Reply – Re: problem with sdf->pdb conversion
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Re: problem with sdf->pdb conversion
— by Geoffrey Hutchison Geoffrey Hutchison

On May 30, 2008, at 6:28 PM, Roni Gordon wrote:

> extract is correct by writing to an intermediate MOL file; however,  
> the
> PDB file that is produced is quite incorrect, with improper
> connectivity, etc., and the corresponding CIF file is also incorrect.

I don't think translating to a CIF is a good idea here -- you're  
taking a MOL file with 2D coordinates only and expecting to have good  
fractional 3D coordinates. As far as PDB, I'd be curious to know what  
you mean by "quite incorrect." The PDB file I generate (attached) has  
connect records, HETATOM, etc. If you can be a bit more specific  
(e.g., version of Open Babel, etc. as mentioned previously) it would  
certainly help.

Cheers,
-Geoff




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