Mike White wrote: > (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.

Since the matrix used for dynamic programming in SALIGN is a linear combination of several other matrices, the gap penalties and matrix offsets are to some extent dependent on the ranges of values present in those individual matrices. The gap penalties used in the iterative alignment are slightly different to those you may use in simple sequence alignment due to the presence of the local conformation feature in the initial phase of the iterative procedure.

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

Yes - it is the quality score, which is a measure of structure overlap.

> (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?

A similar process is employed, although the iterative method is designed purely for structure-structure alignments, hence the name. The iterative alignment also creates an initial alignment and then refines it by pulling in feature 2 (Euclidean distance).

Ben Webb, Modeller Caretaker