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cif to pdb

user_openbabel
Hi

I am triyng to convert cif file obtained from x-ray to pdb file to add hydrogen atoms of water. I am using Avogadro but at the end in the pdb file I lose some bonds (connectivity).

Does anyone know how to solve this problem?
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Re: cif to pdb

Noel O'Boyle
Administrator
The cif file doesn't contain connectivity so Open Babel has to guess.
Sometimes it guess correctly.

- Noel

On 25 January 2017 at 23:46, user_openbabel <[hidden email]> wrote:

> Hi
>
> I am triyng to convert cif file obtained from x-ray to pdb file to add
> hydrogen atoms of water. I am using Avogadro but at the end in the pdb file
> I lose some bonds (connectivity).
>
> Does anyone know how to solve this problem?
>
>
>
> --
> View this message in context: http://forums.openbabel.org/cif-to-pdb-tp4659688.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
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Re: cif to pdb

user_openbabel
The reason why I am using Avogadro is that I want to add hydrogen atoms to oxygen  in a  cif file obtained from x-ray with keeping symmetry.  Is there any suggestion how to do that?

Hanieh
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Re: cif to pdb

Geoff Hutchison
Noel's point is that a CIF file (and a PDB) do not necessarily retain connectivity.

> The reason why I am using Avogadro is that I want to add hydrogen atoms to
> oxygen  in a  cif file obtained from x-ray with keeping symmetry.  Is there
> any suggestion how to do that?


Not necessarily. The hydrogen addition code does not track the space group symmetry. I would probably try CCDC Mercury.

-Geoff
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