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-admin@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 1.46, C-C 1.54 and C2-C4 2.03 !!

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