Marco wrote:
I'm following the basic tutorial and I have a couple of question: a) some times ago Modeller grouped similar structures and scanned against the representative protein of each group: is this still valid?
Sure, you can still do that if you like; see http://salilab.org/modeller/9v7/manual/node372.html
profile.build(), as used in the tutorial, is preferred these days since the older method is very slow when scanning against modern databases.
b) where I find the data on cristallografic resolution of the chosen proteins? The pdball.pir file does not contain this data.
pdball.pir contains only sequence information; for the structural information, look in the corresponding PDB file.
Ben Webb, Modeller Caretaker
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