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.
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.
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.
>
>
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.