[phenixbb] ligand modification / combination in REEL

andre.stiel andre.stiel at helmholtz-muenchen.de
Sat Jan 9 03:38:59 PST 2016


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.



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