[ccp4bb]: Re:

[Garib N Murshudov <garib@ysbl.york.ac.uk>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***

Try to add
BLIM 1.0 500

default minimum B is 2.0. If it does not help could you please send me log 
file I will try to sort it out.

Garib


On Thursday 30 May 2002 1:56 pm, Iain Kerr wrote:
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> I am refining a model constructed  from MAD phases,  vs a native set of
> twinned data treated with DETWIN. The data are merohedrally twinned in P61
> & the twin fraction is estimated to be 0.3 using the Yeates server.
>
> The native data go to 1.2A, but refinement doesn't seem possible beyond
> 1.5A ie. the residuals don't drop any further. The best model (with good
> geometry, at least in REFMAC5) to 1.2 has an Rfree of ~21% and an Rwork of
> 18%. Is this a consequence of loosing some of the signal in the data due to
> the detwinning process ?. I should mention I'm using TLS & CGMAT in
> REFMAC5, refining isotropic Bs to 1.5 & thereafter refining
> anisotropically. ARP/wARP was used to add waters, cycled with REFMAC5 once
> the initial refinement stablised. I've tried dropping the resolution
> steadily from 1.5 to 1.2 but this doesn't help either.
>
> Also beyond 1.5A, REFMAC5 complains about waters having small eigen-values
> when the model is refined anisotropically. Anitropic refinement at 1.5A
> proceeds fine. I've tried using the DAMP 0.5 0.5 flag, but it doesn't help
> & I'm not sure how I should alter the Sphericity restraint, which I though
> might help - is this restraint dependant on the size of the structure or
> the resolution of the data ?.
>
> I'd really appreciate any comments/suggestions, esp. from those that have
> experienced any of the above.
>
> As always, thanks in advance.
>
> Iain
>
> *****************************
>                        Iain Kerr
>      Biomolecular Sciences Building,
>                       3rd floor,
>                  North Haugh,
>                   St.Andrews,
>               The University,
>               Fife KY16 9ST,
>                 Scotland, UK.
>
>         phone: +44 (0)1334 467265
>
> *****************************

-- 
Garib N. Murshudov, Chemistr Department, University of York
Tel: (01904) 432565