Rather then now start mentioning yet 45 other 3D superposition softwares, I think a pointer to the Wikipedia should suffice:
https://en.wikipedia.org/wiki/Structural_alignment The Russian Doll effect (if you align more residues the comparison stats get worse) is best explained (my opinion) by the CATH people (Orengo group), and Arthur Lest is the only one (still, I think) who has been thinking extensively about the cutoff question. Greetings Gert
From: Reza Khayat Sent: Sunday, April 9, 2017 6:07 PM To: CCP4 bulletin board Subject: Structure comparison Hi, I have refined several structures of a protein from different space groups and would like to compare them to one another. Is there a program/software suite that would provide an objective comparison of the structures and identify regions where the structures are sufficiently different from one another to warrant a closer look? I think the most important aspect of the analysis would be defining a threshold (possibly based on resolution and structure statistics) that would identify sufficient difference between structures. Thanks. Best wishes, Reza Reza Khayat, PhD Assistant Professor City College of New York Department of Chemistry New York, NY 10031
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