Once more to those who feel offended by the structures in discussion:
I’d be very careful at judging low resolution structures. This is a tricky business requiring a lot more info than just the PDB validation report. The 3+ to 4 A resolution range is a particularly deceptive one: The crystallographer does not have much data given the model parameters (perhaps consulting his figure showing determinacy for coordinate refinement might help) http://www.ruppweb.org/Garland/gallery/Ch12/pages/Biomolecular_Crystallography_Fig_12-11.htm At this resolution one has about enough data to keep enthusiasm up but at the same time it is not quite yet bad enough to throw up the hands and admit that that one is de facto modelling with a few X-ray restraints (i.e. data), requiring correspondingly suitable refinement protocols (and discipline, aka mental restraints in addition to stereochemical restraints). One is easily spoiled by looking exceptional 2A structures of huge complexes, but nature (I do not mean the journal but the same time would not exclude it) is often cruel. Particularly in Molecular Replacement structures, and here particularly in those with multi- segment/domain models, there are almost always parts that fit well and others that fit poorly - with simply not enough data at the given resolution to improve the poor parts sans additional phase information. Bias issues have been discussed and need not be iterated here. Pavel is correct in pointing out that a model with better geometry is also a more plausible model. What we cannot tell sans supporting density is whether it is a more accurate model, although I have rarely seen an improvement in geometry giving worse density fit. Usually a mess remains a mess - there is (at this resolution) no free lunch. The key question is again – does the model justify the specific conclusions drawn from it? If a poor model is better than no model at all, be it, as long as this is recognized and not used as an excuse for careless work. Facile dictu, difficile factu. Best, BR For every sufficiently complex problem there is an answer that is simple, clear and wrong. LH Mencken From: Narayan Viswam [mailto:nvisw...@gmail.com] Sent: Monday, April 27, 2015 12:02 PM To: b...@hofkristallamt.org Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!! Sorry can't help it. The aggressive replies are mainly from senior PIs from US - friend in need is friend indeed.
