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Re: [ccp4bb]: refinement strategies



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Tommi Kajander wrote:
> 
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> 
> Dear all,
> I would like to know do people routinely use (overal) anisotropic
> b-factor correction and  bulk solvent correction (e.g. as implemetned
> in CNS) throughout the refiment, opinions? Possible pitfalls? At some
> point the was discussion on how/when bulk solvention correction
> should be used during the refiment, to me the way its implemented in
> CNS (at least, sorry  about not discussing CCP4 here) seems pretty
> safe to use all the way..
> Thanks for comments,
> 
> Tommi K.


 Well - I guess the theory is more or less the same for all refinement
packages!

 And yes - in general it is best to use (overal) anisotropic
 b-factor correction and  bulk solvent correction.

 However if your data is not complete, or you have lost the strong
reflections, or some other defect is present, the bulk solvent
correction may not work well ( it is heavily dependent on having
complete low resln terms..) , and the overall anisotropic correction may
try to compensate for other missing data blocks in a rather bizarre
manner . If you look at the plots of your <I> v resolution, wilson plots
etc etc you should know when to be suspicious.

 In particuler - look at all plots from TRUNCATE. in particular the
"amplitude analysis against resln and the Anisotrpy analysis ( FALLOF)

 Then in refmac there are other plots of <Fobs> v <Fcalc> . 
They are labelled 

Rfactor analysis , F distribution v resln   <Fobs> v <Fcalc> 

 Eleanor Dodson



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Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
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