Hi, Cealign's the way to go here. If you have a massively powerful computer you can continue turning off the "guide" which selects special carbons to "guide" the alignment. We need to improve/extend for nucleic acids. Would someone mind filing a feature request on the open-source bug tracker? We also need to standardize the alignment interface as more and more alignment algorithms appear.
Cheers, -- Jason On Fri, Jan 13, 2012 at 8:52 AM, David Hall <li...@cowsandmilk.net> wrote: > 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ 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
