I decided to dig in and answer my own question about what the seq argument does.
seq: positive means use sequence and structure 0 means use only structure negative means only use sequence For super, I assume you only want to use structure, so messing with that argument is silly advice. The problem is that when you use structure, SelectorGetResidueVLA gets an argument of true for ca_only Obviously, nucleic acids don't have any c-alphas, so when SelectorGetResidueVLA searches for residues using strcmp(ai1->name, "CA") == 0 , pymol finds no residues in the selections, then complains to you about "invalid selections" because it thinks the selections are empty. -David On Fri, Jan 13, 2012 at 8:37 AM, David Hall <li...@cowsandmilk.net> wrote: > I think super does not handle nucleic acid sequences well. > > super ec-5s, hm-5s, seq=-1 > > works. > > I'll leave it to someone else to say what that does. I just noted > that align works, super doesn't, guessed it had to do with sequence > and noted that for align, the default value of seq was -1 and for > super, the default value was 0. > > -David > > On Fri, Jan 13, 2012 at 7:44 AM, QT <rdirect...@gmail.com> 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 >> _______________________________________________ >> 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 ------------------------------------------------------------------------------ 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
