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 mercredi 4 juin 2008, Pascal Muller wrote:
> The only difference I see is atoms order. To answer to Vincent, I
> think test.mol is already a 3D conformation, but the molecule is
> mostly planar. Prodrg doesn't transform from 2D to 3D.

  In the test.mol and babel.pdb file, all non-H atoms have 0 as z-coordinate,
but not in the prodrg: the -CH2-OH ligand has its OH group out of the ring
plane, and the O-CH3 ligand has its methyl group out-of-plane.
 ... So there has been a 2D->3D transform, even if it does not really break
the molecule, just reduces steric problems.

  btw rasmol reads both pdb's fine. And both molecules look fine too except
for some steric problems in the original 2D structure.

> By the way, when converting a ligand mol2 in cif, it lost the bond
> type information (openbabel 2.1.1). Is there a way to keep bond type
> in .cif file when converting with openbabel ? Because mol2->pdb->cif
> with eg pdb2cif program is not very useful...

  Well, there is a _chemical_conn_bond_type CIF keyword which we could use for
that. Of course it would require the software that reads the CIF to
understand that keyword.
  Would that be OK ?

(There is also a _geom_bond_multiplicity but that does seem to correspond to a
number of bonds rather than a bond type.)

  See the definitions @
http://www.iucr.org/iucr-top/cif/cifdic_html/1/cif_core.dic/index.html
 
        Vincent
--
Vincent Favre-Nicolin                   http://vincefn.net
UniversitĂ© Joseph Fourier       http://www.ujf-grenoble.fr
CEA/ Institut Nanosciences & CryogĂ©nie  http://inac.cea.fr
ObjCryst & Fox             http://objcryst.sourceforge.net

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