Local refinement - mask is absent

Dear colleagues,

When running the focused local 3D refinement the Real Space Mask Slices Iteration graph seems to be empty.

Although the final result of this focused local 3D refinement seems to be OK but the absence of image in Real Space Mask Slices Iteration graph is a little disturbing.

Do you know if anything is wrong?

Thanks in advance.

Kind regards,

Hi @Dmitry,

Have you set a fulcrum parameter? The slice plots are through orthogonal planes that center on the fulcrum of the refinement, so it appears that the fulcrum here doesn’t cut through the area of the protein with nonzero density.

We’ll make a note to center the slice plots on the actual center of mass of the mask (rather than the fulcrum), which will make visualization better.

You can also try leaving the fulcrum empty and then it will be set to the center of mass of the mask at the start of the refinement – the slices will then better visualize the density.


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thanks you @mmclean.

Yes, I have set the fulcrum parameters, even without values after comma.
Shall I send you the log for the inspection?

I will try without the fulcrum parameters. And report back.

Kind regards,