Reply To: How to define specific residues in alascan ?

[Anonymous]

You seem to have edited your post to remove the qusetion about RepackMinimize, so hopefully this response is still relevant. This is from Sarel Fleishman (who developed these modules).

Dear Park,

RepackMinimize is useful but quite complicated. For many purposes, I use PackRotamersMover in conjunction with MinMover, which together give you the same functionality but with more flexibility and transparency. If you’re interested in repacking and minimizing an interface I would do the following (resfile reading is one of the operations defined below):

this task operation defaults to repacking chain1 and designing chain2 with an interface cutoff of 8A. You can modify any of these choices. See wiki for details
this respects your -ex1 -ex2 -use_input_sc flags on the commandline
your resfile can be specified here

you can set individual degrees of freedom using the movemaps, see wiki for details.