[phenixbb] ligand modification / combination in REEL

[Nigel Moriarty]

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     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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