Re: [ccp4bb]: Riding Hydrogens

[<wgscott@chemistry.ucsc.edu>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***


On Friday, September 6, 2002, at 11:30 AM, 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?
>

If they lower the R, it may be just because you have more adjustable 
parameters.
If they lower the R-free, it is either (a) real or (b) you have more 
than one molecule in the asymmetric unit
and your test and working sets are not therefore strictly independent, 
so having more adjustable parameters will also lower R-free.

In addition, each hydrogen has 1 electron that scatters X-rays, so 
modeling in all the electrons in your molecule and accounting better for 
their
distribution will justifiably lower R-free.

Now if you really want to freak everyone out, truncate your data at 3.0 
Angstroms and then refine with a single TLS group that includes all 
atoms in your structure (only 9 additional adjustable parameters) and 
watch what happens to R-free.


William G. Scott

Associate Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA

phone:  +1-831-459-5367 (office)
                +1-831-459-5292 (lab)
fax:         +1-831-4593139  (fax)

-----BEGIN GEEK CODE BLOCK-----
Version: 3.12
GS dpu s:+ a C--- U*--- P+ L+ E--- W-- N o-- K- w--
O- M+ V- PS+++ PE-- Y+ PGP-- t- 5- X R* tv-- b+++ DI++ D----
G-- e++++ h---- r+++ y++++
------END GEEK CODE BLOCK------