[modeller_usage] origin of blosum62.sim.mat and as1.sim.mat

["Joshua A. Speidel" <jos2036@med.cornell.edu>]

Hello,

I am curious about the origin of the blosum62.sim.mat and as1.sim.mat.

When I look at the blosum62.sim.mat, I can't figure out the relationship
between the numbers there, and the original blosum62 matrix. Initially,
I thought that the Henikoff & Henikoff values were just scaled to
between 0 and 1000, but that didn't seem to work.

I can't find a reference for ALBASE3 mentioned in as1.sim.mat.

Finally, if I wanted to use my own matrix, is it necessary for me to
scale it to between 0 and 1000?

Your help in understanding this is greatly appreciated,

Josh