Seems I am having a bad week with coot.
The smiles string
NC1=C2C(N(CC6(COC6)CO)N=C2C3=CC=C(N=C(OC5CC5)C=C4)C4=C3)=NC=N1
describes the compound in the attached file 1671.png.
However when I feed this string to coot it instead constructs the
molecule shown in the file coot-molecule.png.
Note that the terminal hydroxyl has jumped two carbons over
and a CH2 group has been lost altogether.
If I sketch this molecule ab initio in Calculate->Ligand Builder
then when I select "Tidy up" it is mangled into the same
incorrect isomer as the mis-interpreted SMILES string.
Same thing if I ask coot to export a SMILES string and
read it back in again.
Ethan
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
