[phenixbb] ligand modification / combination in REEL

Nigel Moriarty nwmoriarty at lbl.gov
Wed Jan 20 12:40:46 PST 2016

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



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

On Sat, Jan 9, 2016 at 3:38 AM, andre.stiel <
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
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