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Re: [ccp4bb]: Riding Hydrogens



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One of the ideas of adding hydrogens in their riding positions was that their 
addition in some way is validation of accuracy of the refined atoms. 
Hydrogens are not refined. But they are used for structure factor 
calculations and geometry (bond lengthes, angles, antibumping). Their 
positions are "idealised" during refinement. Usually their addition improves 
overall geometry like torsion angles. Sometimes they are useful in spotting 
"problem areas". Look at the list of vdw outliers. 

As name suggests only those hydrogens for which position can be preicted from 
their parents are included. Other hydrogens have 0 occupancy and do not 
contribute.

Regards
Garib


 
On Friday 06 Sep 2002 7:30 pm, Jason Yano wrote:
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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> Hi All,
>
> Another subject for debate. I am in the process of refining a 2.1 angstrom
> structure using the latest version of Refmac. The default for restrained
> refinement seems to be to generate all hydrogens. This doesn't seem very
> resonable at 2 angstrom resolution. I usually change the default to not
> include the hydrogens, but I was a bit sleepy one afternoon and forgot to
> change the default. Upon noticing that I had set it wrong, I decided to
> re-run refinement again. Surprisingly, I found that adding the hydrogens
> in lowered both R and R free by about 1%. Still skeptical, I tried a 2.3
> angstrom data set, in and early stage of model building, here are the
> results:
>
> without hydrogens:
>
> REMARK   3  FIT TO DATA USED IN REFINEMENT.
> REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
> REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
> REMARK   3   R VALUE     (WORKING + TEST SET) : 0.23753
> REMARK   3   R VALUE            (WORKING SET) :  0.23305
> REMARK   3   FREE R VALUE                     :  0.32008
> REMARK   3   FREE R VALUE TEST SET SIZE   (%) :  5.2
> REMARK   3   FREE R VALUE TEST SET COUNT      :  1196
>
> with hydrogens:
>
> REMARK   3  FIT TO DATA USED IN REFINEMENT.
> REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT
> REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
> REMARK   3   R VALUE     (WORKING + TEST SET) : 0.23091
> REMARK   3   R VALUE            (WORKING SET) :  0.22655
> REMARK   3   FREE R VALUE                     :  0.31141
> REMARK   3   FREE R VALUE TEST SET SIZE   (%) :  5.2
> REMARK   3   FREE R VALUE TEST SET COUNT      :  1196
>
> 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?
>
>
> Thanks,
>
>
> Jason

-- 
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 328252