I have been trying to compute ala-scanning values using the dock design parser applications,
and I also want to specify some residues to be designed (like -resfile option in fixbb design).
Can somebody help me to define specific residues in alanine scanning?
and How to generate output file (.report file)?
Thanks for any help with this problem!
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).
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.
By "see wiki", Sarel means see the RosettaScripts documentation on the Rosetta wiki. The current version of the documentation on the wiki is not available to the general public, but a copy of the version at the time of release is included with the manual (See: http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/Rose...)
With regard to the AlaScan filter, there doesn't appear to be a way to specify a specific set of residues a'la a resfile. Usually the way one will do it is by using a ReadResfile TaskOperation (or other TaskOperation which does something similar), and specifying that in the filter/mover. However, it does not appear that AlaScan is set up to take TaskOperations.
Thanks for the reply! At that time I found that the -resfile option worked well with RepackMinimize script (That's why I modified the question). However, after I performed the docking.xml (simplified script derived from rosetta_deomos/Docking_Design_Scripting/docking.xml of Rosetta 3.1) with my protein structure, it was observed that the hydrophobic core region is exposed maybe due to the packing failure. Is there any reference that describes the detailed actions of RepackMinmize mover?
Thanks in advance!
"Is there any reference that describes the detailed actions of RepackMinmize mover? " - http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/Rose...
Can you be more specific about the core being exposed? Do you mean the protein opened up like a butterfly? This is caused by clashes in the interior being resolved by the minimizer unfolding the backbone instead of the packer repacking the clashes out (it may be possible the packer CAN'T fix them if they're bad enough.)
The protein has horseshoe-like shape consisted of five leucine rich repeats, and the modular repeats pack against each other. After running RapackMinimize, the repeat modules separated (not packed each other) and so the interior region was exposed.
Thank you very much for your help.
This is very likely to be the minimizer undoing clashes. (They could also be backbone-backbone clashes, which the packer can't fix anyway).