Hi niko,
When calculating the difference map, if I apply a negative bfactor to both two 3D volumes before diffmap.exe, the diffmap.exe will run a longer time than no bfactor. So I read the source code, and found you used a VA04 function in diffmap.exe. I remember the VA04 is a Powell minimization subroutine. Can you tell me what you use the VA04 for? To scale the amplitude?
Thank you.

Yes, VA04 is used to scale the amplitudes. It determines a constant A for each resolution zone that minimizes

SUM_OVER_ALL_I[(CABS(F1(I)) - CABS(A*F2(I)))**2]

(F1 and F2 are the Fourier terms in the resolution zone). Then it determines another constant B that minimizes

SUM_OVER_ALL_I[(CABS(F2(I)) - CABS(A*F1(I)))**2]

The final scaling constant is then