ligand/small molecule issues

[LociOiling]

Puzzle 2461: CASP16 Ligand Puzzle L3000 features both the ligand queue and the compound library. There is also a long list of possible ligands, 219 according to the puzzle notes.

Unfortunately, there are a number of issues that get in the way of easily exploring this large space. These issues present challenges for experienced players. Most less-experienced players will probably just give up before learning how to work around the problems.

One general problem is a lack of consistency in how tools operate and what can be done when.

For example, the Tracks window can be opened and closed using a hotkey while the Ligand Queue or another tool is running. However, it's not possible to change tracks or create a new track. This restriction probably makes sense for Wiggle, but it's a limitation for the Ligand Queue.

In contrast, the Compound Library window can't be opened while the Ligand Queue is running. Its icon is dimmed, and the default hotkey H has no effect. If the Compound Library window is already open when the Ligand Queue tool is started, it remains open. In this case, the "Upload Current" button allows submitting a search, and the "Load Library" button will display results.

Comparing the Compound Library and the Ligand Queue, there are a number of inconsistencies.

The Compound Library and the Load Library compound windows are both arranged vertically, and can be expanded vertically. Both can be moved around the screen freely. Load Library Compound shows a rotatable image of each compound.

On the other hand, the Ligand Queue is arranged horizontally. It appears as an overlay, which can't be moved, and not a true window or panel. It can't be expanded, and there's no visualization of the compound.

The Compound Library/Load Library Compound windows and the Ligand Queue tool have a similar function, but very different user interfaces. The differences will probably tend to discourage new players.

Aside from issues of consistency, there are a number of other issues specific to various tools. I'll detail those in a separate post.

(Edit: hit Create Post too soon on the first draft.)

[LociOiling]

Here's a laundry list of things that could be improved. Many of these items have been noted previously. Some of them have suggested solutions here.

While it's a long list, I'm hopeful that some of these items may be low-hanging fruit.

ligand tools (general)

• ligand tools require ligand to be selected
• suggestion: for single ligand at least, just enable the tool icons/hotkeys

ligand queue

• required for CASP16 puzzles
• ligand id appears only in the ligand queue (need small molecule properties afterwards, confusing)
• "initial" ligand is really the last ligand after a selection (confusing)
• must scroll horizontally through list with mouse clicks
• right and left arrows don't work
• if ligand is near the edge of window, Ligand Queue tool appears partly or completely off-screen
• no title bar to move ligand queue tool
• ligand queue does not follow ligand when recentered (Q or Home)
• suggestion: vertical orientation for ligand queue, ala compound library, clickable with preview
• suggestion: additional fields, like molecular weight
• ligand relies on quicksave slots, but key combos necessary to access, no clickable UI (confusing)
• suggestion: new UI element for quicksave slots
• ligand queue uses high CPU even when window minimized/down (bug)

segment information window

• segment information window fixed size
• suggestion: make window resizable vertically/horizontally
• segment note on ligand segment doesn't change when ligand changes (can be confusing) (edit: some players use the segment note differently, and don't want it to change when the ligand is replaced)
• only one segment information window at a time
• suggestion: allow multiple segment information windows

tracks

• one option for organizing a large number of compounds
• tracks menu fixed size
• suggestion: make tracks menu vertically resizable
• tracks menu fixed sort order
• suggestion: allow at least ascending/descending track name order
• changing tracks closes other windows (but not tracks menu itself, small molecule properties, or recipe output)
• suggestion: try to avoid closing everything, as previously noted
• changing tracks slow, always does "refreshing shared solutions" (bug)
• no additional info, such as a description
• suggestion: add optional description, similar to Compound Library and similar
• "default" track can be selected to delete, gets "are you sure" message, then "can't delete" message
• suggestion: just give "can't delete" message up front

small molecule properties

• helpful in knowing which ligand is which
• multiple properties needed to identify a ligand
• no boxes checked by default
• necessary to check each box to get all properties
• suggestion: better if integrated with Segment Information window, always available on ligand segment
• suggestion: plan b: just show everything, eliminate checkboxes
• currently hides behind small molecule view options
• suggestion: give it its own icon/hotkey if properties can't be merged into segment info

compound library/load library compound

• load library compound can be slow (bug?)
• load library compound sometimes fails – network timeout? no error indication
• load library compound quadratic behavior (larger result lists disproportionately slower than smaller)
• load library compound fixed sort order
• load library compound display doesn't change when current ligand changes
• load library compound doesn't display the name or description of the search
• suggestion: display the name and description of the search in load library compound

open/share solutions

• window usually very slow to open (bug/server issue)
• refreshing shared solutions often fails, but gives error message

Lua interface

• function to retrieve small molecule properties (returning dictionary of properties)
• functions for ligand queue (return table of ligand ids, load a particular ligand)
• function to submit named compound library search
• function to get compound library search results (name, description, #, status)
• function to get compound library search details (entry #, similarity)
• function to load single search result
• function to get PDB info shown in segment information window
• add description to save solution function, in addition to title

[rmoretti]

Thanks for the list. It will be helpful when we get the time and manpower to start working on some of these. (Though I can't say when that will be.)