ViewDockX suggestions

[iamkaant@…]

Thank you for your advice, thin cylinder bonds are a good substitution for the wireframe view! However, some atoms are displayed as balls; changing the atom radius doesn’t fix this. Switching to the «Spheres» atom style helps, though.

I have used ViewDockX recently, and here are my thoughts:
All columns from a docking file are displayed by default. I would prefer only molecule name and maybe rating to be displayed initially
Hiding unnecessary columns is quite cumbersome, as the table is updated after each selection/deselection of a tick box. It would be great to be able to select everything one wants first and then update the view after the menu is closed.
It would be nice if the table header was frozen to be visible when you scroll the list down.
My main complaint is the absence of «fixed» buttons to mark compounds. In Chimera’s ViewDock there are three radio buttons at the bottom of the window. In ChimeraX, you must locate the correct number of stars for a specific compound every time you mark it. A kind of solution is: if you don’t scroll the list of compounds, the last one is always at the bottom. However, it gets overlayed by a horizontal scrollbar sometimes.
Additionally, I would love to have 2-3 tiers (Viable/Deleted/Purged) in addition to the stars. My most common action is «mark this compound bad», so this action should be as easy as possible. I have to inspect up to 30K poses routinely, so every delay is multiplied and eats substantial time in the end.
A great improvement would be to have global keyboard shortcuts for «previous/next compound» and «mark compd good/bad». Ideally, these shortcuts should always be active once ViewDockX is active, disregard the part of the ChimeraX window which is in focus. I.e., I should be able to mark a compound «Deleted» even when I’m rotating its 3D view.

[pett]

Elaine's feedback on the suggestions:

Much of this is disliking the ChimeraX ViewDockX interface and wishing it was more like the Chimera one, which I agree with 100%. Like Blast Protein, Conrad used that HTML prefab stuff.

It would be much better after a similar treatment to what Zach did for the Blast Protein results, which includes many of Andrii's requests:

(1) allowing one to choose the set of shown columns and to save it as a preference, regardless the initial default. I think Andrii would be OK with that, he would only have to set it once. Since different programs put out different columns it might make sense for all columns to be shown initially.

(2) header stays in place while other rows scroll

(3) could have buttons across the bottom that apply to chosen rows and are the same actions as in the context menu of that tool. Blast Protein has "Load structures" etc. I'm not a high-volume docking results viewer, obviously, so I don't really understand his wanting 3 levels, but maybe we could even get rid of the stars system and instead ViewDockX could have something like these buttons across the bottom:

Mark chosen entries: [Viable] [Deleted] [Purged]

I don't know if the keyboard shortcuts he suggests are feasible to add, but I have no objection otherwise.

[pett]

Ute Roehrig had some additional suggestions for when the port occurs:

1. When opening a docking results file (format SwissDock/Dock/Vina/Glide), launch the ViewDockX tool automatically
2. In the ViewDockX table, provide the possibility to select several poses by Shift+clicking on several lines in the table (the way it was working in Chimera)
3. Let the user automatize/customize the columns he wants to see by default (provide columns as option in the command line?)

#1 has actually already been implmented.

[pett]

Fixed by re-implemented ViewDock