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Bug #997

open

EMDB to Model memory error

Added by Lauren Fisher about 14 years ago. Updated about 14 years ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
Appion/Leginon Future Version
Start date:
11/04/2010
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Download the EMDB, bin by a factor using itp, convert map back to mrc using tomrc, move map to /ami/data00/temp, then "Upload Model" in Appion.

Description

EMDB to Model fails to properly upload structures that are "very large". The job either crashes due to a memory error or the model density is inverted (i.e. the threshold is negative, and the structure is inside a box when viewed in chimera).

****Example output from /ami/data00/appion/10oct21z/models/emdb/emdb1571-10nov03o02/emdb1571-10nov03o02.appionsub.log:

!!! WARNING: Volume is very large
EMAN 1.9 Cluster ($Date: 2009/02/18 05:12:22 $).
Run '/usr/local/EMAN/bin/volume help' for detailed help.
Min=-2.739318 Max=4.777329 Mean=-0.000000 Sigma=1.000000 Threshold=1.000000

Threshold Mass
1.000000 25473.826080
1.000000 25473.826080
-2.750000 25473.826080
-2.750000 25473.826080
-2.750000 25473.826080
-2.750000 25473.826080
-2.750000 25473.826080
-2.750000 25473.826080
-2.750000 25473.826080

Image has been modified so threshold=1 is 25473.83 kDa
... finished scaling by mass in 1 min 55 sec
!!! WARNING: Volume is very large

****Example command line output from /ami/data00/appion/10oct21z/models/emdb/emdb1571-10nov04k27/modelFromEMDB.log:

... retrieving emdb file: ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1571/map/emd_1571.map.gz
Traceback (most recent call last):
File "/ami/sw/packages/myami-2.1/appion/bin/modelFromEMDB.py", line 214, in ?
emdbmodel.start()
File "/ami/sw/packages/myami-2.1/appion/bin/modelFromEMDB.py", line 181, in start
emdbfile = self.fetchEMDB(self.params['emdbid'], ccp4name)
File "/ami/sw/packages/myami-2.1/appion/bin/modelFromEMDB.py", line 133, in fetchEMDB
g = gzip.open(data,'r').read()
File "/usr/lib64/python2.4/gzip.py", line 218, in read
self._read(readsize)
File "/usr/lib64/python2.4/gzip.py", line 278, in _read
self._add_read_data( uncompress )
File "/usr/lib64/python2.4/gzip.py", line 295, in _add_read_data
self.extrabuf = self.extrabuf + data
MemoryError

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