[Chimera-users] RMSD fit of an object to atom

Eric Pettersen pett at cgl.ucsf.edu
Wed Mar 7 13:54:42 PST 2007

On Mar 7, 2007, at 12:13 PM, Tom Goddard wrote:

>  I didn't understand your explanation of why 4 points are needed  
> for an alignment with the match command.  It looks like only 3 are  
> needed for a unique match.  In your example with points ABC and DEF  
> you suggested that the match could either pair A with D, B with E,  
> and C with F or it could pair A with F, B with E, C with D.  But  
> the match command specifies the desired pairing so only one of  
> those is possible for any match command invocation.

Tom's right in that with the correspondences specified, 3 points is  
enough for a unique superposition.  After some investigation, it  
turns out that back in MidasPlus we used a different superposition  
algorithm and that algorithm required at least four points to work.   
Chimera uses a different algorithm -- and there is no minimum!  It  
will work with one point.  So the 4-point minimum is an unnecessary  
restriction and will be removed in future releases (though it will  
warn about non-uniqueness if you use less than 3 points).

Navnit, I can send you a file with the restriction removed if you  
want.  Let me know.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

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