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.