pose_from_rcsb error

[Anonymous]

I am a newbie with very little experience with linux, conda, python, or pyrosetta. The COVID-19 lockdown finally gave me the time to set this up and start to learn it. I finally have pyrosetta running in a conda python 3.7 environment – I can load pose_from_pdb, clean it, edit it, and view in pymol. But pose=pose_from_rcsb gives the following error: “cannot access network resource, make sure you are connected to the internet”. See the traceback below. I am connected to the internet (I posted this message from the same computer). What’s the matter? Is there something I need to do in python or pyrosetta to connect to the internet? Thanks.

>>> from pyrosetta.toolbox import pose_from_rcsb

>>> pose = pose_from_rcsb(“5OYB.pdb”)

Traceback (most recent call last):

  File “/home/criss/anaconda3/lib/python3.7/site-packages/pyrosetta/toolbox/rcsb.py”, line 36, in download_from_web

    temp = urllib_urlretrieve(url)[0]

  File “/home/criss/anaconda3/lib/python3.7/urllib/request.py”, line 247, in urlretrieve

    with contextlib.closing(urlopen(url, data)) as fp:

  File “/home/criss/anaconda3/lib/python3.7/urllib/request.py”, line 222, in urlopen

    return opener.open(url, data, timeout)

  File “/home/criss/anaconda3/lib/python3.7/urllib/request.py”, line 531, in open

    response = meth(req, response)

  File “/home/criss/anaconda3/lib/python3.7/urllib/request.py”, line 641, in http_response

    ‘http’, request, response, code, msg, hdrs)

  File “/home/criss/anaconda3/lib/python3.7/urllib/request.py”, line 569, in error

    return self._call_chain(*args)

  File “/home/criss/anaconda3/lib/python3.7/urllib/request.py”, line 503, in _call_chain

    result = func(*args)

  File “/home/criss/anaconda3/lib/python3.7/urllib/request.py”, line 649, in http_error_default

    raise HTTPError(req.full_url, code, msg, hdrs, fp)

urllib.error.HTTPError: HTTP Error 404: Not Found

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File “<stdin>”, line 1, in <module>

  File “/home/criss/anaconda3/lib/python3.7/site-packages/pyrosetta/toolbox/rcsb.py”, line 95, in pose_from_rcsb

    load_from_rcsb(pdb_code)

  File “/home/criss/anaconda3/lib/python3.7/site-packages/pyrosetta/toolbox/rcsb.py”, line 70, in load_from_rcsb

    with download_from_web(pdb_url) as pdb_data:

  File “/home/criss/anaconda3/lib/python3.7/contextlib.py”, line 112, in __enter__

    return next(self.gen)

  File “/home/criss/anaconda3/lib/python3.7/site-packages/pyrosetta/toolbox/rcsb.py”, line 39, in download_from_web

    “Cannot access network resource, please check your Internet access.”

OSError: Cannot access network resource, please check your Internet access.

 

 

[Anonymous]

If I do pose = pyrosetta.toolbox.pose_from_rcsb('1UBQ') everything works. But if I do pose = pyrosetta.toolbox.pose_from_rcsb(' 1UBQ') it fails as you get (same with random non-existant Ids). Could you check the len of your Id (in case you have zero-length space)? It is not an PDB Id newness thing, as I tried a brand-new PDB Id and it worked for me (Pyrosetta 4 2020, the newer one with relax.set_movemap_disables_packing_of_fixed_chi_positions(True) feature).

So could you try good old ubiquitin ‘1ubq’?

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