Sure. On 16 October 2012 16:54, Scott McKechnie <mckec...@tcd.ie> wrote: > Excellent, working perfectly now, many thanks. I used your calcrmsd.py > script from an earlier thread as a starting point for my scripts, so to > avoid any future problems a simple canonical conversion of the conformers > can be added in? This might be repetitive if done already but it would save > any potential problems. > > Best wishes, > > Scott > > > On 16 October 2012 16:40, Noel O'Boyle <baoille...@gmail.com> wrote: >> >> See the docs: >> "When aligning molecules, the atoms of the two molecules must be in >> the same order for the results to be sensible." >> >> Try rearranging the atoms into canonical order first: >> obabel C:\Users\noel\Desktop\conf1.mol2 -O tmp.mol2 --canonical >> obabel C:\Users\noel\Desktop\conf2.mol2 -O tmp2.mol2 --canonical >> >> - Noel >> >> On 16 October 2012 16:23, scott_m <js...@cam.ac.uk> wrote: >> > Dear all, >> > >> > I have been using OBAlign() to get rmsd values between conformers but >> > just >> > came across an erroneous value of 3.14 for the molecule N-Acryloyl >> > glycine, >> > the CSD function tormat gives a rmsd of 0 for the two conformers. Any >> > idea >> > what is going wrong here? I've attached the two mol2 files. >> > >> > Thanks, >> > >> > Scott >> > conf1.mol2 <http://forums.openbabel.org/file/n4655579/conf1.mol2> >> > conf2.mol2 <http://forums.openbabel.org/file/n4655579/conf2.mol2> >> > >> > >> > >> > -- >> > View this message in context: >> > http://forums.openbabel.org/OBAlign-error-tp4655579.html >> > Sent from the General discussion mailing list archive at Nabble.com. >> > >> > >> > ------------------------------------------------------------------------------ >> > Don't let slow site performance ruin your business. Deploy New Relic APM >> > Deploy New Relic app performance management and know exactly >> > what is happening inside your Ruby, Python, PHP, Java, and .NET app >> > Try New Relic at no cost today and get our sweet Data Nerd shirt too! >> > http://p.sf.net/sfu/newrelic-dev2dev >> > _______________________________________________ >> > OpenBabel-discuss mailing list >> > OpenBabel-discuss@lists.sourceforge.net >> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss >> >
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