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Well roared, Lion! Just one question: > also, at lower resolution you expect your model to have more > outliers than at higher resolution, so having zero > ramachandran outliers is not a goal you should be pursuing in > the first place. see for instance: > - http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=65 > - http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=39 > - http://xray.bmc.uu.se/cgi-bin/gerard/reprint_mailer.pl?pref=29 The Ramachandran plots you used to define outliers, do they predate the Richardson-Richardson ones? Because, invoking WWW: without the resolution, how can you justify Ramachandran outliers? (The old procheck Rama plot hasn't been updated since 1991, I gather...) > as for the discussion on "desirable" rmsds - i thought we > (the community) had agreed many years ago that the lower the > resolution, the tighter your restraints *must* be. (in the > limit of zero reflections: use constraints) sure, you can > tune the restraints to get an "atomic resolution rmsd" of > 0.02 A or whatever, but you are unable to determine the > individual bond lengths with an accuracy that warrants it. so > you get the "right" distribution, but for the wrong reasons. > i seem to remember (but my memory is write-only nowadays, so > don't take my word for it!) that ian tickle wrote the > definitive posting about this on ccp4bb a couple of years back. He certainly did, it's a longish thread. Go read it. phx.
