Re: [modeller_usage] Basic tutorial

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