Reply – Re: problem with sdf->pdb conversion
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Re: problem with sdf->pdb conversion
— by Vincent Favre-Nicolin-2 Vincent Favre-Nicolin-2
On mardi 03 juin 2008, Roni Gordon wrote:
> 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.

   In the attached test.mol, only 2D coordinates are included ? This can't be
the intermediate mol file used as input ? Unless prodrg does the 2D->3d
transform ?

Vincent Favre-Nicolin
Université Joseph Fourier
ObjCryst & Fox :

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