[phenixbb] scattering factors

Goragot Wisedchaisri goragot at u.washington.edu
Mon Jun 20 10:29:06 PDT 2011

Hi Ralf,

This is a good news for electron crystallography! It looks like you have provided one of the most recent Gaussian fitting of electron scattering factors from Peng et al. Acta Crys A52, 1996 which is supposed to be an improvement to the widely used Doyle and Turner 1968 by using 5 gaussian fittings instead of the 4 + a constant fitting (also used for X-ray scattering factors).

I have a question though. Because electron scattering depends on the velocity of the electron which in turn depends on the acceleration voltage of the microscope. The gaussian parameters need to be corrected using the relativistic electron velocity by multiplying the ai parameters with m/m0 = (1 – v2/c2) ^-1/2 where v is the relativistic electron velocity and c is the velocity of light (for example m/m0 = 1.58707 for a 300keV electron microscope). These days it is probably common for many electron crystallography labs to use 200-300keV microscopes for data collection. Is there a way to implement this correction into Phenix? or alternatively allow users to supply their own parameters?

I normally supply my own files for electron scattering factors of appropriate acceleration voltage in Refmac and CNS  (but can only do so in the 4 gaussian + a constant format). I think the 5-Gaussian fit is more accurate and it would be nice if other refinement programs can support such parameters in the future.

George Wisedchaisri

On Fri, 17 Jun 2011, Ralf Grosse-Kunstleve wrote:

> Hi Andy,
>> Is it possible yet to incorporate user-defined custom X-ray scattering factors?
> No, sorry, we never got to it.
> But we added a table of electron scattering factors:
> http://cci.lbl.gov/cctbx_sources/cctbx/eltbx/e_scattering.py
> Is this the right table for your purposes?
> Your question reminded me to add "electron" as a possible choice for the
> refinement.main.scattering_table=electron
> parameter, which enables use of the table above. This will be in the
> next development build (phenix dev-791 or higher).
> Ralf
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