Reply – Re: problem with sdf->pdb conversion
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Re: problem with sdf->pdb conversion
— by Roni Gordon Roni Gordon
Well, I'm starting from an SDF file, which I presume has correct 3D
coordinates; the reason I used MOL as an intermediate was to use PRODRG
to produce a "valid" PDB file that I know is correct (this was my
previous procedure before I discovered OpenBabel).

I've attached the two different PDB files from babel v2.1.1 vs prodrg
using the same MOL input (in my case, I've included Hs, but it doesn't
seem make a difference).  My modeling software (Coot) doesn't connect
the atoms in the same way, so I'm confused.

Roni

On Mon, 2008-06-02 at 12:55 -0400, Geoffrey Hutchison wrote:

> 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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test.mol (1K) Download Attachment
test-babel.pdb (3K) Download Attachment
test-prodrg.pdb (2K) Download Attachment