Focus Documentation

Defines the small vertical window in Fourier space within which the reference data set will be searched for reference data for alignment of a new image. zstarwin should be 2/ALAT, to achieve highest 3D resolution. There is one case, when a larger zstarwin is needed: If you have a reconstruction from non-tilted data only, and then want to add for the first time data from a tilted image, to initiate a 3D reconstruction, then the tilted data in Fourier space don't find any corresponding reference data in the so-far only non-tilted dataset. In this case, you can set zstarwin to a larger value, e.g. 0.1, so that a tilted image has the range of zstar = +0.1…-0.1 along one lattice line, to find a reference value within a 10A resolution vertical point spread function.

limits in Fourier space the vertical resolution of the reconstruction. It is used in the script Generate Map to calculate the ZMINMAX parameter, which defines the minimum and maximum extensions in reciprocal Z-direction of the range in which the 3D dataset should be considered for generation of the final map. Dimensions in Fourier space, and therefore also the vertical dimensions of the lattice lines, are referred in reciprocal Angstroems. zstarrange should also be given in these units. A zstarrange or 0.5 means that a resolution limitation of 2A will be applied. A zstarrange of 0.1 means a limitation on the vertical resolution of the dataset of 10 Angstroem.

This is the vertical resolution limit to which your 3D reconstruction will be limited. In Angstroems.

Defines if zstarrange should be calculated from the zstarrange_real value, or if the other direction (zstarrange_real from zstarrange) should be calculated. zstarrange is between 0.0 and 0.5, while the real-space zstarrange_real value defines the real resolution in Angstroems.