Hi Chris, Thanks for your reply and apologies for the delayed response. Converting the cif to xyz and viewing the molecule shows the correct structure but converting the xyz file to smi and then generating coordinates and viewing shows the addition of a H atom.
The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1 The other smiles is: C(=O)([C@@H](CC(=O)O)N1C=CNC1)O One strange feature is that there doesn't appear to be a double bond between the N atom in the ring and the C atom, leaving the C atom with only three bonds. The smiles conversion seems to want to add a H here to get the correct bonding. Similarly for an ion, using smiles conversion results in the addition of H's. I've attached the cif file. Many thanks, Scott On 30 November 2012 14:53, Chris Morley <c.mor...@gaseq.co.uk> wrote: > 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 C7H8N2O4 but this changes to C7H9N2O4, which is > no > > longer a zwitterion. > > > > I also noticed that converting an ion to smi and then from smi to xyz > > resulted in the addition of hydrogen atoms. Can this be avoided? > > > > Is the smi conversion of ions and zwitterions known to cause problems? > > Getting added hydrogens right is a recurrent issue. However the > conversion from SMILES to xyz (and other formats) seems ok. Your problem > may be in the conversion of the cif file, but you will need to append it > for somebody (probably not me) to debug. > > obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1 > (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz --gen3D --title "" > --append formula > 21 > C7H8N2O4 > C 2.45602 0.70570 1.56344 > O 3.44592 0.48586 2.25208 > O 1.43656 1.46670 2.00415 > C 2.26356 0.11437 0.19030 > C 3.14546 0.74947 -0.88078 > H 2.84831 0.31396 -1.84634 > C 2.83038 2.27406 -0.99631 > O 1.67090 2.60592 -0.61087 > O 3.79441 2.97728 -1.40748 > N 4.60137 0.42805 -0.71225 > C 5.35900 0.94762 0.25841 > N 6.58789 0.46124 0.10334 > H 7.33992 0.61660 0.75954 > C 6.69161 -0.15933 -1.12882 > C 5.43119 -0.14873 -1.66026 > H 0.84536 1.76580 1.27272 > H 1.20439 0.19509 -0.08254 > H 2.46795 -0.95767 0.27113 > H 5.04774 1.61643 1.05753 > H 7.65241 -0.48371 -1.46628 > H 5.01646 -0.45579 -2.60586 > 1 molecule converted > > Chris > > > ------------------------------------------------------------------------------ > Keep yourself connected to Go Parallel: > TUNE You got it built. Now make it sing. Tune shows you how. > http://goparallel.sourceforge.net > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > >
SOXGES.search2.cif
Description: Binary data
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