<div dir="ltr">Its is very strange that the SMILES string is resulting in an aromatic ring. Can you send me the SMILES?</div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Cheers<div><br></div><div>Nigel<div><br></div><div>---</div><div>Nigel W. Moriarty<br>Building 33R0349, 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" target="_blank">CCI.LBL.gov</a></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On Sat, Jan 9, 2016 at 3:38 AM, andre.stiel <span dir="ltr"><<a href="mailto:andre.stiel@helmholtz-muenchen.de" target="_blank">andre.stiel@helmholtz-muenchen.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
I have a phosphatidyl inositol ligand without an existing CIF file only smiles. When I construct the ligand from the smiles ELBOW regards the sugar as just an aromatic ring.<br>
So I see three possibilities how to end up with a proper constraints file for my ligand (that is: tails like in the smiles but with a proper sugar (chair) conformation on top):<br>
1. Can I edit the aromatic ring in REEL in a way to push it into the desired boat/chair conformation? I did not find a command to that end although he can clearly „see“ this conformation as I know from another ligand.<br>
2. Can I chop the sugar part from the .CIF of another ligand and somehow fuse it to my tails?<br>
3. There is a sugar editor in REEL (which however crashes at the moment for me (Version 1-10-2155)) can I use this to construct the desired sugar and somehow fuse it to the rest… basically like option 2?<br>
I have not found a very extensive documentation on how to play such tricks with REEL.<br>
Or would I have to rebuild a complete ligand with this SCALES?<br>
<br>
Other suggestion how to get my ligand are also welcome.<br>
<br>
Thanks<br>
<br>
André<br>
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