Lsq_improve [old_result] [mol res1 res2](A) [mol res1 res2](B) [atom] [result]
This command can improve on a given transformation. The command employs an algorithm involving a search for structure fragments that can be aligned within a given cutoff limit, and tries to improve the transformation and the matched atoms. The user must specify which transformation currently stored in the database is to be used as the start value that is to be improved. The user then specifies which part of molecule A is being matched with B. The improved transformation operator can be stored in the database (with the same name as the start matrix or as a new entry). The algorithm cycles until either the same set of atoms are selected or until 10 cycles are made. The algorithm used (developed by TAJ) has not been published yet. Roughly speaking, it works by locating the longest matching fragments between the two molecules where each pair of atoms in a fragment fits better than a set value.