You can optimise the geometry with eLBOW. One of the most frequent problems is the quality of the input. The better chemical representation of the molecule, the better eLBOW will work. GIGO.

If you are able, send me the input file directly and I'll help you with the optimisation.

Nigel

On 4/27/10 11:09 AM, r n wrote:

Hi all

I do have crystal structure of my ligand and trying to optimise the geometry using phenix.elbow.
It entirely rotate one of the ring bond to other side and in result of breaking the ring geometry.
Ring contain sulphur and other heavy metal.

Is it any way to optimize with current geometry in phenix.elbow so that it wont ruin the molecule?
Thanks
ram
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-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty@LBL.gov
Fax   : 510-486-5909     Web   : CCI.LBL.gov