Hi all (again!), Warren, I know I half brought this up at the user's meeting but I can't remember if there was a clear answer...so maybe it means not yet, but didn't recall that either.
Question: is there a way to preserve small molecule bond valence information? Background: I know pymol has some recognition of bond valences for standard amino acids, as set valence=1 or starting the "builder" button shows proper valences for backbone carbonyls and aromatic side chains, etc. Also, I can edit a small molecule to get the correct valence (Ctrl-right click to select bond and Ctrl-W to cycle valence to reiterate one of Warren's older posts). If I then add Hydrogens these look correct and I can save the pdb file of the ligand. Reloading the pdb with hydrogens is fine, but if I remove the hydrogens and re-add them, they are regenerated as if all bonds are single bonds indicating it has not preserved the valence info. Is this part of what you aim to incorporate as increased information loading and storage in sd files? Is this an accurate description of current behavior (i.e need to edit bonds each time we want to make a figure of a ligand that way?) or is there some save flag that can store it once edited? If simple, perhaps that would be nice for 1.0! THanks, Seth
