Initial Structure lowpass (Fourier radius)


I tried Ab-initio reconstruction for 30K particles, when I change the parameter Initial Structure lowpass (Fourier radius) to 56 from initially I used 35 for my particles, I see better volumes are generated for the pctls, However, I would like to understand What is the limit of this parameter that I can use for my particles. If more information will be required, I will be happy to share the same


Hi @Rahul,

Thanks for the question. This parameter controls the lowpass radius of the initial structure generated in Fourier space. It is parameterized in Fourier space (rather than in real space), in contrast to the related “Initial resolution (Angstroms)” parameter, which controls the maximum resolution of the Fourier coefficients that the initial SGD update iterations are allowed to change.

To answer your question, it can take on any nonzero value. However, the actual maximum resolution of the current density after the 0th iteration will be limited to whatever is specified in the “Initial resolution (Angstroms)”. So if you see that your data does better with higher resolution initial structures, it might be worth it to also change the Initial resolution (Angstroms) accordingly (i.e., decrease the numeric value of this parameter to start at higher frequencies).