Dear Bernhard,
your email said that the results from refmac5 with automated weighting were
not optimal, and it lists numbers which I think are not the best number for
comparison the goodness of refinement results.
One of my points is that a lower R-values does not indicate a better
structure. The second point is that it is difficult to compare R-values from
different programs because they are calculated quite differently. If you take
a structure refined with program X and ask program Y to calculate its R-value,
it is going to be quite different (usually much higher) than the one
calculcate by program X, although they are calculate from the same structure.
A third point is that you ask how to automate refmac to get the same results
as with phenix, then you list some numbers which don't indicate how similar
the results between phenix and refmac really are. I think it is worth pointing
this out because I often meet scientists at workshops and conferences who
don't distinguish between a good structure and low R-values.
My shorthand phrasing paid respect to your reputation.
Cheers,
Tim
On Wednesday, January 27, 2016 03:33:10 PM [log in to unmask] wrote:
> > I doubt that phenix and Refmac5 produce the same results only because the
>
> R- values are similar - and you surely know this!
>
> ??? Yes, and...your point being what exactly?
>
> > If the geometry (RMS values) deviates from what I am used to
>
> Hmm...I wonder what values those would/should be?
>
> > Did you take a look at the -LL plot vs. cycle to monitor if the refinement
>
> converged?
>
> Yes this was done at convergence, and after the B-factors were adjusted (cf
> Tickle papers)
>
> > In ccp4i2 there is an Advanced Option to "Execute multiple refinement runs
>
> in order to optimise X-ray/geometry weight". How do the figures look like
> when you activate this button?
>
> Can't tell. I was wondering if I should wait for ccp4i2 in Windows - maybe
> ccp4 6.5 is completely deprecated now?
> Then let's put this discussion on hold for now.
>
> Do we have an ETA for WinCCP4i2 or do I need to fire up the trusty VM and
> install linux CCP4i2 there?
>
> Thx,
> BR
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Paul Scherrer Institut
Dr. Tim Gruene
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