When in doubt, try both. In my personal experience, adding hydrogens always works. Especially at low resolution. But don't take my word for it, experiment a little.
Cheers, Robbie Date: Sun, 10 Jul 2011 16:01:59 +0800 From: caiq...@gmail.com Subject: Re: [ccp4bb] low resolution refinement To: CCP4BB@JISCMAIL.AC.UK 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 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! >
