Sun, 05/13/2018 - 19:56
Here are some things I've learned:
- "Ligand Specific" coloring and "Cartoon Ligand" view gives you CPK colors and shows the hydrogens on the ligand.
- You need to see those hydrogens. (White caps.)
- The ligand needs to be selected to enter Ligand Design mode, but selecting tends to obscure the atom colors.
- It's easy to lose ligand design mode, and sometimes you need to get out so you can see the molecule. Use the "back" icon (B) or click on the background to get out on purpose.
- In Ligand Design, you select atoms by (left-) clicking them, control-click and shift-click have no effect.
- Deselect atoms by clicking them again or using "Clear Selection" (broom icon).
- It's easy to select the wrong atom. Zooming in may help.
- Selecting a hydrogen lets you extend the molecule.
- Selecting a heavy atom (non-hydrogen) lets you change that atom.
- Selecting multiple atoms lets you change those atoms, similar to mutate in protein design.
- Selecting two atoms lets you change the bonding between them.
- Selecting two adjacent atoms on a ring lets you add another ring, as in tryptophan.
- Selecting two nearby hydrogens lets you bond them. You can make your own rings this way by chaining carbons, then bonding hydrogens from the first and the last carbon.
- Sometimes the molecule looks squashed, with distorted rings and other problems. The MMFF (Merck Molecular Force Field) wiggle tool can help. The ligand must be selected to use MMFF wiggle.
- The bonding on rings in Foldit often looks different than what you see in the PDB or a separate molecule viewer. This is normal, and has something to do with how Foldit shows "resonance".