search

leginon-org / leginon-redmine-archive

1 stars 0 forks source link

Download map from EMDB does not work for certain model #533

Open leginonbot opened 8 months ago

leginonbot commented 8 months ago

Author Name: Pick-Wei Lau (Pick-Wei Lau) Original Redmine Issue: 533, https://emg.nysbc.org/redmine/issues/533 Original Date: 2010-05-21 Original Assignee: Pick-Wei Lau

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

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2010-05-24T14:51:28Z

Made a more robust XML parsing code.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Pick-Wei Lau (Pick-Wei Lau) Original Date: 2010-06-16T22:00:01Z

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:
FATAL ERROR Could not find file: apChimSnapshot.py

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2010-06-16T22:51:19Z

You are experiencing Bug #609. Try again or tell Christopher to update the code.

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Pick-Wei Lau (Pick-Wei Lau) Original Date: 2010-06-17T15:34:43Z

I'm getting an error with apChimSnapshot. It might be that the code is not updated yet. Can you look into it?

leginonbot commented 8 months ago

Original Redmine Comment Author Name: Christopher Irving (Christopher Irving) Original Date: 2010-06-21T18:19:29Z

Guppy and Goby are both running myami 2.0.1 now which is supposed to fix this problem.

-C