Vince, I started to compile and answer for you, but then it got too long to be appropriate for the list. For a discussion of "fit" and optimal alignment please see the wiki page:
http://www.pymolwiki.org/index.php/Cealign#Fit_vs._optAlign Briefly, PyMOL's "fit" is fast and works well. I believe it's based off the Jacobian, which iteratively arrives at the solution (to within some tiny error). If you have to use something with a known reference then check out the "optAlign" function from the qkabsch.py file that comes with the CEalign package: http://www.pymolwiki.org/index.php/Cealign If not, you can just use "fit" and avoid installing new software. :-) HTH, -- Jason > Message: 4 > Date: Tue, 20 Jan 2009 12:29:20 -0800 > From: "Vincent Chu" <[email protected]> > Subject: [PyMOL] Algorithm for pyMOL's fit and rmsd algorithms > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all -- > > I've been using pyMOL's fit and rmsd commands on small numbers of > structures but now I'd like to use these functions on large numbers of > molecules. > > Does anybody know what algorithm is used in pyMOL to superimpose > molecular structures on top of other ones (i.e., pymol's fit > function). Better yet would be a reference. > > Thanks! > > Vince -- Jason Vertrees, PhD Dartmouth College : [email protected] Boston University : [email protected] PyMOLWiki : http://www.pymolwiki.org/
