[Chimera-users] Chimera: Per-model clipping and contour level

Selenschik, Philipp pselensc at uni-muenster.de
Mon Oct 26 08:47:30 PDT 2020


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 :)

Kind regards

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