cryo-EM driven docking tutorial

Dear support,

I am trying to work through the protein-protein docking driven by cryo-EM tutorial published in Methods of Molecular Biology (EMD1884 & PDB 2YKR) to dock subunits F & R with restraints from a masked map around the two subunits. In the first part (docking subunit F into the map using PowerFit) I get results from the submitted job and produced images of solutions. Although the images show fitting inside the map subvolume; when I check the downloaded results I see the docked solution outside the used map. Not sure what am I missing?

Your comment is appreciated!


Are you using the cropped map or the original one to view the solutions?

For a powerfit tutorial check:

I tried both the coped map and the original one and there is no difference when checking the results. The cropped map overlaps with the original map as expected (it is part of the original map). I did the powerfit tutorial in the link and it worked fine. Then I wanted to do the docking with cryoem restraints that showed the problem.

So you are now referring to the HADDOCK model and not the powerfit ones.
That can indeed be the case as the server transforms the map into an xplor format.

You might then have to fit the HADDOCK models back into the original map using Chimera for example.

I see. So, I need to re-dock the complex into the map. If it is possible to make the transformed xplor map part of the results to download that would be helpful.

Thank you for the clarification.

Not fully sure this is the problem.

But you can recover the map if you download the full archive of the run and check the data/cryo-em directory

Thanks Bonvin for your help.