> Seems I am having a bad week with coot.
Thanks for several very quick offers to send me a mol2 file or
other alternative description of my ligand, but I'm fine on that score.
I have a cif dictionary from the Grade server that works
in both coot and refmac.
I just wanted to point out a glitch in coot's built-in toolchain.
Ethan
>
> The smiles string
>
> NC1=C2C(N(CC6(COC6)CO)N=C2C3=CC=C(N=C(OC5CC5)C=C4)C4=C3)=NC=N1
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> describes the compound in the attached file 1671.png.
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>
>
> However when I feed this string to coot it instead constructs the
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> molecule shown in the file coot-molecule.png.
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> Note that the terminal hydroxyl has jumped two carbons over
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> and a CH2 group has been lost altogether.
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>
>
> If I sketch this molecule ab initio in Calculate->Ligand Builder
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> then when I select "Tidy up" it is mangled into the same
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> incorrect isomer as the mis-interpreted SMILES string.
>
>
>
> Same thing if I ask coot to export a SMILES string and
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> read it back in again.
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>
>
> Ethan
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>
> --
>
> Ethan A Merritt
>
> Biomolecular Structure Center, K-428 Health Sciences Bldg
>
> MS 357742, University of Washington, Seattle 98195-7742
>
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
