Well, that's the reason right there. You have several Open Babel installations, and there is interference. My advice is to delete all of your Open Babel installations, including related Python files. Then install the whole thing locally (including the Python bindings), set your environment variables appropriately, and then test "obabel -H pdb".
- Noel On 6 September 2011 11:22, Daniel Sindhikara <[email protected]> wrote: > Yes it recognizes it, when I check the binary in my unzip directory, > however, it does not. > > 19:21:35 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ obabel -H pdb > Protein Data Bank format > Read Options e.g. -as > s Output single bonds only > b Disable bonding entirely > c Ignore CONECT records > > > Specification at: http://www.wwpdb.org/docs.html > 19:21:39 [danpc: ~/Downloads/openbabel-2.3.0/bin]$ ./obabel -H pdb > Format type: was not recognized > > > On Tue, Sep 6, 2011 at 7:07 PM, Noel O'Boyle <[email protected]> wrote: >> >> Does "obabel -H pdb" show the PDB format? >> >> On 6 September 2011 07:16, Daniel Sindhikara <[email protected]> wrote: >> > Hello, >> > After a long hiatus I got back on this project. After following the >> > instructions I successfully installed openbabel/pybel. >> > However, when I tried testing the program I got a funny error, "pdb is >> > not a >> > recognised OpenBabel format". >> > >> > Enthought Python Distribution -- www.enthought.com >> > Version: 7.1-1 (64-bit) >> > >> > Python 2.7.2 |EPD 7.1-1 (64-bit)| (default, Jul 3 2011, 15:56:02) >> > [GCC 4.0.1 (Apple Inc. build 5493)] on darwin >> > Type "packages", "demo" or "enthought" for more information. >> >>>> import pybel as pb >> >>>> testmolecule = pb.readfile("pdb","mai.pdb").next() >> > Traceback (most recent call last): >> > File "<stdin>", line 1, in <module> >> > File >> > >> > "/Users/sindhikara/Tools/openbabel-install/lib/python2.7/site-packages/pybel.py", >> > line 90, in readfile >> > raise ValueError("%s is not a recognised OpenBabel format" % format) >> > ValueError: pdb is not a recognised OpenBabel format >> > >> > >> > Further, checking the formats variable: >> >>>> pb.informats >> > {} >> > >> > It was empty. >> > Any clues into why this would happen? >> > >> > Thanks in advance! >> > -Dan >> > >> > >> > -- >> > Dr. Daniel J. Sindhikara >> > Institute for Molecular Science >> > E-mail: [email protected] >> > Website: http://sites.google.com/site/dansindhikara/ >> > -- >> > >> > >> > ------------------------------------------------------------------------------ >> > Special Offer -- Download ArcSight Logger for FREE! >> > Finally, a world-class log management solution at an even better >> > price-free! And you'll get a free "Love Thy Logs" t-shirt when you >> > download Logger. Secure your free ArcSight Logger TODAY! >> > http://p.sf.net/sfu/arcsisghtdev2dev >> > _______________________________________________ >> > OpenBabel-scripting mailing list >> > [email protected] >> > https://lists.sourceforge.net/lists/listinfo/openbabel-scripting >> > >> > > > > > -- > Dr. Daniel J. Sindhikara > Institute for Molecular Science > E-mail: [email protected] > Website: http://sites.google.com/site/dansindhikara/ > -- > ------------------------------------------------------------------------------ Special Offer -- Download ArcSight Logger for FREE! Finally, a world-class log management solution at an even better price-free! And you'll get a free "Love Thy Logs" t-shirt when you download Logger. Secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsisghtdev2dev _______________________________________________ OpenBabel-scripting mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
