Hi Martin, I suggest to superpose the conformations with Theseus and use PyMOL for visualization.
http://www.theseus3d.org/ You may also try the PyMOL command "alignto" (not available in older PyMOL version), but I expect better results with Theseus. Cheers, Thomas Martin Breugst wrote, On 04/12/12 19:33: > Dear PyMOL users: > > I want to use PyMOL to generate a nice figure showing six different > transition state structures superimposed in one single picture. I have > already tried to use the commands pair_fit, overlay, and align but I did > not get the results I have expected. Is there any way to tell PyMOL to > overlay three atoms of each structure (in order to define a uniform > plane) and if there is, what specific command do I have to use? > > Thank you very much for your help and suggestions, > > Cheers, > > Martin -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
