Additional display toggles in hit navigator: contacts, surface, electron density

phraenquex commented 4 years ago

(Again, I'm pretty sure I created a ticket on this topic a few weeks ago - again can't find it.)

We need additional display toggle buttons alongside the existing four. They should be, in this order and with these letters:

A --> turn on everything
L --> (for "ligand"): turn on the ligand
P --> (for "protein"): turn on only the lines of what's now called "complex"
C --> (for "contacts"): turn on the dotted lines of what's currently called "complex"
S --> (for "surface"): turn on the surface of only the protein.
D --> (for "density"): turn on the electron density evidence
V --> (for "vectors"): turn on the vectors

Two things: splitting the current "C" (complex) into P and C will apparently require loading things differently (says Rachael) - well, then just do it, because it will also allow S to be rendered correctly. (Rachael will need to talk you through this in detail.)

This is URGENT now, sorry... has bubbled up from several comments of people using for serious work. So I'm going to mark it as "urgent fix". Looking at the swim-lanes, it's definitely more important than the other things in progress (except for #227, if that is as super simple as I think it is).

phraenquex commented 4 years ago

Issue #214 is relevant to this issue; and resolving this one will close #214.

phraenquex commented 4 years ago

Two of the toggles, C and D, might be difficult to do quickly: in that case, just grey them out.

Later: for D, make it so that it allows for the backend to return no data - in which case, just grey it out.

reskyner commented 4 years ago

P --> (for "protein"): turn on only the lines of what's now called "complex" C --> (for "contacts"): turn on the dotted lines of what's currently called "complex"

separate out contacts and lines - check the display controls for the current 'complex implementation' and split the two representations out. Lines -> P and contacts -> C

reskyner commented 4 years ago

S --> (for "surface"): turn on the surface of only the protein.

surface radiusType = covalent; colourScheme = electrostatic

Should be the protein (same object as the lines from above) for the ligand we're clicking the S button for.

Make sure not to include ligand and waters in the surface. (#214 )

reskyner commented 4 years ago

D --> (for "density"): turn on the electron density evidence Needs implementing on Back-end. Rachael to do this ASAP

phraenquex commented 4 years ago

No, Density is not part of the urgent spec. Just make front-end recognise whether it's available, and if not, show the button greyed-out. And if there's back-end work to do, my strong preference is for M2M to do it.

matej-vavrek commented 4 years ago

[x] A --> turn on everything
[x] L --> (for "ligand"): turn on the ligand
[x] P --> (for "protein"): turn on only the lines of what's now called "complex"
[x] C --> (for "contacts"): turn on the dotted lines of what's currently called "complex"
[x] S --> (for "surface"): turn on the surface of only the protein.
[ ] D --> (for "density"): turn on the electron density evidence
[x] V --> (for "vectors"): turn on the vectors

Preview should be always available here: https://fragalysis-matej.apps.xchem.diamond.ac.uk/viewer/react/landing

[x] colour background of image on toggling P not C

matej-vavrek commented 4 years ago

"most important, for this selection we should be using by vDW for radius type" Settings adjusted to this snapshot (could become unavailable), but basicallychanged "radiusType: vdw, opacity: 0.47": https://fragalysis-matej.apps.xchem.diamond.ac.uk/viewer/react/snapshot/2584b52d-c15c-4256-9abe-99a6f305c37d

reskyner commented 4 years ago

Excellent! Can you open PR for the surface?

phraenquex commented 4 years ago

A few things to fix on Display Controls, which are related to this ticket:

in the "Display controls" dialog, everything is named very usefully (Mpro-x0072_0_surface) - except the ligands. Can they be named *_ligand, please.
And sort all Display Controls objects alphabetically (rather than the order in which they were added)

phraenquex commented 4 years ago

Also: we need a toggle on the left side to turn off the cartoon. I suggest something like: a toggle to the right of the overall toggles named "R" (tooltip: ribbon). Leave a little space between the overall [V] and [R] toggles. (But anything else that you feel make sense is fine by me.)

The problem is that "Dispaly controls" is not very noticeable, so many people are unlikely to use it.

phraenquex commented 4 years ago

Last bug: the electrostatic surface is not coming up with the right colour. It's not a blocker, but should be looked at urgently. Do create a new ticket if it turns out to be a Big Bug.

m2ms / fragalysis-frontend

Additional display toggles in hit navigator: contacts, surface, electron density #228