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
> >
> >
>
--
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* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
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* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
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