Hi, Thank you very much.
In the example5 of this page http://www.ysbl.york.ac.uk/~garib/refmac/docs/usage/examples.html#exam5, It seems that for 3A dataset, "MAKE HYDRogens<http://www.ysbl.york.ac.uk/%7Egarib/refmac/docs/keywords/restraints.html#make_hydr>No". Is it mean that the hydrogen just usefull for high resolution data? 2011/7/10 Robbie Joosten <robbie_joos...@hotmail.com> > Hi Qixu, > > > > In CCP4i the option is in the refinement parameters: > > Use hydrogen atoms: ["build all hydrogens"] and [] output to coordinate > file > > > > What is does is build all hydrogens at the expected coordinates and > constrain them in refinement (i.e. adding hydrogens does not add extra > parameters to the model). The effect on explaining your experminetal data is > typically small, but the hydrogens help with the VdW restraints. In effect > they reduce the number of bumps and improve your torsion angles. > > > > You can use a reference structure to generate external restraints: > > http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_news.html#External > > I hope someone else on the BB can explain how. I think it is also explained > in the talk and tutorials of the Refmac website. > > > > HTH, > > Robbie > > > ________________________________ > > From: caiq...@gmail.com > > Date: Sun, 10 Jul 2011 00:44:25 +0800 > > Subject: Re: [ccp4bb] low resolution refinement > > To: robbie_joos...@hotmail.com > > CC: CCP4BB@jiscmail.ac.uk > > > > 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<mailto: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<mailto:caiq...@gmail.com> > > > Subject: [ccp4bb] low resolution refinement > > > To: CCP4BB@JISCMAIL.AC.UK<mailto: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! > > >
