[3dem] amplitude contrast valuesHi,

[Michael Radermacher]

Hi David,

For stain you can also look in:
D. Typke, M. Radermacher, Determination of the Phase of Complex Atomic  
Scattering Amplitudes from Light Optical Diffractograms of Electron  
Microscope Images. Ultramicroscopy, 9, (1982), 131-138

In practice it is most of the time between 0.1 and 0.2 for different  
stains and stain thicknesses. You can also fit it, or, if you cannot,  
repeat the fit with different values. You see if it is a good value by  
checking the fit of the 0s through the full frequency range. From the  
figures in the paper you see how the shape of the transfer function  
changes. At low frequencies the fit of the 0s could almost be  
compensated by a slightly different defocus value, but the function  
has different values especially near the origin. If you cannot fit it  
and have many images under the same conditions, I would carefully  
match it to one and use the same value for the others.

Michael

Quoting David Gene Morgan <dagmorga at indiana.edu>:

> Hi,
>
> 	I'm trying to do some automated defocus determination (initially  
> trying Niko's ctffind3 program) and would like some input on  
> appropriate amplitude contrast values for various types of samples.   
> I know that ice embedded images usually are said to have an  
> amplitude contrast of 0.07 to 0.1.  I also know that with  
> protein/nucleic acid complexes in ice, amplitude contrast may need  
> to be set a bit higher (say to as much as 0.15 for some data I  
> worked on awhile ago).
>
> 	But I don't have any sort of feeling for appropriate values of  
> amp;itude contrast for different sorts of negative stains (either  
> cryo negative stain or standard negative stain).  It should be  
> "high," but I don't know how high might be appropriate.
>
> 	If anyone has either some practical or theoretical insight into  
> this, I'd appreciate some suggestions.  Also, does anyone know about  
> an appropriate amplitude contrast for a standard Au/Pd waffle grid?
>
> 	Thanks in advance for all your help.
>
> -- 
>                  David Gene Morgan
>              Electron Microscopy Center
>                   047D Simon Hall
>                   IU Bloomington
>                812 856 1457 (office)
>                812 856 3221 (3200)
>             http://bio.indiana.edu/~cryo
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-- 
Michael Radermacher, Ph.D., Prof., FMSA
University of Vermont
Dept. Molecular Physiology and Biophysics
HSRF 120 / 149 Beaumont Ave
Burlington, VT 05405
USA