Leginon

This is currently fixed at k = 1, since it does not actually show up at all in the calculation, but you can modify the calculation if you wish. It is in leginon/ice.py. There are two functions:
get_intensity as a function of thickness, and get_thickness as a function of intensity. If you find it useful to modify k, we can add that as a variable input to the calculation.
Jim

I find it more intuitive to have a real life value there. I realize that the calculation has to be done at the same defocus but once it is calibrated these settings have real meaning. What value shows up in the image report i.e. in the database?
Bob

The k value used in the report and in database all use k=1. We will add a user input in the densityreport.php page for you on 2.2 release. In the mean time, you can download the data and do your own calculation.

I should have made a calibration node for this purpose after our 2006 paper (J. Struct. Biol. 154 p303-311) but didn't get to it all these years. The problem was that the k value not only depends on defocus, but also on the insertion of the objective aperture and the lens settings (I will attach that figure after this reply). I suspect that it would even depend on the size of the hole because the interference fringes created by the edge when strongly defocused. These make the calibration by no mean a simple one and I will have to find out the range in which each factor can be allowed to change for one to use the calibration....

Anchi

Here is the figure from the paper