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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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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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On Thu, Jul 24, 2014 at 9:54 AM, L. Costenaro (IBB) < [email protected]> wrote:
PS2: in REEL, the action "Find unique code" make phenix (not REEL) crash (all windows close) without error message
Fixed in next build. -Nat
participants (3)
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L. Costenaro (IBB)
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Nathaniel Echols
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Nigel Moriarty