fix the left part doesn’t work

Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › fix the left part doesn’t work

Viewing 8 reply threads
  • Author
    Posts
    • November 7, 2012 at 8:02 am #1454
      Anonymous

        hello:

        I am using the following protocol which someone used in the forum to build loop based on crystal structure. I am going to fix the left part of the region since they are from crystal structure and I find that all the regions are rebuild by Rosetta. I am just wondering, where is the problem?

        thank you very much

        /opt/rosetta3.4/rosetta_source/bin/loopmodel.default.linuxgccrelease
        -database /opt/rosetta3.4/rosetta_database
        -nstruct $nstruct
        -loops:input_pdb ../crystal.pdb
        -loops:loop_file ../input.loop
        -loops:remodel perturb_kic
        -loops:refine refine_kic
        -loops.max_kic_build_attempts 100
        -loops:fix_natsc true
        -loops:neighbor_dist 0.0
        -loops:relax fastrelax
        -loops:extended
        -ex1
        -ex2
        -out:path:pdb ./
        -out:suffix $i
        -out:file:fullatom
        -out:pdb

      • November 7, 2012 at 3:43 pm #8040
        Anonymous

          Double check your loop file….

        • November 7, 2012 at 3:51 pm #8041
          Anonymous

            What does “left part” mean…?

          • November 7, 2012 at 5:27 pm #8045
            Anonymous

              I checked many times, and I don’t know where the problem it is…..

            • November 7, 2012 at 5:32 pm #8046
              Anonymous

                Is the backbone moving or just the sidechains? What do the occupancies of the moving region look like in the PDB (are they nonzero)? Post the loop file (just paste it into the text box).

              • November 7, 2012 at 6:28 pm #8047
                Anonymous

                  both backbone and side chain moves. I trying to include the hydrogen as the input file, but it always claim loop definition out of range. So, I removed all hydrogen as initial structure. Here is the loop file:

                  LOOP 193 208 200 0 1

                • November 7, 2012 at 6:57 pm #8049
                  Anonymous

                    thanks for kind comments. In fact, I remubered the residues from 1…..

                  • November 7, 2012 at 7:20 pm #8050
                    Anonymous

                      You have fastrelax turned on – try turning that off. I don’t know if fastrelax limits itself to just the defined loop.

                    • November 7, 2012 at 7:56 pm #8051
                      Anonymous

                        IC, it works now. However, I find my disfulde bridge was borken…..
                        THX

                      • November 7, 2012 at 6:45 pm #8048
                        Anonymous

                          If those values are meant to be PDB numberings, you need to include the PDB chain; for example

                          LOOP 193A 208A 200A 0 1

                          Rosetta interprets wthem as 1-indexed residue IDs (whole pose numbered starting from 1) normally.

                      • Author
                        Posts
                      Viewing 8 reply threads
                      • You must be logged in to reply to this topic.