Re: [ccp4bb]: Riding Hydrogens

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Jason Yano wrote:
> 
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> 
> 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


 Well - the hydrogens havent gone away just because your resolution is
limited! I have always thought it is a good idea to add them once you
were confident your structure was more or less correct, but they appear
yo make a reduced contribution to the R factor at lower resolution - I
think the scaling sort of compensates pretty adequately..
 Eleanor
-- 
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Eleanor J.Dodson, York Structural Biology Laboratory,
                  Chemistry Department, 
                  University of York, Y01 5DD Heslington, U.K.
Tel: Work: +44 (1904) 32 82 53  Home +44 (1904) 42 44 49
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