Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Missing “Bio.PDB” module when running “remove_loop_coords.py”
- This topic has 6 replies, 3 voices, and was last updated 9 years, 11 months ago by
Anonymous.
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September 29, 2014 at 11:34 am #2013
Anonymous
Dear friends,
When I tried to run “remove_loop_coords.py”, I was told “ImportError: No module named Bio.PDB”:lanselibai@ubuntu:/mnt/hgfs/Downloads$ python ~/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/remove_loop_coords.py 4KMT.loops 4KMT_clean_0001.pdb 4KMT_clean_0001_no_loop.pdb
Traceback (most recent call last):
File “/home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/remove_loop_coords.py”, line 4, in
import Bio.PDB
ImportError: No module named Bio.PDBHowever, when I tried to install Bio.PDB:
lanselibai@ubuntu:/mnt/hgfs/Downloads$ sudo apt-get install Bio.PDB
[sudo] password for lanselibai:
Reading package lists… Done
Building dependency tree
Reading state information… Done
E: Unable to locate package Bio.PDB
E: Couldn’t find any package by regex ‘Bio.PDB’It still cannot be installed.
Can I ask how to solve this? Thank you very much.
Yours sincerely
Cheng -
September 29, 2014 at 3:23 pm #10347
Anonymous
The Bio.PDB module is part of Biopython; see if you can install Biopython via apt-get.
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September 29, 2014 at 3:42 pm #10348
Anonymous
Hi everyday847,
Thank you. I tried but I was toldE: Unable to locate package Biopython
I also tried biopython, which was the same problem.
Yours sincerely
Cheng -
September 29, 2014 at 8:09 pm #10357
Anonymous
The main website for Biopython is http://biopython.org/wiki/Main_Page which has instructions for manual installation.
From what I can tell, under Ubuntu the package is actually named “python-biopython”. (For Ubuntu, you can go to http://packages.ubuntu.com/ and use the search tool there to see what Ubuntu’s name of the package which provides the program there.) Other distributions may have alternate names for it.
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September 30, 2014 at 11:37 am #10369
Anonymous
Hi R Moretti,
Thank you. “phthon-biopython” can be successfully installed by using:sudo apt-get install python-biopython
However, I was told “ImportError: No module named rosettautil.protein” when I tried:
lanselibai@ubuntu:/mnt/hgfs/Downloads$ python ~/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/remove_loop_coords.py clean.loops clean.pdb clean_no_loop.pdb
Traceback (most recent call last):
File “/home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools/scripts/remove_loop_coords.py”, line 7, in
from rosettautil.protein import util
ImportError: No module named rosettautil.protein1) I tried to search “rosettautil” on http://packages.ubuntu.com/ , but could not find the package.
2) It seems that “rosettautil” is in the following directory:
lanselibai@ubuntu:~/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools$ ls
documentation MANIFEST README rosettautil scripts setup.pyI was assuming I could install “rosettautil” by executing “setup.py”. So I tried:
lanselibai@ubuntu:~/Cheng/rosetta_2014.30.57114_bundle/tools/protein_tools$ python setup.py build
But “ImportError: No module named rosettautil.protein” still exists when running “remove_loop_coords.py”
Thank you very much.
Yours sincerely
Cheng -
September 30, 2014 at 8:22 pm #10375
Anonymous
I believe you also need to run “python setup.py install” rather than just ” python setup.py build”
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October 1, 2014 at 9:13 am #10378
Anonymous
Hi R Moretti,
Thank you. It works for me now after usingsudo python setup.py install
Yours sincerely
Cheng
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