In message <[EMAIL PROTECTED]> Paul Emsley <[EMAIL PROTECTED]> writes: > Hi Mark, > > The issue here is that the dictionary does not define those atoms for e.g. ARG > and GLN. > > For ARG and GLN, the atoms bound to the CG are " HG1" and " HG2" - not Hx3. > i.e. > Coot doesn't know about bonds to those atoms, so it kicks them off with NBC > restraints. > > By what means did you acquire those atoms? There may be a new convention about > hydrogen naming that I don't know about...
After doing a bit of research (talking to Jeff Headd) I find that indeed the convention has changed. The new format for the hydrogen names are indeed Hx2 and Hx3. <grumble>Oh dear oh dear, this is going to be a nightmare... I wonder if the PDB have any idea what problems they have caused... I spoke to Ralf recently, he says (IIUC) that they map input pdb names to the new format on reading the coordinates and then *re-map* the atom names to make them match the dictionary. Urgh! And I will have to do the same...</grumble> Paul.
