Hi James, The "super" method requires CA atoms in the selection because it aligns based on the backbone trace.
You should use "rms" or "rms_cur" to get a side chain RMSD. Cheers, Thomas On 12 Jul 2016, at 10:10, James Starlight <jmsstarli...@gmail.com> wrote: > Dear pymol users! > > I need to estimate how the side-chains dynamics are differs in MD > compared to X-ray structure. > > Assuming that I have 2 structures one from md and another from X-ray > and I select Sidechains from the both as obj1 and obj02 > select xray &! n. n+ca+c+o > select md &! n. n+ca+c+o > > now trying to align both objects with any method I obtain error like > > PyMOL>super obj01, obj02 > ExecutiveAlign: invalid selections for alignment. > > How I can fix it? > > James -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev _______________________________________________ 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
