[modeller_usage] iterative_structural_align question

[Mike White <mwhite AT DrexelMed.edu>]

I noticed that 9v7 has a new command that is designed to obtain the  
best set of parameters (gap_penalties_1d and gap_penalties_3d) for  
aligning two or more structures. Since the reference (Madhusudhan et  
al 2009) is not yet available, I had a few questions based on trying  
the command.

(1) Based on the output log, the first parameter of gap_penalties_1d  
is varied from -150 to 0, and the second is varied from -50 to 0. The  
default values for gap_penalties_1d in for alignment.salign() are  
(-900, -50).  What is the logic for the choice of ranges for  
gap_penalties_1d values in iterative_structural_align()? I always  
assumed that the default values of the various parameters in  
alignment.salign() represent a good starting point for these values.

(2) I assume that the value "final max quality" equivalent to  
"QUALITY_SCORE(percentage)" in the standard output of  
alignment.salign(). Is this correct?

(2) In the Advanced Tutorial the example script "multiple_template/ 
salign.py" runs salign multiple times to first get a rough alignment  
and then refines it by incorporating more information through changes  
in feature_weights. Is feature_weights fixed at (1, 0, 0, 0, 0, 0) in  
iterative_structural_align()? If so, is there any way to use  
iterative_structural_align() in a manner similar to that shown in the  
tutorial?

Thanks!