On 1/10/12 7:34 PM, Ashish Runthala wrote: > Respected Sir, > Are you saying about this line? > for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), > ((1., 0.5, 1., 1., 1., 0.), False, True), > ((1., 1., 1., 1., 1., 0.), True, False)):

That looks like a loop from one of the SALIGN example scripts, which simply calls SALIGN three times. If you look further down in the script you will see this: aln.salign(..., feature_weights=weights)

i.e. SALIGN is being called with the weights given by the first argument in that 'for' statement above.

> What do each of the 6 float constants represent?

They're weights - just numbers that multiply each feature's distance matrix. The distance matrix used by SALIGN is simply a linear combination of these.

> Also tell me What you exactly mean by feature_weights=[0]*6.

I mean exactly what it says - that's elementary Python syntax. [0]*6 is the same as saying [0,0,0,0,0,0]. In other words, all of the features will have zero weight, so SALIGN won't calculate any of them.

Ben Webb, Modeller Caretaker