Dear Herman,
I'm glad we agree, too.
Best,
Tim
On Wednesday, January 27, 2016 02:51:43 PM [log in to unmask] wrote:
> Dear Tim,
>
> There are low resolution structures and low resolution structures. At one
> extreme, the low resolution structure might have a 0.3Å rmsd with a 0.9Å
> native structure, and at the other extreme, the data might be twinned,
> there might only be a remote, incomplete model and the electron density
> maps may look really bad.
>
> In my experience, the programs I work with (Buster, Refmac) do not always
> produce the optimal weights at low resolution in automatic mode and I fully
> agree with Bernard that at low resolution the geometry needs to be tightly
> restrained to prevent model bias.
>
> One could of course activate the button to "Execute multiple refinement
> runs". However, from just pressing buttons one does not learn
> crystallography and one does not get a feeling how reliable and good or bad
> a structure really is.
>
> My 2 cts,
> Herman
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Tim
> Gruene Gesendet: Mittwoch, 27. Januar 2016 14:59
> An: [log in to unmask]
> Betreff: Re: [ccp4bb] Refmac auto weight
>
> Dear Bernhard,
>
> I doubt that phenix and Refmac5 produce the same results only because the R-
> values are similar - and you surely know this!
>
> I tend to integrate data myself and when it seems sound and the integration
> is stable, I would go with the auto weighting scheme in Refmac5. If the
> geometry (RMS values) deviates from what I am used to, I start looking at
> manual weight fitting. At medium to low resolution I would use quite a low
> weight, 0.02 or less, and increase the number of cycles to e.g. 100 or
> more.
>
> Did you take a look at the -LL plot vs. cycle to monitor if the refinement
> converged?
>
> 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?
>
> Best,
> Tim
>
> On Wednesday, January 27, 2016 12:15:30 PM Bernhard Rupp wrote:
> > Dear Developers & Friends,
> >
> >
> >
> > Win CCP4i 6.5.019
> >
> > Win Refmac_5.8.0135 version 5.8.0135
> >
> >
> >
> > I have noticed (as have many others) that occasionally the Refmac
> > auto-weight of restraints does not
> >
> > provide optimal results. I have a simple case (Fab, 1.9A, SG19) where
> > significantly better stats can be obtained by
> >
> > the usual hand-optimization, with the end result Rs and rmsds being
> > almost the same as the auto-weighting
> >
> > obtained by Phenix.
> >
> >
> >
> > So, does any one of the high-volume refiners like Robbie have any
> > indications under
> >
> > what circumstances the refmac procedure is suboptimal? What exactly is
> > the refmac procedure? And if
> >
> > one can do it by hand and phenix automatically gives the same results,
> > could it be implemented in a similar
> >
> > fashion in Refmac?
> >
> >
> >
> > Same coordinate input file
> >
> >
> >
> > Auto : initial final
> >
> > R factor 0.1835 0.1828
> >
> > R free 0.2415 0.2419
> >
> > Rms BondLength 0.0158 0.0157
> >
> > Rms BondAngle 1.9467 1.9511
> >
> >
> >
> > Manual, 0.05:
> >
> > R factor 0.1835 0.1957
> >
> > R free 0.2415 0.2357
> >
> > Rms BondLength 0.0158 0.0070
> >
> > Rms BondAngle 1.9467 1.4095
> >
> >
> >
> > Phenix auto:
> >
> > R factor 0.1902 0.1992
> >
> > R free 0.2444 0.2387
> >
> > Rms BondLength 0.0160 0.0090
> >
> > Rms BondAngle 1.8180 1.1795
> >
> >
> >
> > In any case, I think aiming for small molecule rmsds regardless of
> >
> > resolution and thus data/params is not ideal. Upper limit, yes. Many
> >
> > others have voiced the same, and George Sheldrick once showed a
> >
> > nice graph of restraint weight (or rmsd?) vs resolution as obtained by
> > his
> >
> > 'likelihood by intuition' with a sigmoid curve showing the general
> > trend
> >
> > that lower res needs higher restraint weights. Actually, showing more
> > 'restraint'
> >
> > when modelling at low resolution seems a good idea in general (just
> >
> > to add something vitriolic.)
> >
> >
> >
> > Best, BR
>
> --
> --
> Paul Scherrer Institut
> Dr. Tim Gruene
> - persoenlich -
> OFLC/102
> CH-5232 Villigen PSI
> phone: +41 (0)56 310 5297
>
> GPG Key ID = A46BEE1A
--
--
Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
OFLC/102
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297
GPG Key ID = A46BEE1A
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