Hello,

I really enjoy working with Chimera (version 1.14), however I encounter two  problems:

I fitted the X-ray based crystal structure of apoferritin to my cryo-EM density map, determined the symmetry and based on that the algorithm fits 24 subunits to the map. Really nice.

Now I would like to show a “sliced” image of both map and structure. I tried doing so by “Side view”, enabling “clip”. That works, but I would like to rotate the clipped object.

Then I tried per-model-clipping. Here I can clip the map and structures separately. However, I have to choose all fitted (e.g. 12 out of 24) substructures and the clipping works only partially.

What am I doing wrong?

Also, I tried to figure out the best contour level setting. It seems there is no guide as to which is ideal? Based on a tutorial, I assumed 1 A³/Da for a globular protein, which turns out to be around 620*10³ A³

for my protein. The problem here is: If I slide beyond approx.. 550*10³ A³ all that remains is a square. What’s wrong?

I hope you can help me out J

Kind regards

Philipp