Dear Sir or Madam,
I have recently installed and compiled Rosetta2019.14 (without binaries) on OS Linux OpenSUSE Leap42.3. And I started to study Rosetta in according to file "folding_tutorial.pdf" from the Meiler lab. But after every handling with files and directories on the Rosetta through an Unix terminal that directory becomes unavailable for every operation with it. For example, after running such operation as: "python2.7 /home/ihor/Документи/Rosetta/rosetta_src_2019.14.60699_bundle/tools/protein_tools/scripts/pdb_renumber.py \2LZM_A.pdb 2LZMA.pdb" I tried to save edited PDB-file to a directory, where I work. And I got such error: "The document can not be saved due to a write error to /home/ihor/Documents/Rosetta/rosetta_workshop/protein_folding/2LZM_A.pdb. Make sure you have the right to write to this file and have enough free space." Also, after running such command, as "python2.7 /home/ihor/Документи/Rosetta/rosetta_src_2019.14.60699_bundle/tools/protein_tools/scripts/pdb_renumber.py \2LZM_A.pdb 2LZMA.pdb" I got such error "ERROR: This script requires that Biopython (http://biopython.org) is installed.", despite that biopython had been already installed. Could you tell me more detail, how to solve such problem with the Unix terminal and such error, please? Both commands and their errors are provided on the attached screenshot. I will be sincerely grateful for your response and help, and I am looking forward for it.
|Tutorial for protein folding from Meiler lab||181.39 KB|
|Unix commands and their errors||159.41 KB|
One thing I would be careful with is your path names. Rosetta is developed and tested primarily on systems which are using ASCII only. I don't think we've ever done much testing or support for Unicode in Rosetta. (That's not to say it won't work, just that it hasn't really been tested.) As such, you may see issues related to paths and filenames which have non-ASCII Unicode characters in it.
Regarding the BioPython error, one thing to be careful of is which Python you've installed BioPython for. Your system can have multiple different versions of Python installed, and if you install BioPython for Python3.6, it won't be availible for Python2.7 (or even Python3.5). From your commands, it looks like you've installed BioPython for Python3.6 (which is what your default pip is targeting), but not the Python2.7 with which you're running the script.
many thanks for your answer.
Sorry for not writing earlier.