Stefan, As recommended, I suggest loading the structure in using a file format that contains explicit connectivity information (MOL/SDF or MOL2). PyMOL generally does okay inferring protein connectivity from coordinates alone, but that is about it.
another thing you can do is unbond the atoms, either through picked atoms: unbond pk1, pk2 or explicitly: unbond atom-selection1, atom-selection2 Cheers, Warren -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net on behalf of Gerhardt, Stefan Sent: Fri 3/3/2006 5:06 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] setting correct bond length Dear all, I am trying to display a bound azetidine ring, but pymol is drawing also a bound between the C2 and C4 ring carbons. <<...OLE_Obj...>> bond length N-C 1.46Å, C-C 1.54Å and C2-C4 2.03Å !! See pymol picture attached. Is there a simple way of setting the bond length to be drawn correctly? <<azetidine.gif>> Stefan Gerhardt, Dr AstraZeneca Protein Structure Laboratory 50S38 Mereside Alderley Park, Macclesfield SK10 4TG, UK
