I'm not sure what you mean by pybel or Python to convert to PDB. Do you use the 3D coordinate generation in Pybel? Do you use 2D coordinate generation in Python?
If you're using 3D coordinate generation in Python, it's the same code as babel --gen3d. In this case, I would suspect you have a very old version of libopenbabel with your Python modules. Hope that helps, -Geoff On May 24, 2012, at 6:36 AM, Ting Zhou wrote: > Dear all, > > when I use pybel or openbabel for python to convert > "c1ccc2c(c1)n(c(=O)o2)CC(=O)NC[C@@H]3COc4ccccc4O3" into a pdb file, I > always get a cis amide, which is not good. However when I use the > command "babel -ismi xxx.smi -opdb xxx.pdb --gen3D", I get the correct > trans amide. Does someone know the reason and how to get a trans amide > with the python module. > > Best wishes, > Ting ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
