Besides empirically adjusting the weighting factor for X-ray data to increase the geometric constraints, have you tried jelly-body refinement or refinement with external constraints? The latter two methods can be helpful when refining low resolution data.
Roger Rowlett On Jul 12, 2017 7:33 PM, "Christine Gee" <[email protected]> wrote: > Hi Rhys, > > In Refmac, you can change the weighting of the Xray terms vs the geometry > restraints rather than use what is automatically assigned. Have you tried > this? In Phenix you can use secondary structure restraints (probably you > can do this in Refmac too, but I haven't tried) and try checking the box > optimize stereochemistry/Xray weight. This will probably help if your over > fitting is moving things into density but making the geometry sub optimal. > > Regards > Christine > > On Wed, Jul 12, 2017 at 4:17 PM, Rhys Grinter <[email protected]> > wrote: > >> Dear All, >> >> I'm currently in the process of refining a low(ish) resolution structure >> at 3.2 Ang, with a fair level of anisotropy. I processed the data through >> the anisotropy server (https://services.mbi.ucla.edu/anisoscale/), which >> elliptically truncated the data to 4.0, 3.8 and 3.2 Ang. This really >> improved the maps and allowed me to trace the majority of the chain and >> build most side chains. >> >> The R-factors are reasonable (0.29 work and 0.35 free respectively). but >> I'm having trouble with over fitting in refinement as I continue to refine. >> What parameters/restraints would the community generally use when refining >> this kind of structure? Additionally Refmac doesn't seem to read the >> structure factors from the anisotropy server output file properly, giving >> vastly inflated R values and strange looking maps. >> >> Cheers, >> >> Rhys >> >> -- >> Dr Rhys Grinter >> Sir Henry Wellcome Fellow >> Monash University >> +61 (0)3 9902 9213 <+61%203%209902%209213> >> +61 (0)403 896 767 <+61%20403%20896%20767> >> > >
