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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