[salign] concerning the manual : feature 2 and structure superposition
Dear modellers,
Reading the salign documentation (http://salilab.org/modeller/manual/node300.html) I have troubles understanding a specific paragraph concerning feature 2. The paragraph is the following :
<< The alignment produced within the routine that calculates W^2 does not generally correspond to the alignment calculated based on W. Therefore, the multiply superposed structures are not necessarily superposed based on the final multiple alignment produced by alignment.salign(). If you wish such a superposition, you can use alignment.malign3d() with fit = False and write_fit = True (the meaning of fit is different between alignment.salign() and alignment.malign3d()). >>
And since I am kind of really lost on the interpretation, any clue is welcome. Thanks
--Ben( S.)
On 10/24/11 7:18 AM, Benjamin SCHWARZ wrote: > Reading the salign documentation > (http://salilab.org/modeller/manual/node300.html) I have troubles > understanding a specific paragraph concerning feature 2.
Given that you don't say what you think it might mean, all I can do is restate it and hope it makes more sense. ;) To calculate feature 2, the Euclidean distance between residues in two structures, the structures must be aligned. So SALIGN does this, but that alignment is only a temporary one; it is used only to determine the values of feature 2. The final alignment is done in the regular way, by dynamic programming using *all* features.
Ben Webb, Modeller Caretaker
Hi Ben,
And thank you for that fast answer, as usual :)
> Given that you don't say what you think it might mean, all I can do is restate it and hope it makes more sense. ;)
I didn't expect less… I was really lost ;)
> To calculate feature 2, the Euclidean distance between residues in two structures, the structures must be aligned. So SALIGN does this, but that alignment is only a temporary one; it is used only to determine the values of feature 2. The final alignment is done in the regular way, by dynamic programming using *all* features.
Actually, I think I was able to see clearer thanks to your restatement.
I think it is a matter of juxtaposed terminology and symbols : W^2 designates feature 2, not the Euclidian distance; and W designates the global cost function (the one that uses all features).
Correct ?
So basically, what you told me here, is that the computation of W2 produces another (and temporary) alignment, used to produce a superposition of structures (again a temporary one).
Just to enforce my understanding : What would happen if I set all features to 0 except for feature 2 ? would the two superpositions be the same ?
--Ben( S.)
On 10/24/11 11:04 AM, Benjamin SCHWARZ wrote: > I think it is a matter of juxtaposed terminology and symbols : W^2 > designates feature 2, not the Euclidian distance; and W designates > the global cost function (the one that uses all features). > > Correct ?
No, feature 2 *is* the Euclidean distance, so W^2 designates both. To be more specific, W^2 is a matrix of residue-residue Euclidean distances. There is some scaling done internally so that all the features have roughly the same magnitude, but that's simply equivalent to changing the units of distance.
> Just to enforce my understanding : What would happen if I set all > features to 0 except for feature 2 ? would the two superpositions be > the same ?
Probably. One would hope that an alignment made using a distance matrix that is itself extracted from an alignment would reproduce that alignment, but it's not absolutely guaranteed.
Ben Webb, Modeller Caretaker
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Modeller Caretaker