One can also release structure in the PDB prior to submission - I believe the HPUB option is rarely (if ever) justified.
Ed. On Wed, 2010-10-27 at 22:56 +0200, VAN RAAIJ , MARK JOHAN wrote: > 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 > > -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
