text: user2897: I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms.
  Specifically, I'd like to determine the rough location of side-chain hydrogens in glycine residues, given the CA, C, N, and O coordinates. Is this possible? I don't need too much precision - I just need the general direction relative to the rest of the residue. More specifically, I want a vector originating at the CA that points roughly in the direction of the side chain.
  I've looked at software for generating hydrogen atoms from pdb structures, however, I need to know which ones are glycine side chains, and was wondering if there might be a simpler way to predict hydrogen locations given coordinates of backbone atoms.
  
  user266: Glycine has a single hydrogen atom as its side chain:
  
  All the six bond angles with the CA atom in the middle are about 109°
  (C-CA-N, C-CA-HA3, C-CA-HA2, N-CA-HA3, N-CA-HA2 and HA3-CA-HA2 using the CCD naming convention). This defines the rough direction of the hydrogen atoms.
  But which of the two hydrogens is the side chain?
  If it is a left-handed protein, I'd assume that it's the hydrogen pointing toward the screen, similarly to the side chain in L-alanine:
  
  The images are taken from WikiMedia Commons:
  glycine
  and L-alanine.
  
original_text: 2897: <p>I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms.</p>
  
  <p>Specifically, I'd like to determine the rough location of side-chain hydrogens in glycine residues, given the CA, C, N, and O coordinates. Is this possible? I don't need too much precision - I just need the general direction relative to the rest of the residue. More specifically, I want a vector originating at the CA that points roughly in the direction of the side chain.</p>
  
  <p>I've looked at software for generating hydrogen atoms from pdb structures, however, I need to know which ones are glycine side chains, and was wondering if there might be a simpler way to predict hydrogen locations given coordinates of backbone atoms.</p>
   266: <p>Glycine has a single hydrogen atom as its side chain:</p>
  
  <p><a href="https://i.stack.imgur.com/BKoQT.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/BKoQT.png" alt="Glycine from Wikipedia"></a></p>
  
  <p>All the six bond angles with the CA atom in the middle are about 109°
  (C-CA-N, C-CA-HA3, C-CA-HA2, N-CA-HA3, N-CA-HA2 and HA3-CA-HA2 using the CCD naming convention). This defines the rough direction of the hydrogen atoms.</p>
  
  <p>But which of the two hydrogens is the side chain?</p>
  
  <p>If it is a left-handed protein, I'd assume that it's the hydrogen pointing toward the screen, similarly to the side chain in L-alanine:</p>
  
  <p><a href="https://i.stack.imgur.com/YZjyB.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/YZjyB.png" alt="L-alanine"></a></p>
  
  <p><sub>The images are taken from WikiMedia Commons:
  <a href="https://commons.wikimedia.org/wiki/File:Glycine-3D-balls.png" rel="nofollow noreferrer">glycine</a>
  and <a href="https://commons.wikimedia.org/wiki/File:L-alanine-3D-balls.png" rel="nofollow noreferrer">L-alanine</a>.</sub></p>
  