I have been playing around with Elbow for a while, but I kept having problems generating .cif file. For "Chemical file type" and "Template PDB file", I used the pdb file of the ligand. Since the coordinates in the pdb file corresponds to a conformation desired, I chose "None" for "geometry optimization". After running Elbow, the output pdb file was completely different than the input one -- even double bonds became single bonds and 10-membered ring conformation changed. I have tried Sketcher in CCP4 package, but no good results either. Could anyone tell me how to do this correctly? Any help is appreciated!

Thank you in advance,

Mengbin
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Mengbin Chen