Journal editors need to know when the reviewer they trusted is completely out to lunch. So please don't just silently knuckle under! It may make no difference for Nature, but my impression has been that rigorous journals like JMB do care about review quality. Phoebe
===================================== Phoebe A. Rice Dept. of Biochemistry & Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp ---- Original message ---- >Date: Wed, 27 Oct 2010 15:13:03 -0700 >From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> (on behalf of "Bernhard Rupp >(Hofkristallrat a.D.)" <hofkristall...@gmail.com>) >Subject: Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree) >To: CCP4BB@JISCMAIL.AC.UK > >> Surely the "best" model is the one that the referees for your paper are >happy with? > >That may be the sad and pragmatic wisdom, but certainly not a truth we >should accept... > >> I have found referees to impose seemingly random and arbitrary standards > >a) Reviewers are people belonging to a certain population, characterized by >say a property 'review quality' that follows a certain distribution. >Irrespective of the actual shape of that parent distribution, the central >limit theorem informs us that if you sample this distribution reasonably >often, the sampling distribution will be normal. That means, that half of >the reviews will be below average review quality, and half above. > >Unfortunately, the mean of that distribution is >b) a function of journal editor quality (they pick the reviewers after all) >and >c) affected by systematic errors such as your reputation and the chance that >you yourself might sit on a reviewer's grant review panel >By combining a, b, c you can get a fairly good assessment of the joint >probability of what report you will receive. You do notice that model >quality is not a parameter in this model, because we can neglect marginal >second order contributions. > >> Mind you discussions on this email list can be a useful resource for >telling referee's why you don't think you should comply with their "rule of >thumb". > >I agree and sympathize with your optimism, but I am afraid that those who >might need this education are not the ones who seek it. I.e., reading the bb >complicates matters (simplicity being one benefit of ROTs) and you can't >build an empire wasting time on such things. > >Good luck with your reviews! > >BR > >Simon > > > >On 27 Oct 2010, at 20:11, Bernhard Rupp (Hofkristallrat a.D.) wrote: > >> Dear Young and Impressionable readers: >> >> I second-guess here that Robbie's intent - after re-refining many many >> PDB structures, seeing dreadful things, and becoming a hardened cynic >> - is to provoke more discussion in order to put in perspective - if >> not >> debunk- >> almost all of these rules. >> >> So it may be better to pretend you have never heard of these rules. >> Your >> crystallographic life might be a happier and less biased one. >> >> If you follow this simple procedure (not a rule) >> >> The model that fits the primary evidence (minimally biased electron >> density) >> best and is at the same time physically meaningful, is the best model, >> i. >> e., all plausibly accountable electron density (and not more) is >> modeled. >> >> This process of course does require a little work (like looking >> through all of the model, not just the interesting parts, and thinking >> what makes sense) but may lead to additional and unexpected insights. >> And in almost all cases, you will get a model with plausible >> statistics, without any reliance on rules. >> >> For some decisions regarding global parameterizations you have to >> apply more sophisticated test such as Ethan pointed out (HR tests) or >> Ian uses (LL-tests). And once you know how to do that, you do not need >> any rules of thumb anyhow. >> >> So I opt for a formal burial of these rules of thumb and a toast to >> evidence and plausibility. >> >> And, as Gerard B said in other words so nicely: >> >> Si tacuisses, philosophus mansisses. >> >> BR >> >> -----Original Message----- >> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of >> Robbie Joosten >> Sent: Tuesday, October 26, 2010 10:29 PM >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree) >> >> Dear Anthony, >> >> That is an excellent question! I believe there are quite a lot of >> 'rules of thumb' going around. Some of them seem to lead to very >> dogmatic thinking and have caused (refereeing) trouble for good >> structures and lack of trouble for bad structures. A lot of them were >> discussed at the CCP4BB so it may be nice to try to list them all. >> >> >> Rule 1: If Rwork < 20%, you are done. >> Rule 2: If R-free - Rwork > 5%, your structure is wrong. >> Rule 3: At resolution X, the bond length rmsd should be < than Y (What >> is the rmsd thing people keep talking about?) Rule 4: If your >> resolution is lower than X, you should not >> use_anisotropic_Bs/riding_hydrogens >> Rule 5: You should not build waters/alternates at resolutions lower >> than X Rule 6: You should do the final refinement with ALL reflections >> Rule >> 7: No >> one cares about getting the carbohydrates right >> >> >> Obviously, this list is not complete. I may also have overstated some >> of the rules to get the discussion going. Any addidtions are welcome. >> >> Cheers, >> Robbie Joosten >> Netherlands Cancer Institute >> >>> Apologies if I have missed a recent relevant thread, but are lists of >>> rules of thumb for model building and refinement? >>> >>> >>> >>> >>> >>> Anthony >>> >>> >>> >>> Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 >>> >>> >>> =
