Actually, this isn't quite right yet - since the tabulated values in
atomsf.lib are for f0: so you just need to add f' to C (no need to
adapt it for the value at CuKa). Thanks to Claus Flensburg for
pointing that out to me.
Clemens
On Fri, Aug 10, 2007 at 12:53:05PM +0100, Clemens Vonrhein wrote:
> On Fri, Aug 10, 2007 at 12:32:21PM +0100, Eleanor Dodson wrote:
> > Sorry - Clemens is right.
> >
> > Eleanor
>
> Hi Eleanor,
>
> phew - I was starting to wonder that what I put into (auto)BUSTER
> wasn't right. It should be trivial to put this into REFMAC too
> (Garib!): just add cards like
>
> FPRIme <atom-type> <f'-value>
>
> so that a user can do
>
> FPRIme Se -4.5
>
> REFMAC then corrects C by the difference f'(CuKa)-(-4.5) (after
> reading the f'(CuKa) from atomsf.lib).
>
> And suddenly all those partially substituted Se-MET are becoming 100%
> substituted again ... a kind of 'in-silico expression system'.
>
> Cheers
>
> Clemens
>
> >
> >
> > Clemens Vonrhein wrote:
> > >Hi Eleanor,
> > >
> > >On Fri, Aug 10, 2007 at 10:27:16AM +0100, Eleanor Dodson wrote:
> > >
> > >>If you have significant anomalous scatterering and are using <F> you
> > >>need to modify the scattering factor for that atom appropriately.
> > >>
> > >>Here is an extract from $CLIBD/atomsf.lib
> > >>Se
> > >> 34 34 2.840900
> > >> 17.000599 5.819600 3.973100 4.354300
> > >> 2.409800 0.272600 15.237200 43.816299
> > >> -0.879000 1.139000 -0.178000 2.223000
> > >>
> > >>The values -0.879000 1.139000 are the f' and f" for Cu
> > >>wavelength ( 1.54A)
> > >>
> > >>I you think you have complete substitution and are using data at some
> > >>other wavelength for refinement you should change the f' and f"
> > >>appropriately
> > >>
> > >>( Copy $CLIBD/atomsf.lib to your area and edit it then assign refmac5
> > >>ATOMSF my_atomsf.lib etc )
> > >>
> > >>But in practice this is often less useful than you might expect and you
> > >>still see holes in your maps at the Se. I blame it on incomplete
> > >>substitution
> > >>
> > >
> > >Are you sure this would be the way to work it out in CCP4? As far as I
> > >can see (see top of atomsf.lib), the actual formfactor for an atom
> > >will be calculated as
> > >
> > > Formfactor: a1*exp(-b1*s*s) + a2*exp(-b2*s*s) + a3*exp(-b3*s*s)
> > > + a4*exp(-b4*s*s) + c
> > >
> > >with the coefficients (a1-4, b1-4 and c) given in atomsf.lib as
> > >
> > >AD This contains for each element:
> > >AD ID
> > >AD IWT IELEC C
> > >AD A(4)
> > >AD B(4)
> > >AD CU(2) MO(2)
> > >
> > >So I would be suprised if any program actually uses the tabulated
> > >f'/f" values for CuKa and Mo radiation to calculate formfactors. If
> > >you want to adjust the formfactors for elements that have an f' value
> > >very different from CuKa you need to change the C coefficient -
> > >according to the difference between the f'(CuKa) and
> > >f'(observed). This will have an observable effect then.
> > >
> > >At least that's what we do in BUSTER with good results ...
> > >
> > >Or am I missing something here?
> > >
> > >Cheers
> > >
> > >Clemens
> > >
> > >
> >
>
> --
>
> ***************************************************************
> * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
> *
> * Global Phasing Ltd.
> * Sheraton House, Castle Park
> * Cambridge CB3 0AX, UK
> *--------------------------------------------------------------
> * BUSTER Development Group (http://www.globalphasing.com)
> ***************************************************************
>
--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************
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