On Mon, Jun 21, 2010 at 8:13 AM, Mark A Saper
Could someone explain the difference between the GUI "ligand_identification" routine and the documented command line "find_all_ligands". The latter appears to have more flexible input parameters.
I believe find_all_ligands is just a frontend to LigandFit for searching for multiple different ligands, which you still need to specify. The ligand identification program runs "blind", i.e. it tries all of the most common ligands in the PDB, or all found in ATP-binding proteins, or everything in a directory you supply, etc., and would normally be used to fill mystery blobs in the maps.
I'm not sure the GUI for ligand_identification is working correctly.
sigh. . . Yes, someone deleted a couple of essential lines of my code, so it runs in the wrong directory (and it does still run correctly, but you won't see the results in the GUI). I'll send you the patch. -Nat