I noticed this kind of thing myself a long time ago, and wondered what
refmac was doing to make things worse, so I let it keep going. And
going and going. I was delighted to discover that although R and/or
Rfree could rise over up to hundreds of cycles, it almost invariably
turns around again,
Frank,
Point #1 - fair point; the reason Rfree is popular, though, is because it
is a *relative* metric, i.e. by now we have a sense of what good is. So
I predict an uphill fight for LLfree.
Why? I don't see any difference. As you say Rfree is a relative metric so
your sense of what 'good'
Dear Dr Ian
from your argument i could not understand how many cycles to refine before
submitting the coordinates to the PDB. what is the upper limit 100 or
thousand or million according to my understanding, its more logical to
stop the refinement when over refinement is taking place (when R
and refinement 20 cycles is usually enough
(but more cycles shouldn't hurt).
Cheers,
Robbie
Date: Fri, 26 Aug 2011 20:29:59 +0530
From: proteinchemistr...@gmail.com
Subject: Re: [ccp4bb] number of cycles in refmac
To: CCP4BB@JISCMAIL.AC.UK
Dear Dr Ian
from your argument i could not understand
Hi AR
Please define what you mean by 'over-refinement' as it's not a term I use:
does it mean 'convergence', or 'over-fitting', or 'over-optimisation'
(whatever that means) or something else?
If by LLG is stabilized you mean it has converged then I agree that's a
possible stopping criterion, but
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Hello Ian,
I dare say that the goal is to get phases which match as good as
possible with what is inside the crystal. If this coincides with
maximising the likelihood, why don't we run refinement until the LL
stabilises?
@Garib: I have seen runs
Hello Tim
It was in one or two versions and I did not get consistent results. However
code is there and I can activate it if you want. If you know what criteria you
would like to use I can code that also.
In some cases it happens that R/Rfree go up and then they start coming down. It
may be
TIm,
I dare say that the goal is to get phases which match as good as
possible with what is inside the crystal. If this coincides with
maximising the likelihood, why don't we run refinement until the LL
stabilises?
That's exactly what you should do: any optimisation procedure attains the
Hmm, I used to think I understood this, but I'm feeling a bit dim right
now.
On 25/08/2011 11:07, Ian Tickle wrote:
Since the target function in MX refinement is the total likelihood
(working set + restraints), there's no reason whatsoever why any
another function, such as Rfree LLfree,
Hi Frank
This is self-evident; what is not obvious is why the target function
should be having the final word. Wasn't the word over-refinement
introduced to describe exactly this: that the target function was wrong?
I assumed people were confusing 'over-refinement' with 'over-fitting'; there
Hi Ian
(Yes, your technical point about semantics is correct, I meant
over-fitting.)
To pin down your points, though, you're saying:
1) Don't use Rfree, instead look at LLfree or Hamilton Rfree.
2) Compare only the final values at convergence when choosing
between different
Point #2 would hold if we routinely let our refinements run to
convergence; seems common though to run 10 cycles or 50 cycles instead
and draw conclusions from the behaviour of the metrics. Are the conclusions
really much different from the comparison-at-convergence you advocate?
Which is
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Dear all,
especially at the beginning of model building and/or at low resolution
both Rfree and -LL free as reported in the refmac logfile show a
minimum at a some cycle before rising again.
I am certainly not the only one tempted to first run
Dear Tim
At the moment there is no option to stop refmac prematurely. I can add if it is
necessary. I can only give my experience.
After molecular replacement before running ARP/wARP or buccaneer I usually run
60-100 cycles of refinement with jelly body with sigma set to 0.01.
Then automatic
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