Dear Matthew,
For most of my work with electron diffraction, I used SHELXL for refinement
(e.g. https://doi.org/10.1002/anie.201811318, https://doi.org/10.1107/
S2052252518000945, or http://www.dx.doi.org/10.1107/S2053273315022500).
L Peng ("Electron atomic scattering factors and scattering potentials of
crystals", Micron 30 (1999), 625-648) has published the parameters for
electron scattering factors suitable for SHELXL. Peng used a1-a4, and b1-b4,
i.e. c=0 in the Cromer-Mann-Parametrisation used in SHELXL. Normally I start
with these parameters and fit the full Cromer-Mann-function to the calculated
values from Int. Tables C, Table 4.3.1.1. with gnuplot. There is not a huge
improvement compared to the published values,however, fitting manually has two
advantages for me:
- it is a control, as my gnuplot-script produces a PDF-file for the fit
- I can fit against ionic scattering factors from Table Table 4.3.1.2
For the latter, you have to choose an appropriate low-resolution cut-off, as
for ions, the behaviour at s=0 is not defined. I recommend reading Yonekura eta
l., https://doi.org/10.1107/S2052252518005237
I can send you my current list of scattering factors in SHELX, the gnuplot
script and a selection of PDF-plots if you like.
For small molecules, SHELXL is certainly the program of choice. As additional
information: Refmac5 uses the Mott-Bethe formula for the scattering factors. I
could see not difference between the Mott-Bethe-formula (for non-ions, only as
far as I understand) and the direct parametrisation, and I suggested to George
Sheldrick to incorporate this in SHELXL as well. It is great to hear you are
working on electron crystallography, too, as this might be additional
motivation.
Let me know in case you would like a copy of my list of scattering factors in
SHELX format.
Best regards,
Tim
On Monday, March 4, 2019 9:20:08 PM CET Whitley, Matthew J wrote:
> Greetings all,
>
>
> We have solved a small molecule structure using electron diffraction and
> would like to refine the structure with SHELXL. Coming from a
> macromolecular background, this is our first experience with SHELXL, and we
> are not exactly sure how to proceed. The first thing to do seems to be to
> provide SHELXL the appropriate electron scattering factors for 200 keV
> electrons. Can someone suggest the best way to do this? Or,
> alternatively, if anyone has used a different program to refine small
> molecule structures determined by ED, we would be happy to hear about that
> program too.
>
>
> Thanks in advance for your advice.
>
> Matthew
>
>
> ---
> Matthew J. Whitley, Ph.D.
> Research Instructor
> Department of Pharmacology & Chemical Biology
> University of Pittsburgh School of Medicine
>
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--
--
Tim Gruene
Head of the Centre for X-ray Structure Analysis
Faculty of Chemistry
University of Vienna
Phone: +43-1-4277-70202
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