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Re: [ccp4bb] an over refined structure |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 04 February 2008Subject: Re: an over refined structure From: price {- at -} UCHICAGO {- dot -} EDU price {- at -} UCHICAGO {- dot -} EDU Date: 2008-02-04 should, on the coordinates but not on the Bs)? How does your Ramachandran plot look? You might tighten the geometry even more. Aside from all theoretical arguments about how big the rmsd's should be, if they're rather loose, things that are built incorrectly may be shoved back into density, making mistakes harder to spot. Have you made sure that all your side chains are not just in the density, but in nice, non-strained rotamers? The backbone and side chains are rather couple in refinement, especially if you don't have very high resolution data - this means that if you originally had the backbone slightly wrong, you may have built the side chains in the wrong rotamers. They'll look like they fit the density, but everything will be a bit strained until you fix them. Particularly if your Ramachandran plot is a bit scruffy, try optimizing the backbone geometry (by something such as lego in O), then refitting the side chains. Phoebe Rice At 11:33 AM 2/4/2008, you wrote: >Hi Tim, > >Thank you for your and information and suggestions. There are two >indepdent molecules in the asymmetric unit and one molecule does not >have very good density, especially in the N-terminus. > >Do you think that I should remove the region in the refinement? > >Best, > >Sun > >Tim Gruene >I would agree that the difference is suspiciously high. I. Tickle and >others have published analytical expressions for how to estimate the ratio >between R and Rfree, just google for "tickle rfree" to find the >references. > >You easily achieve a large difference by adding too many waters which just >model noise. There may be other reasons for which more knowledge about the >structure is required. Do you have large unmodelled regions, like loops >that do not show in the density map? > >Tim > > >-- >Tim Gruene >Institut fuer anorganische Chemie >Tammannstr. 4 >D-37077 Goettingen > >GPG Key ID = A46BEE1A > > >On Mon, 4 Feb 2008, Sun Tang wrote: > > > Hello All, > > > > I refined a structure with Refmac in CCP4i and the R/Rfree is > 0.215/0.277. The difference between R and Rfree is too much even > though I used 0.01 for weighting term in the refinement (the > default value is 0.3). The RMSD for bond length and bond angle is > 0.016 A and 1.7 degree. > > > > What may be wrong with the over-refined structure? What is the > reason for leading to an over-refined structure? How to avoid it? > > > > Best wishes, > > > > Sun Tang > > > > > > --------------------------------- > > Be a better friend, newshound, and know-it-all with Yahoo! > Mobile. Try it now. > > > >Be a better friend, newshound, and know-it-all with Yahoo! Mobile. > >it now. --------------------------------------------------------------------------------------------------------------------------- Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 fax 773 702 0439 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 04 February 2008 |
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