<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Nigel,<div class=""><br class=""></div><div class="">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.</div><div class="">Thanks!</div><div class=""><br class=""></div><div class="">André</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">André C. Stiel, Ph.D. (PI)</div><div class=""><br class=""></div><div class="">+49 (0) 89 3187 3972</div><div class="">Office: Building 57, Room 009</div><div class=""><br class=""></div><div class="">Cell Engineering Group</div><div class="">Institute of Biological and Medical Imaging </div><div class=""><br class=""></div></div></div></div></div></div></div></div></div><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">Am 21.01.2016 um 19:12 schrieb Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" class="">nwmoriarty@lbl.gov</a>>:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Andre<div class=""><br class=""></div><div class="">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.</div></div><div class="gmail_extra"><br clear="all" class=""><div class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Cheers<div class=""><br class=""></div><div class="">Nigel<div class=""><br class=""></div><div class="">---</div><div class="">Nigel W. Moriarty<br class="">Building 33R0349, Physical Biosciences Division<br class="">Lawrence Berkeley National Laboratory<br class="">Berkeley, CA 94720-8235<br class="">Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@lbl.gov" class="">NWMoriarty@LBL.gov</a><br class="">Fax : 510-486-5909 Web : <a href="http://cci.lbl.gov/" target="_blank" class="">CCI.LBL.gov</a></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Wed, Jan 20, 2016 at 11:51 PM, andre.stiel <span dir="ltr" class=""><<a href="mailto:andre.stiel@helmholtz-muenchen.de" target="_blank" class="">andre.stiel@helmholtz-muenchen.de</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class=""><div class="">Hi Nigel,</div><div class="">thanks for your time, here you go. And I attached the .cif I obtain from ELBOW</div><span class="">
<br class="">
<div class="">
Helmholtz Zentrum Muenchen<br class="">
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)<br class="">
Ingolstaedter Landstr. 1<br class="">
85764 Neuherberg<br class="">
<a href="http://www.helmholtz-muenchen.de/" target="_blank" class="">www.helmholtz-muenchen.de</a><br class="">
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe<br class="">
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.)<br class="">
Registergericht: Amtsgericht Muenchen HRB 6466<br class="">
USt-IdNr: DE 129521671<br class="">
</div>
<br class="">
</span></div><br class=""><div style="word-wrap:break-word" class=""><div class=""></div><div class=""><br class=""></div><a href="http://www.chemspider.com/Chemical-Structure.28639235.html?rid=ac73301e-ee97-480b-bec0-0ae6de7a505f&page_num=0" target="_blank" class="">http://www.chemspider.com/Chemical-Structure.28639235.html?rid=ac73301e-ee97-480b-bec0-0ae6de7a505f&page_num=0</a><div class=""><span style="font-family:Arial;font-size:16px;line-height:20px;background-color:rgb(244,243,242)" class="">CCCCCCCCCCCCCCCC(=O)</span><span style="font-family:Arial;font-size:16px;line-height:20px;background-color:rgb(244,243,242)" class="">OC[C@H](COP(=O)(O)O[</span><span style="font-family:Arial;font-size:16px;line-height:20px;background-color:rgb(244,243,242)" class="">C@@H]1[C@@H]([C@@H](</span><span style="font-family:Arial;font-size:16px;line-height:20px;background-color:rgb(244,243,242)" class="">[C@H]([C@@H]([C@H]1O</span><span style="font-family:Arial;font-size:16px;line-height:20px;background-color:rgb(244,243,242)" class="">)O)O)O)O)OC(=O)CCCCC</span><span style="font-family:Arial;font-size:16px;line-height:20px;background-color:rgb(244,243,242)" class="">CC/C=C\C/C=C\CCCCC</span></div><div class=""><div class=""><font face="Arial" size="3" class=""><span style="background-color:rgb(244,243,242)" class=""><br class=""></span></font></div><div class=""><font face="Arial" size="3" class=""><span style="background-color:rgb(244,243,242)" class="">cheers</span></font></div><div class=""><font face="Arial" size="3" class=""><span style="background-color:rgb(244,243,242)" class="">André</span></font></div><div class=""><br class="">
</div>
<br class=""><div class=""><blockquote type="cite" class=""><div class="">Am 20.01.2016 um 21:40 schrieb Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" target="_blank" class="">nwmoriarty@lbl.gov</a>>:</div><br class=""><div class=""><div dir="ltr" class="">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" class=""><div class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Cheers<div class=""><br class=""></div><div class="">Nigel<div class=""><br class=""></div><div class="">---</div><div class="">Nigel W. Moriarty<br class="">Building 33R0349, Physical Biosciences Division<br class="">Lawrence Berkeley National Laboratory<br class="">Berkeley, CA 94720-8235<br class="">Phone : <a href="tel:510-486-5709" value="+15104865709" target="_blank" class="">510-486-5709</a> Email : <a href="mailto:NWMoriarty@lbl.gov" target="_blank" class="">NWMoriarty@LBL.gov</a><br class="">Fax : <a href="tel:510-486-5909" value="+15104865909" target="_blank" class="">510-486-5909</a> Web : <a href="http://cci.lbl.gov/" target="_blank" class="">CCI.LBL.gov</a></div></div></div></div></div></div></div>
<br class=""><div class="gmail_quote">On Sat, Jan 9, 2016 at 3:38 AM, andre.stiel <span dir="ltr" class=""><<a href="mailto:andre.stiel@helmholtz-muenchen.de" target="_blank" class="">andre.stiel@helmholtz-muenchen.de</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br class="">
<br class="">
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 class="">
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 class="">
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 class="">
2. Can I chop the sugar part from the .CIF of another ligand and somehow fuse it to my tails?<br class="">
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 class="">
I have not found a very extensive documentation on how to play such tricks with REEL.<br class="">
Or would I have to rebuild a complete ligand with this SCALES?<br class="">
<br class="">
Other suggestion how to get my ligand are also welcome.<br class="">
<br class="">
Thanks<br class="">
<br class="">
André<br class="">
<br class="">
Helmholtz Zentrum Muenchen<br class="">
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)<br class="">
Ingolstaedter Landstr. 1<br class="">
85764 Neuherberg<br class="">
<a href="http://www.helmholtz-muenchen.de/" rel="noreferrer" target="_blank" class="">www.helmholtz-muenchen.de</a><br class="">
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe<br class="">
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.)<br class="">
Registergericht: Amtsgericht Muenchen HRB 6466<br class="">
USt-IdNr: DE 129521671<br class="">
<br class="">
<br class="">
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Helmholtz Zentrum Muenchen<br>
Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH)<br>
Ingolstaedter Landstr. 1<br>
85764 Neuherberg<br>
www.helmholtz-muenchen.de<br>
Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe<br>
Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Dr. Alfons Enhsen, Renate Schlusen (komm.)<br>
Registergericht: Amtsgericht Muenchen HRB 6466<br>
USt-IdNr: DE 129521671<br>
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