Hi Kristof
The trivial, and it turns out only, answer is "as many as it takes to
converge". Unfortunately for everyone carrying out optimisations, or
indeed almost any kind of computation, Alan Turing proved (1936) -
Google for "Turing halting problem" - that a general algorithm to solve
the halting problem for all possible program-input pairs cannot exist,
or to put it another way, there's no way to know in advance what a
program will do without actually running it.
The number of iterations required will obviously depend on how far away
the starting parameters are from the optimum which clearly cannot be
known in advance. In any case, if you don't like the result that the
program produces then the answer doesn't lie in changing the number of
iterations: rather the answer lies in changing the input and starting
conditions, since an optimisation procedure is valid only if carried
through to convergence (otherwise the starting assumptions are not
satisfied), i.e. taking as many (or as few) iterations as it needs to
satisfy the stopping criteria. Of course you could change the stopping
criteria but they determine how accurate the result will be, so the
question then would be "how accurate do you want it?".
So much for the theory, on a practical note I've noticed that for some
reason structure idealisation with Refmac requires a very large number
of iterations to converge (I have not tried it with other refinement
programs though, maybe I should), given that the stopping criteria are
that the RMSDs for bonds and angles should be essentially zero (they can
only be non-zero in the case that the restraints are inconsistent with
each other, e.g. rings don't close under the restraints), so maybe
someone can answer why that is, it has baffled me for a while.
Cheers
-- Ian
> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
On
> Behalf Of Kristof Van Hecke
> Sent: 25 March 2009 10:42
> To: bulletin_ccp4
> Subject: Structure idealisation Refmac_5.5.0072
>
> Dear,
>
> I want to optimize a DNA-helix with the function "Structure
idealisation"
> in Refmac_5.5.00782 (CCP4_6.1.1).
> My question, is this performing just a geometry optimization (against
a
> library), or is there also an energy-optimization of some kind
> involved,..?
>
> And according to the number of cycles (default 10) used, different
> structural results are obtained, hence is there a means of estimating
the
> ideal number of cycles to use..?
>
> Many thanks
>
> Kristof Van Hecke
>
> --------------------------------------
> Kristof Van Hecke, PhD
> Biomoleculaire Architectuur
> Celestijnenlaan 200 F
> B-3001 Heverlee (Leuven)
> Tel: +32(0)16327477
> --------------------------------------
>
>
>
>
>
> Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more
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>
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