Jerome If you are using a PDB file without hydrogens, there can often be ambiguous bonding assignments so it can be better to add hydrogens or use a "better" chemical input like SMILES, Mol2 etc that explicitly states the bonding. You can also use REEL to define bond orders and run eLBOW. Either way, send me the input file (off list) and I'll take a look. Nigel On Fri, Mar 11, 2011 at 11:15 AM, Jerome Nwachukwu wrote:

Hi all: For some reason, phenix.elbow converts a specific double-bond (C=C) in my ligand to a single bond (C-C) and therefore generates a wrong .cif file. Is there away to avoid or correct this problem? Thank you, -Jerome

Jerome C. Nwachukwu, PhD Kendall Nettles' Lab Dept. of Cancer Biology The Scripps Research Institute-Florida 130 Scripps Way, 2C1 Jupiter, FL 33458

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