Fails to make a universe from 2Y2N.pdb

[kaceyaurum]

When a universe should be created, a KeyError is raised.

---

KeyError Traceback (most recent call last)
in ()
----> 1 mda.Universe(path + '2Y2N.pdb')

/usr/local/lib/python2.7/dist-packages/MDAnalysis/core/AtomGroup.pyc in init(self, _args, *_kwargs)
4337 try:
4338 with parser(self.filename, universe=self) as p:
-> 4339 self._topology = p.parse()
4340 except IOError as err:
4341 raise IOError("Failed to load from the topology file {0}"

/usr/local/lib/python2.7/dist-packages/MDAnalysis/topology/PDBParser.pyc in parse(self)
88 structure['atoms'] = atoms
89
---> 90 bonds = self._parsebonds(atoms)
91 structure['bonds'] = bonds
92

/usr/local/lib/python2.7/dist-packages/MDAnalysis/topology/PDBParser.pyc in _parsebonds(self, atoms)
181 atom, atoms = _parse_conect(line.strip())
182 for a in atoms:
--> 183 bond = tuple([mapping[atom], mapping[a]])
184 bonds.add(bond)
185

KeyError: 3635

import MDAnalysis as mda

u = mda.Universe('2Y2N.pdb')

[jdetle]

Hi @kaceyreidy, I'd be happy to try help. Are you able to share the 2Y2N.pdbfile such that I can try to reproduce the error? Also, if you could please run python -c "import MDAnalysis as mda; print(mda.__version__)" and share that info and let us know what OS you are running that can't hurt either.

[dotsdl]

@jdetle this is a file for a structure on the PDB, namely 2Y2N. You can download it from here.

[kaceyaurum]

Ubuntu 14.04.

On Monday, August 15, 2016, David Dotson [email protected] wrote:

@jdetle https://github.com/jdetle this is a file for a structure on the
PDB, namely 2Y2N. You can download it from here
http://files.rcsb.org/download/2Y2N.pdb.

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[orbeckst]

@jdetle , see #810 (comment) :

import urllib 
downloader = urllib.URLopener()

def fetch_pdb(pdb_id, download_url="http://files.rcsb.org/download"):
    filename = "{0}.pdb".format(pdb_id.lower())
    downloader.retrieve("/".join([download_url, filename]), filename)
    return filename

# get file
pdb = fetch_pdb("2y2n")

# load pdb
u = mda.Universe(pdb)

[jdetle]

@dotsdl, @orbeckst, the issue seems to be caused by the TER statement on line 8045. The comments in the _parse_bonds function alludes to problems with multiframe PDBs and the CONECT statements being given at the end of the file. It looks like this is a case where the error isn't caught. Any help?

[richardjgowers]

So looking into this, there's a CONECT record between atoms and the TER record. As the TER record doesn't represent a real Atom, would a good fix for this be to ignore bonds to the TER location?

[orbeckst]

I think so, yes. I don't really know why one would have these pseudo bonds but it won't matter for MDAnalysis if they are there. It might be an issue when writing PDB files but I am willing to wait for someone to raise an issue for the PDBWriter about this…

On 20 Aug, 2016, at 05:46, Richard Gowers [email protected] wrote:

So looking into this, there's a CONECT record between atoms and the TER record. As the TER record doesn't represent a real Atom, would a good fix for this be to ignore bonds to the TER location?

Oliver Beckstein * [email protected]
skype: orbeckst * [email protected]