Re: [ccp4bb]: Refmac vs Ramachandran (low resolution)

[Anastassis Perrakis]

On Aug 23, 2006, at 9:59, Clemens Vonrhein wrote: But what should be those values? I guess at 1A resolution I'd expect a rmsd(bond) of 0.02 or larger. And at 3.5A I'd expect a rmsd(bond) of 0.005 or smaller. But these are personal choices (same as I/sig(I) or Rmerge cut-offs in data-reduction). But maybe I'm completely wrong here ... correct me please? Although i think Clemens is very far from being wrong, as usual, I cant help contributing another set of personal choices and a brief justification. Most important, and as Clemens explains, RMSD on bond lengths   and standard deviation of the Engh&Huber distributions, are different things.  However, there must be some correlation: if (to exaggerate) a certain type of bond is  in the dictionary 1.0 +/- 0.1 A, I would doubt if it makes sense to restrain it in a way that the deviation of the distribution of this type of bonds in a 3.5 A structure is 1.0 +/- 0.001. Thats just intuition and I have a concern that this is one of the things that intuition serves you wrong and statistics would say otherwise. But, i would be curious to see why this is  wrong/right. I will go and read the Cruickshank paper that Dirk pointed out to us ... I also think that beside personal preferences, Rfree would have one or two things to say here. Should we simply aim for an RMSD between 0.005-0.020, that also gives minimal Rfree ? I did a quick experiment with our current favorite nightmare at 3.3 A resolution, 360 residues, no NCS. I am reporting the achieved RMSD, the Rfree and the number of residues flagged by procheck as Rama outliers. The model I started with is 'towards the end' and had an initial 'original' rmsd of about 0.016 when I started this test. RMSD Rfree Nres 0.020 31.2 31 0.016 31.3 27 0.010 31.4 23 0.007 31.9 20 0.005 32.2 22 from that I would say, that - for our structure - the middle job is best: i would expect that after quickly fixing 4-5 residues in the graphics and running a job that would give an RMSD about 0.015 to be the best at the end. But, of course now I am tempted to take the 0.007 model, look at it, and then slowly 'release it' towards the end. ;-) Having said these I want to iterate one point that was made: Use hydrogens. It can only help and  it costs nothing. And to make a new point: use TLS. The major reason that some crystals do not diffract at high enough resolution, should be rigid body motions and TLS describes exactly that, while being very 'cheap' in parameters, so use it. for the above structure is makes a huge difference. btw: i found torsional refinement as implemented in CNS not useful compared with refmac5 / phenix or Buster. I was a bit surprised by that, but ... A.