I'm sorry, I can't simply drop this thread, not when it keeps ignoring
the physics of diffraction:
In order to attempt any (rigorous) scientific conclusions from a
structure, one needs the "best" model, the one that's converged against
the data.
When you run real-space refinement, you're refining against maps that
come from a set of phases - but phases are *derived* data: derived from
the starting model -- from ALL of the starting model. Which real-space
refinement has now changed. So to achieve *convergence*, you have to
recalculate the phases. From ALL of the starting model.
I'm mystified how this procedure can be considered local to a few
atoms. (Even if it is intensely pleasing to watch RSR make a model snap
into some bothersome density.)
phx.
P.S. The availability of spectacular experimental phases *should* allow
convergence purely through real-space refinement, of course. But I've
seen a lot of phasing, and I've never encountered this situation.
On 28/08/2010 00:19, Gerard Bricogne wrote:
> Dear Pavel,
>
> Yes, I may indeed have been focussed too much attention on your
> "subversive"-looking last paragraph, without fully seeing it in the context
> of the whole thread. I am also sorry that I was so strident in my criticism:
> I should not be writing e-mails on this topic late on a Friday night :-)) .
>
>
> Have a nice weekend.
>
> Gerard.
>
> --
> On Fri, Aug 27, 2010 at 03:48:03PM -0700, Pavel Afonine wrote:
>
>> 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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