Hi Rex,

There is a simple fix to that: just break a bond somewhere in the ring using

> unbond atom1, atom2

where '>' means the PyMOL command line, and 'atom1', 'atom2' are selections corresponding to two adjacent atoms in the ring. Then make your adjustments to the ring geometry and finally close the ring again using

> bond atom1, atom2

Be sure to check the length of the recreated bond, just in case you missed an angle somewhere...

Best regards,
Thomas

On 15 Jun 2008, at 18:34, Rex Palmer wrote:

From a high resolution X-ray study we have detailed geometry of a seven membered ring which is a feature of a modified steroid.
The same compound has been studied by NMR and the particular 7-membered ring has been described
as having a different conformation from the X-ray structure. The NMR measurements have provided torsion angles
with respect to the CH2 groups in the ring. These are vicinal torsion angles of the type H-C-C-H and there are six of
them in total. We would like to modify the vicinal torsion angles of the X-ray conformation in order to transform the
ring conformation to that found in solution from NMR. It was suggested that it may be possible to do this with PyMOL
but so far our efforts have not proved successful. Does any one know how to do this? Help with this would be most appreciated
as we would very much like to study the detailed solution conformation of the ring which is not presented in the NMR paper.
 
Rex Palmer
Brkbeck College
London
   
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