[phenixbb] problems with clashes
PAfonine at lbl.gov
Mon Jul 30 09:59:04 PDT 2007
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.
Lari Lehtio wrote:
> 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.
More information about the phenixbb