how to use backrub in rosetta3.1

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    • January 11, 2010 at 10:43 pm #415
      Anonymous

        I installed rosetta3.1 on my system. Based on the backrub documentation, I did exactly the things as it said:
        > cat << END_RESFILE > 2YPI.resfile

        then I input the content as the documentation showed.
        >backrub -database rosetta3_database -s 2YPI.pdb -ignore_unrecognized_res -resfile 2YPI.resfile
        -pivot_residues 127 128 129 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178

        the system showed following error message:
        -bash: backrub: command not found

        So, what is wrong? Why I could not repeat the example on rosetta3.1 website and why it could not even recognize the backrub command? Thanks a lot.

      • January 12, 2010 at 3:15 pm #4305
        Anonymous

          You have a bash shell error message, not a rosetta error message. I would guess either you don’t have a backrub executeable in your current directory (or a symlink to one), or your lookup path does not include the current directory.

          Try ./backrub instead of just backrub. That usually fixes my problems when I use the bash shell.

        • January 12, 2010 at 6:43 pm #4306
          Anonymous

            Thank you very much for your help! I got it.

            I found that when the backrub worked, it output structures with the tag as _last and _low, how to understand the meaning for those tags? The manual for backrub online is too simple. Thanks again.

            > I installed rosetta3.1 on my system. Based on the backrub documentation, I did exactly the things as it said:
            > > cat 2YPI.resfile
            >
            > then I input the content as the documentation showed.
            > >backrub -database rosetta3_database -s 2YPI.pdb -ignore_unrecognized_res -resfile 2YPI.resfile
            > -pivot_residues 127 128 129 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178
            >
            > the system showed following error message:
            > -bash: backrub: command not found
            >
            >
            > So, what is wrong? Why I could not repeat the example on rosetta3.1 website and why it could not even recognize the backrub command? Thanks a lot.
            >
            >

          • January 13, 2010 at 2:52 pm #4308
            Anonymous

              I would guess that last and low are Monte Carlo designations – last is wherever the trajectory ended, and low is the lowest-energy structure seen along the course of the trajectory.

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