I have a cryo-EM map that I want to segment. I have structures surrounding the density of interest from all sides. I did a molmap in chimera and subtracted everything the molmap. I then cleaned the excess density around my protein using volume eraser.

Now the map that I get opens fine in Chimera. But I tried to open a model and my density in Coot, the screenshot is what I got:

1) the structure is not fitted

2) the density appears to have multiple copies of my proteins, it's supposed to be only one unit there

What is wrong here exactly, I'm suspecting it's the volume eraser! Is there a better way to segment the density given how I have atomic models for all the surrounding densities, but not the density of interest?

Regards.