein (where most molecular simulations will wind up holding hydrogens rigid via SHAKE anyway) it is fine.
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