Appion

You get to this by:
1. running an eman reconstruction
2. Upload the recon
3. selecting the option to remove jumpers

Here is a sample command:
makegoodaverages.py --reconid=1 --iter=4 --mask=100 --hard=25 --stackname=goodavgs.hed --make3d=threed.mrc --zoom=1 --mass=375 --avgjump=0 --eotest --rundir=/ami/data00/appion/10sep01b/recon/emanrecon4/eulers/refine4_10oct14o45 --runname=refine4_10oct14o45 --projectid=274 --expId=7989 --jobtype=makegoodavg

It will be very important to note that the default value for avgjump is 0. This will most likely not return any particles and the function will fail to produce results. read #947 for more information.