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
unbond atom-selection1, atom-selection2
From: firstname.lastname@example.org on behalf of Gerhardt, Stefan
Sent: Fri 3/3/2006 5:06 AM
Subject: [PyMOL] setting correct bond length
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?
Stefan Gerhardt, Dr
Protein Structure Laboratory
Alderley Park, Macclesfield
SK10 4TG, UK