Appion

EMDB to Model does not seem to be working. I also am having errors with PDB to Model. Small pdbs are no problem, but large PDB files do not have a PDB gz file and use XML or mmCIF.

A workaround that I used was to: 1) download the map or pdb, 2) manually use EMAN or SPIDER to create a volume with the right box/pixel size and 3) use Upload model tool.

Example of EMDB to Model error:

Job: emdb1022-15aug24i23.appionsub.job (ID: 38)
name: emdb1022-15aug24i23.appionsub.job
user: eeng
appion path: /emg/data00/appion/eeng/jchase/15aug18h/models/emdb/emdb1022-15aug24i23
submit time: 2015-08-24 08:24:09
status: Done
Show last lines of log file

emdb1022-15aug24i23.appionsub.log:

... Time stamp: 15aug24i24
... Function name: modelFromEMDB
... Appion directory: /opt/myamisnap/lib
... Using split database
Connected to database: 'nyap_45'
... Committing data to database
... Looking up symmetry for input: 7
... Selected symmetry group: C3 -- C3 (z)
... Looking up session, 15aug18h
... Run directory: /emg/data00/appion/eeng/jchase/15aug18h/models/emdb/emdb1022-15aug24i23
!!! WARNING: directory '/emg/data00/appion/eeng/jchase/15aug18h/models/emdb/emdb1022-15aug24i23'
already exists.
... Writing function log to: modelFromEMDB.log
... Uploading ScriptData....
... Found 1 processors on this machine
... Running Appion version 'trunk'
Naming EMDB model: /emg/data00/appion/eeng/jchase/15aug18h/models/emdb/emdb1022-15aug24i23/emdb1022-15aug24i24

... retrieving emdb file: ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1022/map/emd_1022.map.gz

... downloaded file of size 489.3k
... retrieving emdb XML file: ftp://emdb.rutgers.edu/structures/EMD-1022/header/emd-1022.xml
Traceback (most recent call last):
File "/opt/myamisnap/bin/modelFromEMDB.py", line 215, in
emdbmodel.start()
File "/opt/myamisnap/bin/modelFromEMDB.py", line 185, in start
self.getXMLInfoFromEMDB(self.params['emdbid'])
File "/opt/myamisnap/bin/modelFromEMDB.py", line 85, in getXMLInfoFromEMDB
tmpfile = urllib.urlretrieve(xmlurl)[0]
File "/usr/lib64/python2.6/urllib.py", line 93, in urlretrieve
return _urlopener.retrieve(url, filename, reporthook, data)
File "/usr/lib64/python2.6/urllib.py", line 239, in retrieve
fp = self.open(url, data)
File "/usr/lib64/python2.6/urllib.py", line 207, in open
return getattr(self, name)(url)
File "/usr/lib64/python2.6/urllib.py", line 524, in open_ftp
host = socket.gethostbyname(host)
IOError: [Errno socket error] [Errno -3] Temporary failure in name resolution

Example of PDB to Model error:

Job: pdb4V6X-15aug24i30.appionsub.job (ID: 91)
name: pdb4V6X-15aug24i30.appionsub.job
user: eeng
appion path: /emg/data00/appion/eeng/aferguson/15jun25a/models/pdb/pdb4V6X-15aug24i30
submit time: 2015-08-24 08:31:18
status: Done
Show last lines of log file

pdb4V6X-15aug24i30.appionsub.log:

... Time stamp: 15aug24i31
... Function name: modelFromPDB
... Appion directory: /opt/myamisnap/lib
... Using split database
Connected to database: 'nyap_24'
... Committing data to database
... Looking up symmetry for input: 1
... Selected symmetry group: C1 -- C1
... Looking up session, 15jun25a
... Run directory: /emg/data00/appion/eeng/aferguson/15jun25a/models/pdb/pdb4V6X-15aug24i30
!!! WARNING: directory '/emg/data00/appion/eeng/aferguson/15jun25a/models/pdb/pdb4V6X-15aug24i30'
already exists.
... Writing function log to: modelFromPDB.log
... Uploading ScriptData....
... Found 1 processors on this machine
... Running Appion version 'trunk'
Naming PDB model: /emg/data00/appion/eeng/aferguson/15jun25a/models/pdb/pdb4V6X-15aug24i30/pdb4V6X-15aug24i31

... retrieving pdb file: http://www.rcsb.org/pdb/files/4V6X.pdb1.gz
Traceback (most recent call last):
File "/opt/myamisnap/bin/modelFromPDB.py", line 311, in
pdbmodel.start()
File "/opt/myamisnap/bin/modelFromPDB.py", line 281, in start
pdbfile = self.fetchPDB()
File "/opt/myamisnap/bin/modelFromPDB.py", line 171, in fetchPDB
g = gzip.open(data, 'r').read()
File "/usr/lib64/python2.6/gzip.py", line 212, in read
self._read(readsize)
File "/usr/lib64/python2.6/gzip.py", line 255, in _read
self._read_gzip_header()
File "/usr/lib64/python2.6/gzip.py", line 156, in _read_gzip_header
raise IOError, 'Not a gzipped file'
IOError: Not a gzipped file