Leginon

Hello,

we are having trouble running FindEM through Appion.

Traceback (most recent call last):

  File "/usr/local/bin/appion/templateCorrelator.py", line 8, in <module>

    imgLoop.run()

  File "/usr/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 90, in run

    results = self.loopProcessImage(imgdata)

  File "/usr/lib/python2.6/site-packages/appionlib/particleLoop2.py", line 104, in loopProcessImage

    self.peaktree = filterLoop.FilterLoop.loopProcessImage(self, imgdata)

  File "/usr/lib/python2.6/site-packages/appionlib/filterLoop.py", line 87, in loopProcessImage

    peaktree = self.processImage(imgdata, self.filtarray)

  File "/usr/lib/python2.6/site-packages/appionlib/apTemplateCorrelator.py", line 169, in processImage

    cclist = self.runTemplateCorrelator(imgdata)

  File "/usr/lib/python2.6/site-packages/appionlib/apTemplateCorrelator.py", line 141, in runTemplateCorrelator

    ccmaplist = apFindEM.runFindEM(imgdata, self.params, thread=self.params['threadfindem'])

  File "/usr/lib/python2.6/site-packages/appionlib/apFindEM.py", line 171, in runFindEM

    apDisplay.printError("findem.exe did not run or crashed.\n")

  File "/usr/lib/python2.6/site-packages/appionlib/apDisplay.py", line 62, in printError

    raise Exception, colorString("\n *** FATAL ERROR ***\n"+text+"\n\a","red")

Exception: 

 *** FATAL ERROR ***

findem.exe did not run or crashed.

Looking at the apFindEM.py file I see the program should be executed on line 58, but on line 57 there is a sys.exit()

for i, templatename in enumerate(params['templatelist']):
        classavg = i + 1

        # First round: normal findem: template x image
        numstr = "%03d" % (100 + classavg)
        ccmapfile1 = "cccmaxmap" + numstr + ".mrc" 
        apFile.removeFile(ccmapfile1)
        params["startang" + str(100 + classavg)] = params["startang" + str(classavg)]
        params["endang" + str(100 + classavg)] = params["endang" + str(classavg)]
        params["incrang" + str(100 + classavg)] = params["incrang" + str(classavg)]
        if len(dwnimgname) > 76:
            feed = findEMString(100 + classavg, templatename, randlink, ccmapfile1, params)
        else:
            feed = findEMString(100 + classavg, templatename, dwnimgname, ccmapfile1, params)
        sys.exit()
        execFindEM(feed)

Am I correct in thinking this is a mistake or am I not understanding what this is doing (Which is quite possible)

Thank you

Chris Lilienthal