1) Ligand Queue requires too many clicks for me. Going through 30 ligands and stopping at each one takes over 500 clicks. (If there's a shortcut to avoiding clicking 30 times to get to ligand 30, I don't know it.) Maybe a way to jump to a ligand? An option to "show last viewed" would help too.
2) Ligand Queue info that falls outside the black box just beneath the buttons requires me moving a dark part of the puzzle to use as a background. Can the background be sized to the text so it isn't white on white sometimes?
3) When I open the Ligand Queue after closing it, the Quicksaves are gone. Could they be saved?
Letting us save the present ligand while the Ligand Queue is running would reduce many of the clicks ucad describes in (1) above. It seems like right now, you have to stop running the Ligand Queue in order to save the latest ligand it is showing. Also, after saving something in puzzle 2363, it seemed like I always had to restart the Ligand Queue from puzzle 2363's starting ligand, even if I wanted to reach the 30th ligand in the sequence given by the Ligand Queue. Any crash during the 500 clicks in (1) above has been very annoying, because when you then restart the crashed client, the order given in the Ligand Queue seems to be entirely scrambled from what it was before the crash. Letting us save multiple different ligands from a single run of the Ligand Queue would certainly help.
I had ucad's problem (2) from above as well because I like using a light background. My best solution was to switch to a dark background. Then I could see things like 3/31 and the smiles format for each ligand.
Today while using the Ligand Queue in Puzzle 2366, I thought it would be nice if we could click the left arrow to switch from compound 1/31 in the Ligand Queue to compound 31/31. It would also help if we could click the right arrow to switch from compound 31/31 to 1/31. In addition, if there was a textbox that let us pick the first # in 7/31 and switch it from 7 to 1-31, that would also be helpful. These would reduce the # of clicks needed to load all 31 of the compounds in the Ligand Queue.
In reranking puzzles like 2366, it would help if we could use the Ligand Design tools. I know the purpose of these reranking puzzles is to let us only optimize certain compounds, but the Ligand Design tools are helpful for reliably finding certain ligands, like if we had a specific ligand from puzzle 2360 or 2363 that we wanted to examine more. With the Ligand Queue + Compound Library system in 2366, many things are shuffled around so that it isn't easy to find specific compounds from 2360 or 2363. Letting us rebuild specific ligands from scratch would help us find them and their relatives in the library sooner. Letting us load solutions from previous puzzles would also help in this regard.
Another benefit of the Ligand Design tools is that sometimes you can fix bad torsions by replacing atoms in the ligand with themselves; for example, replacing a carbon with a carbon somehow changes the nearby bond lengths and angles, and sometimes this fixes bad torsions. You can get similar effects by replacing oxygens with oxygens, nitrogens with nitrogens, etc.
The only problem would be to discourage too much exploration on ligands that aren't among the specific ones listed in the Ligand Queue or Compound Library. Perhaps an even larger library bonus or even no credit for non-library compounds would be enough to discourage such exploration.
If there will be more reranking puzzles, another thing that would help would be to eliminate from the Ligand Queue and Compound Library certain ligands that were overly-explored in previous puzzles. This would help us focus our efforts on the remaining, less-explored ligands. Then, as our exploration becomes more evenly distributed, ligands removed from one puzzle could be restored in a later puzzle to allow them to be explored more.
I agree with jeff101 that keeping the ligand design tool would be useful, especially with the current alignment method of a new molecule from ligand queue or compound library. The design tool is a useful workaround to keep the desired pose and orientation while changing the compound, as discussed also by other players.
