Hi, External structure atomic bond distance restraints for use in refmac are generated using ProSMART. The webpage is here: http://www.ysbl.york.ac.uk/mxstat/Rob/index.html
Email me if you want a pre-release version. Regards, Rob On 9 Jul 2011, at 18:00, Robbie Joosten wrote: > 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! >>
