Nigel, crazy thing, I repeated the ELBOW run with the exact same smiles for: 1.10-2155 and 1.10.1-2155 and it gives different results. With the newer version addressing the sugar correctly, as you said. Thanks! André André C. Stiel, Ph.D. (PI) +49 (0) 89 3187 3972 Office: Building 57, Room 009 Cell Engineering Group Institute of Biological and Medical Imaging

Am 21.01.2016 um 19:12 schrieb Nigel Moriarty :

Andre

I note that you use 1.10-2155. It works correctly with the latest nightly build. You could also try 1.10.1-2155 if you are more comfortable with major releases. Version 1.10-2155 was replaced with 1.10.1-2155.

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov http://cci.lbl.gov/ On Wed, Jan 20, 2016 at 11:51 PM, andre.stiel mailto:[email protected]> wrote: Hi Nigel, thanks for your time, here you go. And I attached the .cif I obtain from ELBOW

Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de http://www.helmholtz-muenchen.de/ Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

http://www.chemspider.com/Chemical-Structure.28639235.html?rid=ac73301e-ee97-480b-bec0-0ae6de7a505f&page_num=0 http://www.chemspider.com/Chemical-Structure.28639235.html?rid=ac73301e-ee97-480b-bec0-0ae6de7a505f&page_num=0 CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O[C@@H]1[C@@H]([C@@H]([C@H]([C@@H]([C@H]1O)O)O)O)O)OC(=O)CCCCCCC/C=C\C/C=C\CCCCC

cheers André

...

Am 20.01.2016 um 21:40 schrieb Nigel Moriarty mailto:[email protected]>:

Its is very strange that the SMILES string is resulting in an aromatic ring. Can you send me the SMILES?

Cheers

Nigel

--- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 tel:510-486-5709 Email : [email protected] mailto:[email protected] Fax : 510-486-5909 tel:510-486-5909 Web : CCI.LBL.gov http://cci.lbl.gov/ On Sat, Jan 9, 2016 at 3:38 AM, andre.stiel mailto:[email protected]> wrote: Hi,

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. 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): 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. 2. Can I chop the sugar part from the .CIF of another ligand and somehow fuse it to my tails? 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? I have not found a very extensive documentation on how to play such tricks with REEL. Or would I have to rebuild a complete ligand with this SCALES?

Other suggestion how to get my ligand are also welcome.

Thanks

André

Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de http://www.helmholtz-muenchen.de/ Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671

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Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.) Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671