Hi Quyen, unfortunately, the super command does a selection on CA atoms internally. Maybe this should be considered a bug. If you have the latest svn version of PyMOL, I recommend cealign for this task (older versions of cealign do select CA atoms as well).
Cheers, Thomas On 01/13/2012 01:44 PM, QT wrote: > Dear all, > > I'm having a tough time using the super command correctly. I want to > superimpose two 5S structures. > > In pymol, I'll do the following > > load 2awb.pdb > load 3cc2.pdb > > create ec-5s, 2awb and chain a > create hm-5s, 3cc2 and chain 9 > > If I issue /super ec-5s, hm-5s/ then the cryptic error "ExecutiveAlign: > invalid selections for alignment. would appear." > > Issuing /super /ec-5s//a, /hm-5s//9/ does not help either. > > What am I missing? /align /ec-5s//a, /hm-5s//9 /works just fine though... > > Any help from the community would be very appreciated. > > Best, > Quyen > > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Mar 27 - Feb 2 > Save $400 by Jan. 27 > Register now! > http://p.sf.net/sfu/rsa-sfdev2dev2 -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen ------------------------------------------------------------------------------ RSA(R) Conference 2012 Mar 27 - Feb 2 Save $400 by Jan. 27 Register now! http://p.sf.net/sfu/rsa-sfdev2dev2 _______________________________________________ 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
