[Open Babel] Smiles conversion problems with Ion and Zwitterion

Dear all, The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a .cif file to .smi and subsequent generation of coordinates from the .smi file results in the addition of an extra H to one of the ring C atoms. The original cif formula is C7H8N2O4 but this changes to C7H9N2O4,

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

On 30/11/2012 12:03, scott_m wrote: Dear all, The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate from a .cif file to .smi and subsequent generation of coordinates from the .smi file results in the addition of an extra H to one of the ring C atoms. The original cif formula is

Re: [Open Babel] Tidying up files

Hi, I never knew this option existed, as far as I can tell it is not mentioned on the wiki and it does not appear when you type babel -H It does look as if it could be exactly what I want ;-) Cheers ChrisS On 30 Nov 2012, at 14:53, openbabel-discuss-requ...@lists.sourceforge.net wrote: