Hi Andreas, In your case, it sounds like a reasonable strategy would be to use external restraints for a few rounds of refinement (as you have done), but then release them and instead use jelly-body restraints. This two-stage process will help to initially hold your model in a sensible conformation using external restraints, but then gently release the structure in order to reduce further bias in later rounds. The immediate subsequent use of jelly-body restraints after external restraints will ensure that the model won't deviate too far from that sensible conformation, unless the data suggests otherwise.
Of course, if certain regions lose their sensible conformations in subsequent rounds of refinement, you can continue to use external restraints just in these regions. > I substantially rebuilt a surface loop that I don't want to restrain by the > model. In this case, I would recommend re-generating the external restraints, this time telling ProSMART not to generate restraints for these particular residues/regions. This can be done using the -restrain and -restrain_rm keywords, as described in the documentation (let me know off-board if you want help with this). If you enable map sharpening then the single output MTZ file should be the sharpened map… I'm not sure why you are finding that the map is not displayed… do you see any difference between enabling/disabling map sharpening? Cheers, Rob On 25 Sep 2012, at 11:19, Andreas Förster wrote: > Dear all, > > I'm making first steps in the desolate world of low-resolution refinement. > With dodgy 3.8A data, the magic of Phaser was able to solve the structure of > a complex by MR with its components as MR models. Jelly-body refinement does > wonders for R free. There are three issues that I would like to get some > advice on: > > 1) Using external restraints calculated with ProSMART improved the structure > further, but I'm worried that using restraints derived from the structures > used for MR gets me into a sinkhole of model bias. Should it be either > molecular replacement or homology restraints? > > 2) Do I recalculate restraints at each round of refinement? In particular, > I substantially rebuilt a surface loop that I don't want to restrain by the > model. > > 3) Activating map sharpening results in mtz files that look just normal and > open in coot after the typical map calculation break, but no maps are > displayed. This is independent of the sharpening factor I choose (between 5 > and 60). > > Thanks for your help. > > > Andreas > > > -- > Andreas Förster, Research Associate > Paul Freemont & Xiaodong Zhang Labs > Department of Biochemistry, Imperial College London > http://www.msf.bio.ic.ac.uk
