Re: [modeller_usage] Question about alignment.check()

On 5/5/12 10:13 AM, M wrote: > Using the superimposed templates and a visualisation program (pymol), > the measured distance between the mentioned pairs is only 0,6 A. The > problem is the same for other pairs. I've checked the alignment pir > file many times and there are no errors in it, the sequences are > aligned correctly. How can this be explained?

The distances are those from the superposition as implied by the current alignment, not those from an "ideal" structural alignment. You can see the former by using selection.superpose() to fit one structure onto another.

Ben Webb, Modeller Caretaker