Dear Gerard,
I guess you simply did not understand my email, at all. It's in the
archive, you may read it again -:)
All the best!
Pavel.
P.S. Are you saying people producing (nearly manually) first
macromolecular structures BEFORE the era of cool refinement packages
were all doing "2hr0"s ? I would stay away from such a strong statements.
On 8/27/10 3:35 PM, Gerard Bricogne wrote:
> Dear Pavel,
>
> I must say that I find some of the statements in your message rather
> glib and shallow, especially on the part of a developer. Where is all the
> Bayesian wisdom that Phenix is advertised to have absorbed? Your last
> paragraph is shocking in this respect. The whole idea of Bayesian inference
> is precisely that it isn't good enough to pull out of a hat, by means of a
> trick/blackbox, "a" model that corresponds to the data, but that one needs
> to see how many models would do fare more or less as well and to give some
> rough probability distribution over them; and if your are going to finally
> deliver a single model, it had better be as representative as possible of
> that weighted ensemble of possible ones, rather than just "a" model that
> happens to have been persuaded to fit the data by hook or by crook.
>
> Closer to practicalities, the procedure by which a model that ends up
> being deposited should be reproducible by third parties as the endpoint of a
> refinement calculation from the deposited coordinates and X-ray data,
> conducted according to the author's description of their own refinement
> procedure. That procedure, however, should always end with a justifiable
> purely computational step. It seems very dangerous to state that a model in
> which some manual moving around of atoms was given the last word is as good
> as anything else. If you start encouraging such casual attitudes, you may
> end up with 2hr0.
>
>
> With best wishes,
>
> Gerard.
>
> --
> On Fri, Aug 27, 2010 at 02:02:48PM -0700, Pavel Afonine wrote:
>> Hello,
>>
>>>>> The requirement sounds extremely suspect: every atom in the structure
>>>>> contributes to every reflection, so refining "only some atoms" makes as
>>>>> little mathematical sense as refining against "only a subset of
>>>>> reflections".
>>>>>
>>>> I agree with you that the requirement sounds dubious.
>>>> But the specific argument you make is not quite right.
>>>>
>>>> Two common counter-examples are real-space refinement and rigid-body
>>>> placement of a known fragment relative to an existing partial model.
>>> Not so: they're tricks to get out of local minima and maybe improve
>>> phases, but they're /not/ useful for generating the model that "best" fits
>>> the data,
>> I completely agree with Ethan. Although the overall goal of refining
>> B-factors only for a subset of atoms is not clear (there are at least three
>> example where I do it in phenix.refine - I won't go into technicalities
>> here, it's hidden under the hood and no-one knows -:) ), doing so makes
>> perfect sense in general.
>>
>>> Or would one deposit a model for which real-space refinement has been the
>>> final step?
>> Of course you would. Refinement - in whatever space - is just a
>> trick/blackbox to get your model to correspond to the data, and how you do
>> it: in real, reciprocal or both spaces, manually moving atoms or letting
>> minimizer or grid search do that - it does not matter.
>>
>> Pavel.
>>
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