Re: [phenixbb] scattering factors

Hi Ralf, Hmm... You raised a very good point. Multiplying a_i by a constant would be the same effect as scaling Fcalc, and that should be fine as scaling is normally done during the refinement anyway. I will be curious to test this with electron diffraction data. Hint: electron diffraction data to 1.9A resolution is available from pdb under accession code 2B6O. George On Mon, 20 Jun 2011, Ralf Grosse-Kunstleve wrote:

Hi George,

...

No, the factor m/m0 is independent of atom types

Can anomalous (f') and dispersive (f") contributions be ignored?

Ignoring these the structure factor equation is

f_calc += f0 * dw * occ * sym_weight * exp(2 * pi * i * x * h)

dw = isotropic or anisotropic Debye-Waller factor occ = occupancy factor (between 0 and 1) sym_weight = usually 1 except for special positions x = fractional coordinate of atom h = Miller index

f0 = Sum[a_i * exp(-b_i * stol**2)]

If you scale all the a_i by a constant factor, it is the same as scaling the final f_calc by the same constant factor. Therefore the m/m0 will just change the overall isotropic scale factor, which we determine dynamically inside phenix.refine; the value isn't usually interesting. I.e. I'd expect that you can use phenix.refine as-is.

But maybe I'm missing something important? I've never worked with electron diffraction data.

Ralf

On Mon, Jun 20, 2011 at 1:45 PM, Goragot Wisedchaisri wrote:

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Hi Ralf,

No, the factor m/m0 is independent of atom types for the same acceleration voltage (m0 is electron rest mass, m is relativistic mass of electron which depends on acceleration voltage. The Guassian ai and bi coefficients already take care of fitting scattering factor f(e) for each atom type. In another word, if you can implement a function that calculates and multiplies m/m0 to all the ai coefficients for all atom types in the table, users will only need to input the acceleration voltage.

Thanks,

George Wisedchaisri

On Mon, 20 Jun 2011, Ralf Grosse-Kunstleve wrote:

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Hi George,

...

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).

Is the factor m/m0 different for each atom type?

Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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