As a former cryoEM researcher, using 0.141 for visualization jumped out at me. I worried it was taking away from your argument, but it actually reinforces it.

Thanks for the clarification. The use of 0.141 as a threshold is oddly specific and likely indicates that the authors do not understand the different thresholds. This further detracts from the overall quality of the map.

I agree that the lack of ligand density is a problem. However, the Fourier Shell Correlation (FSC) threshold of 0.141, which is used to estimate the resolution of the map, should not be related to the electron density visualization threshold in ChimeraX. These thresholds serve different purposes.