They do send both, if you explicitly ask as a referee and threaten otherwise not to review, but who
a) has and takes the time to make a map and look at the parts relevant to discussion b) knows how to do that properly and with confidence (otherwise it’s worthless) A suggestion to Nature to always pair a crystallographic technical reviewer with no stake in the subject of study with those evaluating the biological or whatever thematic merits are, was not deemed worthy of response. It would admittedly require intimate knowledge of the field and quite some work for the editor, that is for sure. BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of VAN RAAIJ , MARK JOHAN Sent: Wednesday, October 27, 2010 1:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rules of thumb (was diverging Rcryst and Rfree) perhaps we should campaign for it to be obligatory to provide the pdb and structure factor file to the journal, and thus referees, upon submission? Then he can look for himself to see that building and refinement have been performed satisfactorily. Mark > Surely the "best" model is the one that the referees for your paper > are happy with? > > I have found referees to impose seemingly random and arbitrary > standards that sometime require a lot of effort to comply with but > result in little to no impact on the biology being described. 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". > > 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 >>> >>> >>> = > Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoléculas Centro Nacional de Biotecnología - CSIC c/Darwin 3, Campus Cantoblanco 28049 Madrid tel. 91 585 4616 email: mjvanra...@cnb.csic.es
