I was using the simulator in cisTEM of alpha version (pre-compiled) with the tutorial written on the cisTEM-dev website: https://bhimes.github.io/cisTEM_docs/docs/sim/tutorials/tutorials.html
Section 3, calculate a stack of noisy particles, in that tutorial shows steps to simulate an isolated protein. I followed the instructions and I could reproduce Figures 1 A and B by modifying and executing bgal_flat.sh on my ubuntu 20.04. However, for Figure 1 C, after removing the flag, --save-detector-wavefunction, from optional_args in shell script (bgal_flat.sh), the generated image does not look identical with Figure 1 C which is very dark. In fact the generated image looks similar to Figure 1 B. I have no clue why this difference happened.
Could you help me with this situation? I attached the simulated image in png and my output messages shown on the terminal after runing the simulator.