Hi,
lets say I have a set of docked conformations and want to compare them with the conformation observed in a crystal structure (aka redocking). How can I get pymol to calculate RMS values for pairs of small molecules that probably don't have the same numbering? For now I tried to use the rms_cur command, but it fails telling me that there were no atoms selected. How do I convince pymol to compare the two structures without any fit while they are non-peptidic? Paul
