Symmetric Minimization

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  • This topic has 5 replies, 3 voices, and was last updated 12 years ago by Anonymous.
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    • December 17, 2012 at 7:45 pm #1487
      Anonymous

        Hi!

        Two questions:

        1) Is it possible to minimize specified residues? I do not want different rotamers? So I do not want to use NATAA in the resfile, but if I use NATRO then specify minimize_rotamer – will that have the expected behavior?

        2) Secondly, does symmetry work with minimization. For example, can I do something like this:
        /Users/aroop/rosetta31/bin/fixbbSym.macosgccrelease -nstruct 1 -s n191.pdb -database /Users/aroop/rosetta31/rosetta_database -in:file:fullatom -symmetry:symmetry_definition n191.sdef -symmetry:initialize_rigid_body_dofs -packing:preserve_c_beta -packing:use_input_sc -minimize_sidechains

      • December 17, 2012 at 8:54 pm #8242
        Anonymous

          Aroop – are you really asking for 3.1? Or for 3.4? I don’t have a copy of 3.1 installed anymore.

        • December 17, 2012 at 9:09 pm #8243
          Anonymous

            Assuming 3.4,

            1) No. The code uses TaskAwareMinMover, which will see NATRO and assume you want a fixed rotamer.

            2) It appears that -minimize_sidechains is compatible with symmetry, but -min_pack is not. This is from casual inspection of fixbb, not testing.

            If you want behavior 1), the fastest way to get it is just comment out most of fixbb.cc. Comment out all the packing routines and leave the TaskAwareMinMover present, and you’ll have a resfile-selectable sidechain minimization routine. Possibly faster would be to write a RosettaScript that contains only TaskAwareMinMover with a ReadResfile operation (and InitializeFromCommandLine, as desired), plus whatever hookup it needs for symmetry.

          • December 18, 2012 at 3:29 pm #8247
            Anonymous

              Dear Steven & T (sorry I do not know your name :( ),

              I think this makes sense. I am no RosettaScripts pro, but have recently started to dabble in it. Hopefully I will be able to use your XML script shortly.

              Thank you,
              Aroop

            • December 17, 2012 at 9:16 pm #8244
              Anonymous

                Here’s an (untested) script that will do the task-based sidechain minimization part. I don’t know how to incorporate symmetry. Someone who does said they’d offer a comment.

              • December 17, 2012 at 9:28 pm #8245
                Anonymous

                  I don’t think you can do task aware minimization with symmetry. To do global minimization you would have a mover section like:

                  {MOVERS}
                  {SetupForSymmetry name=sym definition=*symmetry_def_file* /}
                  {SymMinMover name=min bb=false /}
                  {/MOVERS}

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