Hi All, a couple of comments about hydrogens: 1) A few people will argue today the fact that although the contribution of hydrogen atoms to X-ray scattering is weak or nearly invisible (depending on resolution), the H atoms are still present in real structures. Including them into a model makes other model atoms aware of their positions which removes non-physical (bad) contacts at no cost (depending on H model used). This is irrespective of data quality (resolution, for instance). 2) We *strongly* encourage to not remove hydrogen atoms from your output PDB file after refinement since it will make the refinement statistics (R-factors, etc...) irreproducible without repeating exactly the same refinement protocol. It is *really* bad to do the refinement using hydrogens and then remove them before the deposition to PDB. Pavel. Lari Lehtio wrote:
Sorry,
It was just an attempt to be sarcastic about my 2.8 Å data. In refmac you do not see riding hydrogens although it uses them.