Tom, Because the number of atoms in the alignment can vary with each pairwise structure comparison, the RMS number returned by align cannot be considered valid criterion except perhaps if presented along with the number of atoms in each comparison. E.g.:
RMS over X atoms 0.5 1451 0.3 1273 0.4 1343 But remember, each final RMS value will involve a different set of atoms...and that's the root of the problem...there's no common reference point. Therefore, I must recommand against using 'align' for this purpose -- it's just not the right tool for the job. Cheers, Warren > -----Original Message----- > From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] > Sent: Thursday, October 29, 2009 4:56 PM > To: Warren DeLano > Cc: Thomas Evangelidis; pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] how to get RMSD from align command > > Warren, > > before I write something incorrect into Methods section, do you think > the overall RMSD returned by align command is a valid criterion to > select which structure of the family is most similar? > > Tom > > > Tom, > > > > Apologies for the confusion, but there really isn't any way to > > measure overall structural similarity in PyMOL other than pair_fit, > > but you have to do the work of explicitly stating which pairs are to > > be aligned. > > > > The pair_fit selections don't have to be identical, but they do have > > to correspond in a pairwise fashion. In other words, you can > > compare any number of C-alpha positions so long as the same number > > of atomic positions are specified in each structure. > > > > Cheers, > > Warren > > > > -----Original Message----- > > From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] > > Sent: Thu 10/29/2009 5:24 AM > > To: Warren DeLano > > Cc: pymol-users@lists.sourceforge.net > > Subject: Re: [PyMOL] how to get RMSD from align command > > > > Hi Warren, > > > > Now I am more confused. I used align command to measure the overall > > RMSD between homologous structures. Apparently align is not > > appropriate if not sufficient sequence similarity is present. I later > > came across CEalign plugin, which does structure-based > > superimposition. This command also returns an RMSD value, which > > happens to be higher for the set of homologous structures I analysed. > > Based on this I concluded that align command is more appropriate to > > measure measure structural similarity, but I'm not sure now. > > > > My objective is to select between a small set of homologous structures > > (co-crystallized with ligands), the one with the highest structural > > similarity and use it to place a dummy ligand into one where it's > > missing. I.e. "1ebh" lacks a ligand, so I compared it with "1ebg", > > "1els", "1one", "2one", "5enl", "6enl", "7enl" which have > > co-crystallized ligands. According to both align and cealign, 5ENL is > > the most similar with overall RMSD 0.246 and 0.420907 respectively. > > The question is which command produces the best superimposition > > provided that these proteins belong to the enolase family and thus > > have high sequence and structural similarity? Based on the RMSD > > values, align does, but as you said this value pertains to only a > > subset of atoms after refinement. > > > > Apparently pair_fit command cannot be used for my purpose as it > > requires identical selections. > > > > Tom > > > > > >> Tom, > >> > >> The complication with cmd.align() is that it is doing a whole lot > >> more than a simple alignment. The first number is in fact the RMS, > >> but it covers only the subset of the input atoms remaining after > >> refinement is completed. The count of aligned atoms is the second > >> field. > >> > >> If you're looking for exact RMS fit values over a well-defined set > >> of atoms, try using cmd.pair_fit(sele1, sele2) instead, for example: > >> > >> load $TUT/1hpv.pdb > >> > >> create loopA, A/46-55/ > >> > >> create loopB, B/46-55/ > >> > >> show sticks, loop* > >> > >> print cmd.pair_fit("loopA////CA", "loopB////CA") > >> > >> Cheers, > >> Warren > >> > >> -----Original Message----- > >> From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr] > >> Sent: Wed 10/28/2009 8:09 PM > >> To: pymol-users@lists.sourceforge.net > >> Subject: [PyMOL] how to get RMSD from align command > >> > >> Simple question, it must have been answered before but couldn't find > >> it so far: > >> > >> how can I get the RMSD value from the align command in a python > >> script? cmd.align() returnes a tuple of 8 numbers and none of them is > >> the actual RMSD value I get when I align these 2 structures manually. > >> > >> thanks,Tom > >> > >> > >> ----------------------------------------------------------------------- > ------- > >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA > >> is the only developer event you need to attend this year. Jumpstart > your > >> developing skills, take BlackBerry mobile applications to market and > stay > >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! > >> http://p.sf.net/sfu/devconference > >> _______________________________________________ > >> 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 > >> > >> > >> > >> > >> > >> > >> > > > > > > ----- End message from war...@delsci.com ----- > > > > > > > > ------------------------------------------------------------------------ > ------ > > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > > is the only developer event you need to attend this year. Jumpstart your > > developing skills, take BlackBerry mobile applications to market and > stay > > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > > http://p.sf.net/sfu/devconference > > _______________________________________________ > > 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 > > > > > > > > > > > > > > > > > ----- End message from war...@delsci.com ----- > > > > > ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. 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