Chimera- How to go about changing the threshold of the EM map?

Question

[MicrobePrincess]

It is my first time using Chimera. I have uploaded a PDB file on to Chimera and opened it up on the software. I need to change the threshold of the EM map so that I can analyze what the EM map would look like with a threshold too high and too low.

Please let me know if you have any suggestions.

Thanks

Answer 1

[Jiyao Wang]

If you use iCn3D (e.g., https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=6hjr), you can change it in the menu "Style > EM Density Map". These two images are 30% and 50% of max EM value, respectively: