Dear Bryan, The factor 0.9 is a purely empirical term. It serves two functions. One is to soften the minimas when atoms coalesce and to also prevent taking the logarithm of a negative number. The closer it gets to zero the more accurately it pinpoints the global minimum when the MLAD score is used for identifying the best superposition betweent two molecules. But if it becomes two small chances are that the landscape of MLAD values will be dotted with many very deep local minima which might lead to wrong results. The square boxes under the min, max symbols are typos to be ignored, sorry. There are currently no plans to publish further details about find_alt_origin_sym_mate. Regards, Robert Oeffner On Wed, Feb 15, 2012 at 4:33 PM, Bryan Lepore <bryanlepore at gmail.com> wrote:
will the find_alt_origin_sym_mate article in CCN Jan. 2012 be described in any other publications?
... e.g. Acta Cryst., because I am interested in particular : 1. what is the significance of the factor of 0.9 2. is the MLAD a novel formula also, the 'min' and 'max' on p. 6 have small boxes under them [*] as if missing a character - are these integrals? -Bryan [*] tried evince and Adobe Reader on Linux, Adobe Acrobat on OSX 10.5.8 -- Robert Oeffner, Ph.D. Research Associate Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162