<div dir="ltr">Lionel<div><br></div><div>Can you send the SMILES directly to me?</div><div><br></div><div>Cheers</div><div><br></div><div>Nigel</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jul 24, 2014 at 9:54 AM, L. Costenaro (IBB) <span dir="ltr"><<a href="mailto:lionel.costenaro@bioinf.uab.es" target="_blank">lionel.costenaro@bioinf.uab.es</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Dear all, <br><br></div>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: <br>
<br></div><div>Atom input_chirality input_smiles output_vol_sign output_R/S output_chirality_pdb<br></div><div>C20 S C@H negative S S<br></div>
<div>C37 R C@@H positive S S<br><br></div><div>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.<br>
<br></div><div>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?<br><br></div>
<div>Best regards, <br></div><div>Lionel<br><br></div><div>PS: phenix version 1.9-1692, linux X86_64<br><br></div><div>PS2: in REEL, the action "Find unique code" make phenix (not REEL) crash (all windows close) without error message<br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br>Nigel W. Moriarty<br>Building 64R0246B, Physical Biosciences Division<br>Lawrence Berkeley National Laboratory<br>Berkeley, CA 94720-8235<br>Phone : 510-486-5709 Email : NWMoriarty@LBL.gov<br>
Fax : 510-486-5909 Web : <a href="http://CCI.LBL.gov">CCI.LBL.gov</a>
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