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
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