Roberto steiner has told you how to use these new REFMAC5.6 features, Rob Nicholls has suggested how to generate secondary structure restraints, and Martyn Winn given a page to install a new interface to make it easier to use them..
But with such limited data it isnt surprising that the FreeR climbs steadily. Scaling Fcalcs and Fobs together at this resolution is tricky, and you should look at your plots of Rfactor and Fo/Fc at the end of refinement. There may be anomalies at the top or bottom resolution.. There really isnt a general rule for a fix. You need to "know your data". You can still get useful information from the maps. Eleanor On Sat, 9 Jul 2011 16:59:29 +0800, 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!
