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 BiotecnologĂ­a - 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

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