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:[log in to unmask]] On Behalf
> Of Robbie
> Joosten
> Sent: Tuesday, October 26, 2010 10:29 PM
> To: [log in to unmask]
> 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
>>
>>
>> =
|