But aren't the bump restraints re-evaluated at each iteration? That was
my understanding (but I could be wrong), after all it's not a big deal
to compute interatomic distances. One contribution that is not
re-evaluated every iteration but only at iteration 1 is (I believe, but
again I could be wrong) the solvent contribution, I guess because the
assumption is that it doesn't change much.
All the same it's interesting that you mention that idea, because I have
been trying precisely that with regular refinement and in some cases I
get significantly lower final R-factors for the same total number of
iterations if I split it into a series of short jobs of maybe only 3 or
4 iterations each (doesn't help every time though), each time feeding
the output PDB from one job into the next one as you describe. I've no
idea why it works though!
Cheers
-- Ian
> -----Original Message-----
> From: [log in to unmask] [mailto:[log in to unmask]]
On
> Behalf Of James Holton
> Sent: 26 March 2009 01:08
> To: Kristof Van Hecke
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] Structure idealisation Refmac_5.5.0072
>
> Kristof Van Hecke wrote:
> > 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,..?
> What's the difference?
> >
> > 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..?
> >
> I generally keep re-inputting the output PDB back into refmac until
the
> input and output PDB files are "identical" to, say, withing 0.001 A.
> This is my definition of "convergence". It is important to use a
small
> number of cycles for each run because if you don't atoms can move far
> enough to start "bumping" into atoms that were not close enough to
> trigger a "bump" restraint at the beginning. At least, this is how it
> was back in "my day".
>
> -James Holton
> MAD Scientist
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