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On 03/04/14 04:45, Oliver Clarke wrote: > Hi all, > > Is the functionality of ‘Calculate-->Merge Molecules’ available from the scripting interface? Yes. > > I couldn’t find it in the manual. There is a function named merge_molecules, but I don’t know what arguments it takes and it does not do what I would expect - I’d like it to take two mol_ids and merge the second one with the first, but that does not seem to be the case. Recall that you can merge many molecules with a "first" molecule, then you're golden. merge_molecules(imol_ref, [imol_daughter]) Although not written in python, I believe that the documentation hints that the second argument is a list of molecule numbers. > > I’d like this function so I can write a little shortcut that will allow me to click on two fragments and join them, rather than having to scroll through the list of mol_ids of various newly placed helices etc. > > I guess I could use replace_fragment if I add a dummy atom to the first molecule and then replace it with the second - Yikes! :-) HTH, Paul.