One can also use:
$ gemmi fprime Sr --wavelength=1.2782
Element E[eV] Wavelength[A] f' f"
Sr 9699.91 1.2782 -0.63756 1.3067
or
$ $CCP4/lib/py2/cctbx/bin/cctbx.eltbx.show_fp_fdp --wavelength=1.2782
--elements=Sr
Wavelength: 1.2782 Angstrom
Element: Sr
Henke et al. : f'=-0.665752, f''=1.332521
Sasaki et al. : f'=-0.75942 , f''=1.306888
diff f''=-0.97 %
As you see, all these commands give slightly different values. I was
told that nowadays XrayDB (not in CCP4) provides the most accurate
values:
$ python3 -c "import xraydb; print(xraydb.f1_chantler('Sr', 9699.91))"
-0.657390314908364
Crossec is the original code from Don Cromer. Gemmi, one of the cctbx
tables, and I think Ethan's server also use code that stems from it,
but with corrections added later when this code was circulating, such
as Kissel & Pratt, Acta Cryst. A46, 170 (1990).
Marcin
On Fri, 22 Jan 2021 at 21:40, Mitchell D. Miller
<[email protected]> wrote:
>
> You can also use the ccp4 legacy program crossec ---
> http://legacy.ccp4.ac.uk/html/crossec.html
>
> for your case --
>
> echo -e "NWAV 1 1.2782\nATOM Sr\nEND\n" | crossec | grep SR
>
> Atom symbol and number SR 38
> $TABLE:Wave length v F' and F"- SR :
> $GRAPHS:Lambda v F' and F" SR :A:2,3,4: $$
> SR 1.2782 -0.7663 1.3068
>
>
> I often ran it from a script to lookup the f'/f" for various elements via
> a script crossec.sh which takes arguments of wavelength followed by a
> list of elements
>
> #!/bin/bash
> #egrep '^ATOM|^HETATM' | cut -c77-78 file.pdb | sort -u`
>
> for atom in "$@"
> do
> if [ "$atom" != "$1" ]
> then
> echo -e "NWAV 1 $1\nATOM $atom\nEND\n" | crossec | awk '/^
> Lambda F/ {getline ; getline ; print $0}'
> else
> echo "Atom_type Lambda F"\'" F"\"
> fi
> done
>
>
>
> Quoting Bernhard Rupp <[email protected]>:
>
> > ...or you can use the old anoweb app
> >
> > http://www.ruppweb.org/new_comp/anomalous_scattering.htm
> >
> >
> >
> > http://www.ruppweb.org/cgi-bin/anoweb_linux?Element=Sr
> > <http://www.ruppweb.org/cgi-bin/anoweb_linux?Element=Sr&iano=1&nresi=100&iwavl=K&w1=Cu&w2=1000&w3=2&w4=1&w5=700&anoweb=Submit>
> > &iano=1&nresi=100&iwavl=K&w1=Cu&w2=1000&w3=2&w4=1&w5=700&anoweb=Submit
> >
> >
> >
> > HTH, BR
> >
> > From: CCP4 bulletin board <[email protected]> On Behalf Of rohit kumar
> > Sent: Friday, January 22, 2021 11:36
> > To: [email protected]
> > Subject: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom
> >
> >
> >
> > Hello All,
> >
> >
> >
> > I have data collected at Wavelength: 1.2782 (For Sr Heavy atom) with
> > a resolution of 1.6 A. I was trying to run Crank in ccp4 for SAD
> > phasing and It asks me to fill the values of (scattering factors) f
> > and f" for the heavy atom.
> >
> > Can anyone please help with this, how to calculate or where to find
> > these f and f" values for Sr heavy atoms?
> >
> >
> >
> > Please let me If you need any information from my side.
> >
> >
> >
> > Thank you in advance
> >
> >
> >
> >
> >
> >
> > --
> >
> > Regards
> > Dr. Rohit Kumar Singh
> >
> > Postdoctoral fellow
> >
> >
> >
> >
> >
> >
> >
> > _____
> >
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