When I ran "pdb_renumber.py", I got the " ERROR: This script requires that Biopython (http://biopython.org) is installed." Acutally I installed Biopython. Is there any suggestion.
The most common case would be that you installed Biopython in a different enviorment than the one you are running rosetta in.
Thanks for your viewpoint. It looks biopython is at "/usr/local/li64/python3.6/site-packages". How can I use it for "pdb_renumber.py?
That error message comes up when the script attempts to import the `Bio.PDB` module and fails.
As ajasja mentions, if you don't have Biopython installed in the particular python you're using, then it wouldn't work. You should be able to check if things are installed correctly by just running python by itself and see if "import Bio" and "import Bio.PDB" work at the Python terminal you get.
Note that the script uses the "/usr/bin/env python" technique when launched directly. If the python which you have Biopython installed for isn't what you get when you type "python" on the command line, you may have to explicitly type the path to the python executable first. (e.g. "/path/to/my_python/bin/python pdb_renumber.py")
Thanks for your feedback. biopython is in "/usr/local/lib64/python3.6/site-packages". When I type "python2.7" here, "import Bio" works, but "import Bio.PDB" doesn't. I have no idea about how to incoporate biopython into python. When I input "python2.7 ~/Downloads/rosetta_src_2021.16.61629_bundle/main/tools/protein_tools/scripts/pdb_renumber.py --norestart 3GBM_AB.pdb 3gbm_HA.pdb", it still shows " ERROR: This script requires that Biopython (http://biopython.org) is installed."
The script is looking specifically for the Bio.PDB package -- if your installation of Biopython doesn't have the PDB module, it may be a very old one.
What does `import Bio` and then `print Bio.__version__` give you? The most recent versions of Biopython which work with Python2.7 are in the 1.7X range. If you're much earlier than that, it may be that your version of Biopython is too old. Alternatively, you may only have a partial version of Biopython installed.
In either case, the solution may be to (re)install a newer version of Biopython. If you have administrator access to the machine, you may be able to update the system-installed version of Biopython you're using. If not, it might be worth installing Conda in your home directory. Done properly, it will give you access to multiple version of Python, each with their own set of installed packages, so you can install whatever version of Biopython you want. (Its particularly useful these days, as many of the machine learning packages for biomolecular modeling are set up to be installed with Conda.)
Thanks a lot for your suggestion. Biopython was successfully installed after python was upgraded to 3.7.