How to reconstruct full atom structure from silent file

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  • This topic has 7 replies, 2 voices, and was last updated 16 years ago by Anonymous.
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    • #297
      Sally Ride
      Participant

        Hi,

        I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.

        Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).

        I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.

        Is there any dedicated protocol?

      • #3980
        Anonymous

          You can use the extract.pl scripts in rosetta_scripts package to extract PDB from a silent mode file.

          > Hi,
          >
          > I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
          >
          > Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
          >
          > I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
          >
          > Is there any dedicated protocol?
          >
          >

        • #3981
          Sally Ride
          Participant

            Well, yes I could but extract.pl returns only backbone. I think rosetta -extract only reformats torsion angles to Cartesian.

            What I am looking for is a crude reconstruction of side chains using rosetta and starting with backbone only structures in silent format.

            > You can use the extract.pl scripts in rosetta_scripts package to extract PDB from a silent mode file.

          • #3983
            Anonymous

              I believe that if you use the command-line flag -fa_input flag, rosetta++ will extract
              full-atom coordinates. If that doesn’t work, please let me know

              > Hi,
              >
              > I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
              >
              > Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
              >
              > I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
              >
              > Is there any dedicated protocol?
              >
              >

            • #3986
              Sally Ride
              Participant

                I guess you meant -fa_output.

                I tried this and it does not work with -extract but it does work with the -refold -score which extract.pl uses. So the final rosetta command which works looks like that:

                rosetta.gcc -refold -score -fa_output -scorefile test -silent_input -nstruct 1 -s test.out -l tagfile

                Thanks a lot for a hint!

                > I believe that if you use the command-line flag -fa_input flag, rosetta++ will extract
                > full-atom coordinates. If that doesn’t work, please let me know
                >

              • #3990
                Anonymous

                  I’m forwarding an expert suggestions;

                  Here’s the command line to extract fullatom PDBs:

                  rosetta.gcc -extract -s test.out -all -paths ~/paths.txt -fa_input

                  You can replace -all with -l , or with -t .

                  Cheers,

                  > Hi,
                  >
                  > I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
                  >
                  > Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
                  >
                  > I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
                  >
                  > Is there any dedicated protocol?
                  >
                  >

                • #3991
                  Sally Ride
                  Participant

                    Hmm, this does not work for me at all. I get a parse error:

                    parse error2: S_0001_8516 1 1 1 1 158

                    parse error2: S_0206_1379 1 1 1 1 158

                    parse error2: S_0207_4013 1 1 1 1 158

                    parse error2: S_0208_8411 1 1 1 1 158

                    EOF error?

                    STOP:: couldnt open silent-file!!

                    ERROR:: Exit from: pose_main.cc line: 256

                    But anyway, the other solution (-refold) seems to work.

                    > I’m forwarding an expert suggestions;
                    > —
                    > Here’s the command line to extract fullatom PDBs:
                    >
                    > rosetta.gcc -extract -s test.out -all -paths ~/paths.txt -fa_input
                    >
                    > You can replace -all with -l , or with -t .
                    >
                    > Cheers,
                    >
                    > —
                    >
                    > > Hi,
                    > >
                    > > I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
                    > >
                    > > Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
                    > >
                    > > I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
                    > >
                    > > Is there any dedicated protocol?
                    > >
                    > >

                  • #3992
                    Anonymous

                      Hi, Kosa,

                      Can you forward the silent file to the user support email? Or you can attach it here. We could look at it in more detail.

                      Yi

                      > Hi,
                      >
                      > I am looking for the quickest way for __crude__ (re)constructing full atom decoys (backbone + side chains) from the silent format file.
                      >
                      > Lets say I have generated silent file using -silent rosetta flag and now I want to get all full atoms decoys in PDB format (with crude reconstruction of side chain).
                      >
                      > I have tried several approaches but: rosetta -extract gives only the backbone. -relax takes too long. -loops could work but requires additional input files.
                      >
                      > Is there any dedicated protocol?
                      >
                      >

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