Hi Everyone,

How can we interpret these plots from the Ab-initio and Homo Refine jobs?

What are the x and y axes and the heatmap like plots ?

I would appreciate your help.

Thanks!

Ab-initio:

Homo Refine:

Hi Everyone,

How can we interpret these plots from the Ab-initio and Homo Refine jobs?

What are the x and y axes and the heatmap like plots ?

I would appreciate your help.

Thanks!

Ab-initio:

Homo Refine:

Dear @Ashwin-Dhakal,

In refinement jobs, these plots show heatmaps of the real-space density being actively solved by the algorithm. Specifically, each subplot shows a density slice along one of the coordinate planes: z-y, z-x, and y-x, respectively. The color is proportional to the scalar density value at each voxel. If you are familiar with UCSF ChimeraX, you can obtain a similar visualization by using the orthoplanes functionality in their volume viewer.

In ab-initio jobs, these are projections of the density. Instead of slicing the density along a plane, the density is summed (integrated) along the normal to that plane, and the resulting sum is displayed.

Michael

and units of axes are pixels of the box - and ab initio is often binned internally. 0-255 means 256 box