RE: [PyMOL] setting correct bond length

[Warren D. <wa...@de...>]

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: pym...@li... on behalf of Gerhardt, =
Stefan
Sent: Fri 3/3/2006 5:06 AM
To: pym...@li...
Subject: [PyMOL] setting correct bond length
=20
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.
=20
 <<...OLE_Obj...>>    bond length N-C 1.46=C5, C-C 1.54=C5 and C2-C4 =
2.03=C5 !!

See pymol picture attached. Is there a simple way of setting the bond =
length
to be drawn correctly?
 <<azetidine.gif>>=20


  Stefan Gerhardt, Dr
AstraZeneca
Protein Structure Laboratory
50S38 Mereside
Alderley Park, Macclesfield
SK10 4TG, UK