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:[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
>>>
>>>
>>> =
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