Lionel Can you send the SMILES directly to me? Cheers Nigel On Thu, Jul 24, 2014 at 9:54 AM, L. Costenaro (IBB) < [email protected]> wrote:

Dear all,

I am making the restraints file (CIF) for a ligand with two chiral carbons, using eLBOW (AM1 QM, output: retain original chirality) from a SMILES description and obtain the following:

Atom input_chirality input_smiles output_vol_sign output_R/S output_chirality_pdb C20 S C@H negative S S C37 R C@@H positive S S

Although the volume_sign in the output cif file correspond to the input chiralities, the output pdb has the wrong chirality for the carbon C37: S instead of the desired R.

I think the "retain original chirality" option is what I need to keep the input chirality, but apparently it doesn't. How should I proceed to get a pdb with the correct chiralities?

Best regards, Lionel

PS: phenix version 1.9-1692, linux X86_64

PS2: in REEL, the action "Find unique code" make phenix (not REEL) crash (all windows close) without error message

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