Re: [ccp4bb]: Riding Hydrogens

["David J. Schuller" <djs63@cornell.edu>]

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On Fri, 6 Sep 2002, Jason Yano wrote:

> So I am unclear on on the requirements for adding the hydrogens on in
> refinement. At what resolutions do they become justified? Why are they
> lowering my R and R-free?

1) your protein actually has hydrogens, that is why adding hydrogens to 
the model brings it closer to reality, i.e. lowers R and Rfree.

2) as mentioned in your subject header, these are "riding hydrogens". 
they 'ride' in a set position relative to the other atoms.  the positions 
of the hydrogens themselves are not independently refined. that is why 
your number of refined parameters has not gone up, which might have 
led to over-refinement and increase of the R : Rfree split.

cheers,

=======================================================================
"Life is a struggle, not against sin, not against the Money Power, not
against the malicious animal magnetism, but against hydrogen ions."
                                                - H.L. Mencken


"Being a true scientist, Ralph wanted to make his own dangerous experiments."
                                                      - Hugo Gernsback
=======================================================================
                        David J. Schuller
                        modern man in a post-modern world
                        MacCHESS, Cornell University
                        djs63@cornell.edu