Appion

We are trying to run topology alignment at Northwestern and we do not have a copy of IMAGIC.

The classification crashed at the end of the last iteration, presumably during generating the final unmasked averages.

topologyAlignment.py \
  --projectid=8 --rundir=15may20a/align/topol1 \
  --description=meanfilt6_109to433_mask30 --runname=topol1 --stack=8 \
  --lowpass=10 --highpass=2000 --num-part=186947 --start=109 \
  --end=433 --bin=1 --mask=30 --iter=5 --itermul=10 --learn=0.01 \
  --ilearn=0.0005 --age=25 --mramethod=eman --msamethod=can --nproc=16 \
  --msaproc=8 --premask --classiter --commit --expid=205 --jobtype=partalign 

Traceback (most recent call last):
  File "/tank/software/myami-3.1/appion/bin/topologyAlignment.py", line 1129, in <module>
    topRep.start()
  File "/tank/software/myami-3.1/appion/bin/topologyAlignment.py", line 1104, in start
    imagicFilters.takeoverHeaders("mrastack",self.params['numpart'],self.workingboxsize)
  File "/tank/software/myami-3.1/appion/appionlib/apImagic/imagicFilters.py", line 22, in takeoverHeaders
    myIm = pymagic.ImagicSession("stand/testim.e")
  File "/tank/software/myami-3.1/appion/appionlib/pymagic.py", line 51, in __init__
    apDisplay.printError("$IMAGIC_ROOT directory is not specified, please specify this in your .cshrc / .bashrc")
  File "/tank/software/myami-3.1/appion/appionlib/apDisplay.py", line 65, in printError
    raise Exception, colorString("\n *** FATAL ERROR ***\n"+text+"\n\a","red")
Exception: 
 *** FATAL ERROR ***
$IMAGIC_ROOT directory is not specified, please specify this in your .cshrc / .bashrc

Even when using the flags, "--mramethod=eman --msamethod=can" it still uses IMAGIC at the end. Is there any way around this?