Bug #533: Download map from EMDB does not work for certain model - Appion - Electron Microscopy Group

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Bug #533

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Download map from EMDB does not work for certain model

Added by Pick-Wei Lau almost 14 years ago. Updated almost 14 years ago.

Status:

In Test

Priority:

Normal

Assignee:

Pick-Wei Lau

Category:

Python scripting

Target version:

Appion/Leginon 2.0.0

Start date:

05/21/2010

Due date:

% Done:

100%

Estimated time:

Affected Version:

Appion/Leginon 2.0.1

Show in known bugs:

Workaround:

Description

I tried downloading different models:

My dicer model EMD-1646 gave this error

... retrieving emdb XML file: ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1646/header/emd-1646.xml

Traceback (most recent call last):
File "/opt/appion/bin/modelFromEMDB.py", line 207, in ?
emdbmodel.start()
File "/opt/appion/bin/modelFromEMDB.py", line 179, in start
self.getXMLInfoFromEMDB(self.params['emdbid'])
File "/opt/appion/bin/modelFromEMDB.py", line 98, in getXMLInfoFromEMDB
apDisplay.printMsg("file has a pixel size of .3f A/pix"(apix))
UnboundLocalError: local variable 'apix' referenced before assignment

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Updated by Neil Voss almost 14 years ago

Category set to Python scripting
Target version set to Appion/Leginon 2.0.0

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Updated by Neil Voss almost 14 years ago

Status changed from New to In Code Review
Assignee set to Amber Herold

Made a more robust XML parsing code.

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Updated by Amber Herold almost 14 years ago

Status changed from In Code Review to In Test
Assignee changed from Amber Herold to Pick-Wei Lau
% Done changed from 0 to 100

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Updated by Pick-Wei Lau almost 14 years ago

Assignee changed from Pick-Wei Lau to Neil Voss
Affected Version set to Appion/Leginon 2.0.1

I'm getting an error with apChimSnapshot

Traceback (most recent call last):
File "/opt/appion/bin/modelFromEMDB.py", line 209, in ?
emdbmodel.start()
File "/opt/appion/bin/modelFromEMDB.py", line 200, in start
apChimera.renderSnapshots(mrcname, contour=1.0, zoom=1.0, sym=self.params['symdata']['eman_name'])
File "/usr/lib64/python2.4/site-packages/appionlib/apChimera.py", line 208, in renderSnapshots
chimsnappath = getSnapPath()
File "/usr/lib64/python2.4/site-packages/appionlib/apChimera.py", line 31, in getSnapPath
apDisplay.printError("Could not find file: apChimSnapshot.py")
File "/usr/lib64/python2.4/site-packages/appionlib/apDisplay.py", line 56, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: