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?