Hi everybody, as I did not find a final solution to the hydrogen restraints problem (flying or exploding during real space refinement) in any of the mailing lists, I wanted to pick this topic up again.
If one adds hydrogens by phenix.ready_set or reduce the labels for these hydrogens on let's say a Cbeta atom will be HB2 and HB3 (according to the pdb v3.2 convention). However, the coot/ccp4 library names them HB1 and HB2, so there are no restraints for HB3 atoms. I see that probably this naming problem can be overcome by using phenix.reduce -OLD, or renaming them manually in the pdb file (but if one deposits the structure to PDB does one have to name them back again?). Is there already some new solution? And how about hydrogen restraints for the most N-terminal amino acid, where one has H1, H2 and H3? How are these handled? There seem to be no restraints for those as well, because they also fly around during real space refinement. I'm using Coot 0.6-pre-1 (Durham (revision 2264)) and phenix GUI 1.5.2... Thanks for any suggestions! Sara
