It is probably an error in the cif file due to the wrong number of hydrogens. If you can define a SMILES string, (c1ccccc1 is benzene, C1CCCCC1 is cyclohexane), you should be able to get the right thing. Aromatic rings should be planar to within 1 degree or so. Visually, they should appear flat. You can generate a proper SMILES string with a java molecular editor. http://www.molinspiration.com/jme/ Claudia Scotti wrote:
Dear list,
I've refined a protein at 2.0 A resolution with its ligand, a small molecule which includes a phenyl group. For this, I used elbow to generate the cif file, and in this file the atoms of the phenyl ring are correctly defined as "aromatic". However, the pdb output of the refinement shows a boat configuration for the 6 carbon atoms ring, with a very nice fit to the electron density. This would suggest a flexible cyclohexyl- substituent instead of the expected, typically planar phenyl ring.
As my chemistry is poor, I'd really need some suggestions on where I'm wrong: did I give the wrong cif file or does phenix recognise a better fitting in a boat structure, indicating that my ligand phenyl moiety has been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the phenyl group not so planar as I've supposed it to be until now?
Any help would be very appreciated.
Many many thanks,
Claudia
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673
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