Re: [ccp4bb] Against Method (R)

[Bart Hazes]

On 10-10-29 12:03 AM, Robbie Joosten wrote: Hi Bart, I agree with the building strategy you propose, but at some point it stops helping and a bit more attention to detail is needed. Reciprocal space refinement doesn't seem to do the fine details. It always surprises me how much atoms still move when you real-space refine a refined model, especially the waters. I admit this is not a fair comparison. Does the water move back to its old position if you follow up the real-space refinement with more reciprocal refinement. If so, the map may not have been a true representation of reality. Basically what I was implying is that if the required model changes "details" are such that they fall within the radius of convergence then the atoms should move to their correct positions; unless something is keeping them from moving such as an incorrectly placed side chain that causes a steric conflict. Fix the incorrect side chain and your "details" will take care of themselves. I don't imply that I can always spot an easy error to fix and sometimes end up rebuilding several different ways in the hopes that one will resolve whatever was the problem. If that doesn't happen at some point you need to give up, especially if it does not affect a functionally important region. I do think it is good practice to point out regions in the model that are problematic and have never had reviewers complain about that if it is clear you made the effort to get it as good as possible given the data. High resolution data helps, but better data makes it tempting to put too little effort in optimising the model. I've seen some horribly obvious errors in hi-res models (more than 10 sigma difference density peaks for misplaced side chains). At the same time there are quite a lot of low-res models that are exceptionally good. Can't blame the data for that, in the end each person (and supervisor) need to take responsibility for the models they produce and deposit. Same applies to sequence data bases that are full of lazy errors. If humans are involved both greatness and stupidy are likely outcomes. Bart Cheers, Robbie > Date: Thu, 28 Oct 2010 16:32:04 -0600 > From: bart.ha...@ualberta.ca > Subject: Re: [ccp4bb] Against Method (R) > To: CCP4BB@JISCMAIL.AC.UK > > On 10-10-28 04:09 PM, Ethan Merritt wrote: > > This I can answer based on experience. One can take the coordinates from a structure > > refined at near atomic resolution (~1.0A), including multiple conformations, > > partial occupancy waters, etc, and use it to calculate R factors against a lower > > resolution (say 2.5A) data set collected from an isomorphous crystal. The > > R factors from this total-rigid-body replacement will be better than anything you > > could get from refinement against the lower resolution data. In fact, refinement > > from this starting point will just make the R factors worse. > > > > What this tells us is that the crystallographic residuals can recognize a > > better model when they see one. But our refinement programs are not good > > enough to produce such a better model in the first place. Worsr, they are not > > even good enough to avoid degrading the model. > > > > That's essentially the same thing Bart said, perhaps a little more pessimistic :-) > > > > cheers, > > > > Ethan > > > > Not pessimistic at all, just realistic and perhaps even optimistic for > methods developers as apparently there is still quite a bit of progress > that can be made by improving the "search strategy" during refinement. > > During manual refinement I normally tell students not to bother about > translating/rotating/torsioning atoms by just a tiny bit to make it fit > better. Likewise there is no point in moving atoms a little bit to > correct a distorted bond or bond length. If it needed to move that > little bit the refinement program would have done it for you. Look for > discreet errors in the problematic residue or its neighbors: peptide > flips, 120 degree changes in side chain dihedrals, etc. If you can find > and fix one of those errors a lot of the stereochemical distortions and > non-ideal fit to density surrounding that residue will suddenly > disappear as well. > > The benefit of high resolution is that it is much easier to pick up and > fix such errors (or not make them in the first place) > > Bart > > -- > > ============================================================================ > > Bart Hazes (Associate Professor) > Dept. of Medical Microbiology& Immunology > University of Alberta > 1-15 Medical Sciences Building > Edmonton, Alberta > Canada, T6G 2H7 > phone: 1-780-492-0042 > fax: 1-780-492-7521 > > ============================================================================ -- ============================================================================ Bart Hazes (Associate Professor) Dept. of Medical Microbiology & Immunology University of Alberta 1-15 Medical Sciences Building Edmonton, Alberta Canada, T6G 2H7 phone: 1-780-492-0042 fax: 1-780-492-7521 ============================================================================