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 > > > =
