Request - show nearby residues when selecting residue in Ramachandran plot

[olibclarke]

Hi Paul, when navigating the main Ramachandran plot interface, clicking on a residue recenters on that residue. It would be useful if there were a way to then see just which residues (general or outliers) are nearby in either sequence or 3D space. The rama HUD does this during refinement, but it would be useful to have access to a similar tool outside of refinement when identifying problem regions.

Also, is there any possibility of flagging "dubious" residues on the ramachandran? Not outliers per se but outliers given structural context. E.g., a residue in the middle of a helix that has "allowed" but non helical phi/psi...?

Cheers Oli

[pemsley]

when navigating the main Ramachandran plot interface, clicking on a residue recenters on that residue. It would be useful if there were a way to then see just which residues (general or outliers) are nearby in either sequence or 3D space. The rama HUD does this during refinement,

by using Rama spheres, is that what you mean?

but it would be useful to have access to a similar tool outside of refinement when identifying problem regions.

So, put Rama spheres around the current central residue in normal view mode - is that what you mean?

Also, is there any possibility of flagging "dubious" residues on the ramachandran? Not outliers per se but outliers given structural context. E.g., a residue in the middle of a helix that has "allowed" but non helical phi/psi...?

Not any time soon.

[olibclarke]

Hi Paul, no I mean on this plot:

When I click on a residue, it recenters on a residue. What I am suggesting is to (a) highlight the currently centered residue on the plot and (b) indicate nearby residues (either in sequence space or 3D) on the plot. This would help give a quick indication of whether an outlier is a one-off, or part of a more problematic cluster. Does that make sense? This would also give a quick idea of whether the structural context makes sense - e.g. if one is centered on the middle of a helix, all the residues nearby in sequence should be clustered in the alpha-helical region of the plot, and if there is one that isn't it may be a baddie, even if in an "allowed" region.

(In Coot 0.98, the residue is highlighted with a green box - this doesn't seem to happen in 1.0 - is it supposed to?)

[pemsley]

I see what you mean now - that would be useful.

In the rewrite a good many things got dropped. The green box was one of them. It would be nice to have it back.