Hi, Thank you for your papers. I will read them carefully.
2011/7/9 Elizabeth McSweeney <elizabeth.mcswee...@duke.edu> > Hi > > I highly recommend reading the two Brunger papers below: they will explain > the important factors to take note of when refining low-resolution > structures. I found them very useful when I was learning about > low-resolution refinement. > > I would suggest using the deformable elastic network with simulated > annealing in CNS, and then follow that with refinement in PHENIX using tight > geometery restraints and doing TLS and grouped-B factor refinement. Your > problem is that at low resolutions, the data to parameters ratio is low, and > you need to use a number of restraints along with good bulk-solvent and > anisotropic corections in order to keep your R-factor and R-free values > within 3-4%. Perhaps you could send your PHENIX input file and we could see > what you did and maybe point what needs to be corrected. > > Hope that was helpful. good luck! > > Schroder, Levitt, Brunger, Super-resolution biomolecular crystallography > with low-resolution data Nature. 2010 Apr 22;464(7292):1218-22 Brunger, AT > et al. X-ray structure determination at low resolution. Acta Cryst D. 2009 > Feb;65(Pt 2):128-33 > > > On Sat 07/09/11 4:59 AM , Qixu Cai <caiq...@gmail.com> wrote: > > Dear all, > > Recently, I refine two low resolution structures in refmac 5.5. Their > resolutions are 3A and 3.5A respectively. > For 3A structure, after MR by phaser and rigidbody refinement&restraint > refinement by refmac5.5, I got R factor 25% and R free 35%. And then > each time, after my model building in coot and restraint refinement by > refmac 5.5, the R factor stays 25%, but R free increases to 38%, even 39%. > For 3.5A structure, the R factor stays 27%, but R free increases from > 37% to 42% after my slightly model building in coot. > Could you help me to find the reason? > > Maybe the reason is the overfit of the structure? I found that new > version of refmac 5.6 has many new features for low resolution > refinement, such as jelly boy, secondary structure restraints. But I > don't know how to use these new features in old version ccp4i (6.1.13)? > > I also used phenix.refine with the "reference model" ( I have high > resolution model for one domain of the low resolution protein) and > "secondary structure restraints", but it seams the same. Any suggestion? > > BTW, is that simulator annealing not suitable for low resolution > structure? I used the simulator annealing method of CNS and > phenix.refine, but the geometry of the structure is always destroyed > seriously. > > Could you help me? > > Thank you very much! > >
