Hi, Thank you for your suggestion. Could you tell me what is "riding hydrogens"? And it seems there is not "reference model" function in refmac5.6?
2011/7/9 Robbie Joosten <robbie_joos...@hotmail.com> > Dear Qixu, > > > > refamac 5.6 works well at these resolutions. You can add commands to your > refinement in CCP4i by using the 'Run and view command script' (or something > like that) option and just typing in the extra commands. Jelly-body has > worked very well for me (although I use tigheter restraints than the > default). Also local NCS works well (provided you have NCS). I never used > reference structures, but I heared good things about it. Don't forget to use > riding hydrogens, for some reason it is not the deafault. > Perhaps you should also switch of the automatic X-ray weighting in favour > of optimizing the matrix weight yourself (start with 0.05 and compare > refinements for higher and lower values). > > > > HTH, > > Robbie > > > > > ---------------------------------------- > > Date: Sat, 9 Jul 2011 16:59:29 +0800 > > From: caiq...@gmail.com > > Subject: [ccp4bb] low resolution refinement > > To: CCP4BB@JISCMAIL.AC.UK > > > > 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! >
