[phenixbb] ligand modification / combination in REEL

Thu Jan 28 12:55:55 PST 2016

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 <nwmoriarty at lbl.gov>:
> 
> 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 : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov <http://cci.lbl.gov/>
> On Wed, Jan 20, 2016 at 11:51 PM, andre.stiel <andre.stiel at helmholtz-muenchen.de <mailto:andre.stiel at helmholtz-muenchen.de>> 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 at H](COP(=O)(O)O[C@@H]1[C@@H]([C@@H]([C at H]([C@@H]([C at 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 <nwmoriarty at lbl.gov <mailto:nwmoriarty at lbl.gov>>:
>> 
>> 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 : NWMoriarty at LBL.gov <mailto:NWMoriarty at lbl.gov>
>> 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 <andre.stiel at helmholtz-muenchen.de <mailto:andre.stiel at helmholtz-muenchen.de>> 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

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