Enrico, At the time it was written, the RMS code was tested against other tools and confirmed to produce equivalent numbers. Our superposition algorithm is implemented using center of geometry translation followed by an iterative three-way Jacobi rotation of the correlation tensor to shrink the off-diagonals to within an adjustable tolerance within an adjustable number of cycles. RMS is then computed using the converged rotation matrix. I believe VMD has since adopted our code for this task because of its robustness, though you'd have to check their sources to be sure (at the time John pointed out a minor bug that has since been fixed). PyMOL's dynamic programming 1D/3D "align"-ment algorithm has not been subjected to similar head-to-head testing, but the output of an adaptive fitting routine is subjective and to some extent arbitrary. In other words, though the algorithm itself is definite, the decisions it makes in terms of number of refinement cycles, and the RMS cutoff for outliers will very based on the shape and noise in the distributions. Other "magic fit" algorithms will almost certainly produce slightly different fits because they make different arbitrary decisions.
Ultimately, with PyMOL the proof is in what you see on the screen. If two proteins aren't well superimposed, that fact should be painfully obvious. As for publishing numbers, the safest way is to cite the program, version, and the number and identity of atoms over which the RMS value was generated. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Enrico Malito > Sent: Friday, February 24, 2006 3:30 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] align/fit > > Hi all, > I'm using macPyMOL 0.99rc1 and found very useful the commands > align&pair_fit to do superposition. I'm just wondering which > specific algorithm they use, if somebody never used them to > do superposition of Ca trace for publications, and if there > is a specific reference to them. > Thanks in advance, > Enrico. > > -- > Enrico Malito > Dept. of Biochemistry and Molecular Genetics University of > Illinois at Chicago 900 S. Ashland Ave. > Molecular Biology Research Building, Room 1116 Chicago, IL > 60607 - U.S.A. > Tel (312) 996-6299 > Fax (312) 355-4535 > > > > ------------------------------------------------------- > This SF.Net email is sponsored by xPML, a groundbreaking > scripting language that extends applications into web and > mobile media. Attend the live webcast and join the prime > developer group breaking into this new coding territory! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=110944&bid=241720&; > dat=121642 > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
