Ligand Viewing Options menu confusing

Case number:954892-2001503
Topic:Developer Preview
Opened by:Susume
Status:Open
Type:Suggestion
Opened on:Tuesday, November 24, 2015 - 04:04
Last modified:Tuesday, November 24, 2015 - 20:30

When you change to Ligand Viewing Options mode, the menu does not appear until you click. This is counterintuitive - you would only change to that mode if you wanted to change the viewing options, so the menu should appear as soon as you enter the mode.

When Ligand Viewing Options menu first appears, you can check the boxes of the various grids, but you can't see the grids because the sliders are all the way to the left. It would make more sense to have them all the way to the right or in the middle by default so that checking the boxes causes the grids to appear.

When the grids are visible and you switch to Ligand Design mode, they stay visible until you change an atom to C or N, when they disappear. It would make more sense for them either to disappear when you change mode (if they are not supposed to be visible in ligand design mode), or to stay visible until you explicitly turn them off.

When the viewing options menu reappears after re-entering viewing options mode, the grids do not reappear even if their boxes are checked and their sliders are all the way to right. The grids do not reappear until you move their sliders. They should reappear as soon as you enter viewing options mode, if their boxes are checked. Or they should stay visible in other modes until you turn them off.

Many players always use the black background for folding. The black repulsive grid does not show up against the black background - could it please have a different color?

Where are the grids supposed to be? They appear as little clouds that are not centered on the protein or the ligand, or the donors or acceptors, or the hollow space inside the protein.

(Tue, 11/24/2015 - 04:04  |  1 comment)


Joined: 01/12/2015
Groups: None

Excellent feedback Susume. I really appreciate your thoughts and am really excited to fix the things you mentioned!

1) I guess I never thought about the fact that you shouldnt have to click on ligand in order to get the ligand viewing options to open up. It should appear as soon as you click the button, maybe it should even be available through a right click on the ligand?

2) I am not sure why the grids do not appear when you click the check box, but I will figure it out and make sure it works in the next release!

3) The grids disappearing is also a little odd. That is not something I intended and have not observed. I will go back and check what is going on.

4) Once again, another weird bug. I will check why they do not reappear.

5) Sure, what color? Do you want the choice to pick colors?

6)The grids are supposed to highlight spots between the protein and ligand that will help you make design decision. For example, while designing a ligand, you will want to place a donor in the vicinity of the red spheres (acceptors). The black spheres are another way of viewing clashes. The goal is to expand this interface to include QSAR scores, which are kind of like a representation of a bunch of features squashed into one feature.

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