>2) when I submit this to referees will they think my structure is appropriate to draw these conclusions?".
Particularly question 2) can rarely be answered w/o looking at electron density. Binding site details, ligand geometry, all have practically no effect on the Rules of Thumb. > It is whilst asking these two questions that rules of thumb become somewhat handy, especially when they coincide with the rules of thumb used by the referees. Keep also in mind that every atom contributes to every reflection. So fixing ANY error WHEREVER will improve you refinement - also in the part you are actually interested in. You point is correct however that once your question is answered you could stop. That however does not necessarily deliver a publishable structure that might be used by others for purposes you initially did not intend. Pharma industry does this all the time quickly looking for ligands and abandoning pointless structures early - but they don't publish the unfinished models. br On 28 Oct 2010, at 10:28, Eleanor Dodson wrote: > Oh cynic! > Eleanor > > > > On 10/27/2010 09:01 PM, Simon Kolstoe wrote: >> 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 >>>> >>>> >>>> =
