[phenixbb] eLBOW / REEL and chirality

Nigel Moriarty nwmoriarty at lbl.gov
Thu Jul 24 10:06:47 PDT 2014


Can you send the SMILES directly to me?



On Thu, Jul 24, 2014 at 9:54 AM, L. Costenaro (IBB) <
lionel.costenaro at bioinf.uab.es> 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 at 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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> phenixbb at phenix-online.org
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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 at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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