Re: [Open Babel] cif to pdb

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 h

Re: [Open Babel] cif to pdb

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 -- View this message in context: http://forums.openbabel.org/cif-to-pdb-tp4659688p4659690.html Sent fro

Re: [Open Babel] cif to pdb

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 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

[Open Babel] cif to pdb

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