[phenixbb] problems with clashes

Pavel Afonine PAfonine at lbl.gov
Mon Jul 30 09:59:04 PDT 2007

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.


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.

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