I also have a question regarding MLAD score. Why do you take the sum of absolute dr_i components? This is not orientation invariant. The attached screenshot is like figure 3 from the article, but rotates the system from 0 to 90 degrees. I think this: |dr_i,x| + |dr_i,y| + |dr_i,z| needs to be replaced by this: |dr_i| right? Regards, Thomas On 02/21/2012 01:31 AM, R.D. Oeffner wrote:
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
-- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
