How to do ligand puzzles - A short guide

Started by Floddi

Floddi Lv 1

@rmoretti sorry for answering a bit late:
I can also recommend the preset. I think it's pretty much the same with some minor adjustments.

What's missing is some information of hydrogen bonds which can be important for high scores.
I also like to see "exposed" sometimes for pi-pi-stacking or van-der-Waals bonding.

This isn't static in any way :D For the 2715 I changed the view settings to "Binding site" instead of "Cartoon ligand" because the protein is big and I'll stay in the center anyways. I've also disabled voids.

It would be nice if voids and others wouldn't have collision as it can be a bit annoying when adding bands. Same for clash warnings. Those spikey balls are blocking bands. Imo there is no reason why collision is nessecary.

More info can be overwhelming but is also pretty useful if you're working on something hours at a time.
I think the preset is designed well enough to be used by the majority but as you're improving, more information is more of an advantage than a disadvantage.
The preset shouldn't be changed in any way imo! It's well done!

Bruno Kestemont Lv 1

@Elfi @moretti I see in the PDB you showed that the ligand sometimes is in 2-3 pieces (2-3 ligands ?). It would be helpfull to be able to build separate ligands (then if needed to join them in one ligand).

rmoretti Staff Lv 1

@"Bruno Kestemont" The ability to work with multiple disconnected fragments (rather than a single totally connected ligand) and combine them back together is on the wish list. It's just that this requires a rework of the backend which we haven't yet found time to undertake.

Elfi Lv 1

Thank you, @"Bruno Kestemont"! This is super helpful. I wish I had found this when I started the ligand puzzles. I had a really hard time understanding what to do. Now I also see what the x-ray tunnel function is good for. Plus how to use the compound library properly. I hadn't figured that bit yet.