Small Molecule Design tools crashes and inconsistencies

Case number:845829-2012536
Opened by:LociOiling
Opened on:Saturday, December 18, 2021 - 21:07
Last modified:Wednesday, December 22, 2021 - 19:30

There are several issues with how the small molecule design tools work.

Switching puzzle types

From a small molecule design puzzle, the Small Molecule View Options and Small Molecule Properties windows remain open when switching to another type of puzzle.

If any options are checked on Small Molecule Properties at the time of the switch, a crash occurs. Checking one of the properties after the switch also causes a crash.

For Small Molecule View Options, "Show IsoSurface" doesn't cause a crash before or after switching puzzle types. "Cation Pi Interactions" and "Pi Pi Interactions" do cause a crash.

The Small-Molecule Design window closes when switching puzzle types. This is the expected behavior.


The Small-Molecule Design window opens and closes with repeated clicks on its action bar icon.

The Small Molecule View Options and Small Molecule Properties windows remain open with repeated clicks on their shared action bar icon. This is inconsistent.


The action bar icon "Design Ligand!" opens the "Small-Molecule Design" window. Both spots should say either "Small Molecule" or "Ligand".

The action bar icon "Ligand Properties!" opens the "Small Molecule View Options" and "Small Molecule Properties" windows. Again, sticking to either "Small Molecule" or "Ligand" would be better.

The term "small molecule design" is used to describe the type of puzzle, so maybe "Small Molecule" should be the default.

MMFF wiggle

The "MMFF Wiggle" tool has been assigned the default hotkey M. The same hotkey is used for "mutate to specific amino acid" in protein design puzzles.

The "MMFF wiggle" action bar icon now floats to the top row, away from the other small molecule options.


Small molecule design is partially a mode, but not entirely.

The small molecule design and small molecule properties windows require the ligand to be selected before they can be opened. But they remain open if the ligand is deselected, which seems inconsistent.

Requiring the ligand to be selected makes little sense on puzzles where the protein is entirely locked, such as the VHL ligand design series. On the VHL series, Ctrl+A selects just one segment, the ligand.

If the small molecule design tool is open, clicking on the ligand currently selects the ligand if it's not already selected, in addition to selecting an atom. So there doesn't seem to be an advantage to requiring the user to select the ligand before opening the tool in the first place.

For MMFF wiggle, selecting the ligand also seems unnecessary in the VHL series. Perhaps on puzzles with movable protein sidechains, a selection requirement would make more sense.

Other tools, including recipes, are available regardless of whether the ligand is selected, even if some of the ligand tools are open.

(Sat, 12/18/2021 - 21:07  |  2 comments)

phi16's picture
User offline. Last seen 1 day 38 min ago. Offline
Joined: 12/23/2008

How does one open The Small-Molecule Design window ?

LociOiling's picture
User offline. Last seen 7 hours 36 min ago. Offline
Joined: 12/27/2012

First, select the ligand by clicking on it. (I don't think this step should be necessary, but it is, at least for now.)

Then, the Ligand Design button on the action bar will be active. Click on it to open the tool. The keyboard shortcut L (really lower case "l") also works.


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons