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Bug #5405

closed

Rubinstein particle alignment web gui did not validate stack nor ddstack

Added by Zhening Zhang almost 7 years ago. Updated almost 7 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Carl Negro
Category:
-
Target version:
-
Start date:
01/02/2018
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.3
Show in known bugs:
No
Workaround:

Description

I submit a job to do a per particle alignment in Appion. I got these error msg:

[zzhang@SEMC-head micrographs_hd]$ /opt/myamisnap/bin/appion polishStack.py --commit --micrographs_per_job=30 --particleradius=200 --expweight --localavg --localavgsigma=500 --framefirstali=0 --framefirstave=0 --smooth=1.0 --exaggerate=10 --rmax1=500 --rmax2=20 --bfactor=2000 --runname=rpp1 --rundir=/gpfs/appion/afeklistov/17dec20a/rpp/rpp1 --projectid=333 --expid=5605 --jobtype=particlepolishing

... Time stamp: 18jan02n48
... Function name: polishStack
... Appion directory: /opt/myamisnap/lib
... Processing hostname: SEMC-head
... Using split database
Connected to database: 'nyap_333'
... Committing data to database
... Using split database
Connected to database: 'nyap_333'
Traceback (most recent call last):
File "/opt/myamisnap/bin/polishStack.py", line 428, in <module>
polisher = stackPolisherScript()
File "/opt/myamisnap/lib/appionlib/appionScript.py", line 85, in init
self.checkConflicts()
File "/opt/myamisnap/bin/polishStack.py", line 97, in checkConflicts
apDisplay.printError("stackid was not defined")
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 65, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception:
  • FATAL ERROR ***
    stackid was not defined
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 #1

Updated by Anchi Cheng almost 7 years ago

  • Status changed from New to Assigned
  • Assignee set to Carl Negro
  • Priority changed from Urgent to Normal
  • Affected Version changed from Appion/Leginon 3.2 to Appion/Leginon 3.3

This program requires an unaligned but gain-corrected movie stack as well as particle coordinate.

Zhening, You will need to run MotionCor-Purdue but uncheck the "align" checkbox to generate the former.

Carl, please write validation that prevent people from constructing the command if there is no required movie stack.

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 #2

Updated by Anchi Cheng almost 7 years ago

  • Subject changed from John Rubinstein particle alignment to Rubinstein particle alignment web gui did not validate stack nor ddstack
  • Status changed from Assigned to Closed

added validation for unaligned ddstackid requirement in 0b356f84

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