Yes, agree overall.
What I plan to implement in phenix.refine and then play with at some
point is that loop I wrote before:
for cycle in cycles (until convergence):
- do real space refinement (minimize T = Exray*weight +Egeom w.r.t.
model params);
- do reciprocal space refinement (minimize T = SUM(rho_obs -
rho_calc)^2*weight +Egeom w.r.t. model params)
(- do other things, like we do now: model bulk and ordered solvent,
etc...)
Based on the literature review, the overall feeling is that this should
work better than either one separately: real or reciprocal space
refinement.
Pavel.
Anastassis Perrakis wrote:
>
> On 10 Aug 2007, at 20:12, Pavel Afonine wrote:
>
>>
>>
>> Anastassis Perrakis wrote:
>>> On 10 Aug 2007, at 18:59, Pavel Afonine wrote:
>>>
>>>> Hi Mike,
>>>>
>>>> the best is to do both in a loop:
>>>>
>>>> for cycle in cycles:
>>>> - do real space refinement;
>>>> - do reciprocal space refinement
>>>
>>> Well - thats what we all do - right ?
>>> The real space refinement can be done either with the tools from
>>> Chapman at al,
>>> or interactively by the user or by (here I go again ... ) ARP/wARP
>>> or Resolve etc etc.
>>> In all cases we fit the model to the map ... only the tools differ.
>>
>> I was not clear enough, sorry. By refinement I meant the
>> mini(maxi)mizer-driven optimization of a goal function w.r.t. model
>> parameters, and not atoms re-shuffling manually (looking at map) or
>> using a program.
>
> Clear clarification ... but there is hardly a difference I would say.
>
> What ARP/wARP, or Coot, or O, or I am sure Resolve, do at some point
> is exactly to use a mini(maxi)mizer-driven optimization of a goal
> function w.r.t. model parameters to fit the model to the real space
> density better.
>
> ARP/wARP uses a simplex minimizer with a real space correlation
> function and a torsional parameterization, and if I remember Michael
> Chapman's papers
> he uses a powell minimizer in a simulated annealing protocol and a
> cartesian parameterization, and if I again recall Paul uses the BDGFS
> minimizer in cartesian space, but they all do the same things at one
> point or another, which what you describe. If before that one used the
> mouse or a clever algorithm to build a model, this is always refined
> as you describe in real space, before entering 'real' refinement.
>
> Tassos
>
>> Pavel.
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