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.
|