Im very grateful to the community for supporting me with so interesting
information!
Now my understanding of the subject is much better!
With best regards,
Ivan Shabalin
Yes, in my gnuplot "form factor" functions, "x" is the real-space
distance from the center of the atom in Angstrom and the "return value"
is electron density in electrons/A^3.
I did not realize the gnuplot file would be so interesting! If anyone
wants the reciprocal-space version (which is si
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 r
James - you are fantastic!
This is so educational..
Eleanor
On 11/02/2011 02:36 AM, James Holton wrote:
On Tue, Nov 1, 2011 at 3:32 PM, Ivan Shabalin 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 possible the
calculations).
With best regards,
Sacha Urzhumtsev
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Pavel
Afonine
Envoyé : jeudi 3 novembre 2011 04:40
À : CCP4BB@JISCMAIL.AC.UK
Objet : Re: [ccp4bb] atomic scattering factors in REFMAC
Continuing on the
Just for the record, except for charge density studies most small molecule
structures are refined with neutral atom scattering factors even when ions such
as Cl- are present. For example SHELX uses "4 Gaussian plus const:
International
Tables for Crystallography (1992)". Users rarely input ionic
Continuing on the subject, as far as I know there are at least
three flavors of form-factors currently used in refinement programs:
"4 gaussian plus const":
International Tables for Crystallography (1992)
"5 gaussian plus const":
D. Waasmaier & A. Kirfel. Acta Cryst. (1995). A51, 416-431. "New an
Ivan,
it might be helpful/instructive to have a look at this review on the
subject you seem to be actively interested:
Acta Cryst. (2004). A60, 19-32.
and some basic educational illustrations here:
http://phenix-online.org/newsletter/CCN_2011_01.pdf
(see "Electron density illustrations" articl
Hi James!
Thank you very much for the gnuplot-ish version of ${CLIBD}/atomsf.lib!! It
works very nice and is very useful for education!
As I understand, the form factor is the Fourier transform of electron charge
density. It is plotted as f(electrons) vs sin(tetta)/lambda and is approximated
a
On Tue, Nov 1, 2011 at 3:32 PM, Ivan Shabalin 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 d
Thanks everybody for the profound answers!
As a summary, I can list the following reasons for the negative density defects
at Se atoms:
1) the default scattering factors for Se are incorrect for wavelengths that are
not close to CuKA, even though it may be not the major source of errors. Also,
James,
this may be one of those physics-vs-math arguments again. Surely the
occupancy can be used to account for everything, but it makes it a fudge
factor. I'd say the right way is to use the adjusted scattering factors
first (after all, that is something we do know about the experiment),
and i
Collecting "close to the edge" where the cross section of Se is higher
does indeed increase the absorbed dose per scattered photon (Muray et
al. JSR, 2005), but wavelength has absolutely no impact on the relative
"rate" of Se-C bond breakage (Holton JSR 2007). The number of Se-C
bonds broken i
On Mon, 2011-10-31 at 15:57 +, Ivan Shabalin wrote:
> As a result, red peeks around Se are significantly lower, Se B-factors are a
> bit smaller (like 25.6 and 23.1), and Rf is lowered by a bit more than 0.1%
> with the same input files.
Hope others will comment to clarify my confusion:
It
That is correct. We saw this in every selenomethionyl protein structure that
was determined at CESG. There are two reasons for the negative density defects
at Se atoms. As you note, the default scattering factors for Se are incorrect
for these experiments, as f' is large in Se SAD experiment
Hi, personally I didn't find that changing scattering factors for Se,
Br, I etc made a big difference to the maps. The more likely
explanation seems to be site occupancy disorder due to
radiation-induced breaking of covalent bonds, in which case you need
to refine the occupancy. But maybe it's a
Dear Refmac users,
I noticed that if I refine a structure containing SeMet, then Se atoms usually
have big negative (red) peeks of difference map and high B-factors. As I
understand from the diffraction theory and from some discussions at CCP4bb,
that may result because in REFMAC the atomic sca
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