# Mon Dec 31 13:17:56 PST 2007 Kevin Karplus

Change picture generation at end to show models 1 through 5.

make_alignments needs to make multi-track alignments even for
sequences not in template library (as long as they have basic-setup done).

Make template library multi-track HMMs.
Add alignment methods for multi-track template HMMs.

Add consensus-based scoring for template models.
	[[ Tue Jan  1 13:49:13 PST 2008 Kevin Karplus
		Done for single-track HMMs, still need to do
		multi-track template-based scoring!
	]]


Add consensus-based scoring for target models
	[[ Tue Jan  1 13:32:34 PST 2008 Kevin Karplus
		Done for multi-track, but not w0.5 model.
	]]

Really need 2 scoring methods for each HMM:
	1) real sequence and structure for all of PDB (basic-setup)
	2) consensus sequence and real structure for template library


Modify undertaker script and  to do 5 optimizations: one with all the
alignments, the next 4 with just the first 4 templates.

Modify rasmol display of solution to have coloring script controlled
by the Make.main file.  Better still, replace the static pictures with
jmol or other display technique.