Normalise greyscale / intensity levels of external references

Cryo-EM Data Processing
1

Dear all,

I am processing a heterogenous dataset, and would like to use various maps from the EMDB as references for heterogenous refinement. The maps have different greyscales ( = intensity thresholds when opened in ChimeraX), which I would like to normalise before using them as references. Is there a way to do this, or does this happen internally anyhow?

Thanks a lot,
Matthias

2

The option “Re-estimate greyscale level of input reference” (which is enabled by default) does this.

One caution, though; if using maps which come from different greyscales in heterogeneous refinement, you can expect odd behaviour to occur with particle assignments.

3

Thanks for the response! As far as I can see, this option does not exist for heterogenous refinement. I tried to normalise densities in ChimeraX, but I am not sure if this is the perfect solution. How would you make use of the “Re-estimate greyscale level of input reference” option that exist in Homogenous refinement for heterogenous refinement?

Cheers, Matthias