James, this doesn't take the effect of resolution cut-offs into
account, right? You appear to be assuming that you have data to
atomic resolution (~ 1 A) or better. The integral of the scattering
factor should be confined to the experimental resolution range,
otherwise it's not going to be very realistic, in fact the calculated
profile is not going to show the observed resolution dependence (and
where the density can go negative). See slides 13 & 14 here
http://www.cse.scitech.ac.uk/events/CCP4_2011/talks/tickle.pdf for the
resolution-dependent version.
Cheers
-- Ian
On Wed, Nov 2, 2011 at 2:36 AM, James Holton <jmhol...@lbl.gov> wrote:
> On Tue, Nov 1, 2011 at 3:32 PM, Ivan Shabalin <shabali...@inbox.ru> wrote:
>> Does that mean, that with Bf>10 we cannot distinguish Mg and water by
>> electron density peak profile? Even if oxygen in water has twice as much
>> bigger radius than Mg2+?
>
> Yup. Pretty much.
>
> An "Mg+2" with B=10 is almost exactly the same density profile as a
> single point electron (atom type "Ano") with occ=9.72 and B=12.7. You
> can also fit "water" (an "O" with two "H" atoms on top of it) to Mg+2,
> and get a pretty good fit with occ=1 and B=15 for the "water". If you
> want to play around with this, I have placed a gnuplot-ish version of
> ${CLIBD}/atomsf.lib at:
>
> http://bl831.als.lbl.gov/~jamesh/pickup/all_atomff.gnuplot
>
> in gnuplot you can type:
> load 'all_atomff.gnuplot'
> plot Mg_plus_2_ff(x,20), O_ff(x,15)+2*H_ff(x,15)
>
> and stuff like that.
>
> -James Holton
> MAD Scientist
>
