how to keep native structure when do loop modeling

Member Site Forums Rosetta 3 Rosetta 3 – General how to keep native structure when do loop modeling

  • This topic has 4 replies, 2 voices, and was last updated 15 years ago by Anonymous.
Viewing 4 reply threads
  • Author
    Posts
    • #293
      Anonymous

        I am trying to do model a loop using loopmodeling mode and want to keep the rest structure rigid. when I run loopmodel.linuxgccrelease. A lot of WARNING lines like

        core.io.pdb.file_data: [ WARNING ] discarding 3 atoms at position 17
        in file . Best match rsd_type.
        core.io.pdb.file_data: [ WARNING ] discarding 9 atoms at position 30 in file . Best match rsd_type

        I found that some positions in other regions were changed after loop modeling.

        I tried -loops:natsc and -loop:refine_only. seems both changes the side chains

        Thanks.
        Johnny

      • #4075
        Anonymous

          It’s probably balking because something is wrong with the sidechains at those positions – most likely either the hydrogens are labeled improperly (and ignored) or there are heavy atoms missing, or both. Rosetta won’t tolerate missing atoms and will build them back in; it then repacks the sidechain to ensure the newly built atoms don’t clash.

          These changes are probably occuring at the time of PDB read-in, not within loop modeling (thus loops: natsc didn’t work).

          Try -pack::pack_missing_sidechains false. It defaults true so you need the false.

          If the moving sidechains are far from your loop you they won’t affect its conformation – you can also just fix them by editing the PDB later.

        • #4076
          Anonymous

            Seems it worked. BUT I always had a lot of WARNING lines like
            discarding atoms at position in file Best match rsd_type

            Is this step of discarding some atoms of each residue and best match rsd_type required?

            Johnny

          • #4083
            Anonymous

              It’s not “required”, in the sense that a perfectly formatted PDB will not produce these warnings. That said, it’s probably nothing to worry about. You could try stripping all the hydrogens from your input file and see if that makes the warning go away.

            • #4084
              Anonymous

                After I further checked out. I still saw slight movement of sidechains of many residues. the positions of alpha C are same. what is the reason. thanks

                args are
                -database /usr/local/rosetta3/rosetta3_database/
                -in:file:fullatom
                -in:ignore_unrecognized_res
                -loops:fix_natsc true
                -loops::input_pdb template.pdb
                -loops:loop_file template.pose_loops
                -loops::frag_sizes 9 3
                -loops::frag_files fragment9 fragment3
                -loops::remodel quick_ccd
                -loops::refine refine_ccd
                -packing:pack_missing_sidechains false
                -packing:resfile
                -nstruct 1

                Resfile
                NATRO
                start

            Viewing 4 reply threads
            • You must be logged in to reply to this topic.