I put in a fix in apFindEM.py, which creates a soft link inside the directory using a random 10-letter filename, then feeds that link into FindEM. Everything else in the directory is the same.
The code was tested using a single, long micrograph in directory: /ami/exdata/appion/12dec03f/extract/test_Dmitry
Amber: please review code.
Julia: You should be able to use / test the fix tomorrow (February 13), when it gets updated on the nightly build. If you would like to test it on a single micrograph, you could use the command below (note that currently the --runname and --rundir options are set to --runname=test_fix, --rundir=/ami/exdata/appion/12dec03f/extract/test_fix)
/opt/myami-2.2/bin/appion templateCorrelator.py --projectid=377 --session=12dec03f --runname=test_fix --rundir=/ami/exdata/appion/12dec03f/extract/test_fix --no-rejects --no-wait --no-commit --continue --maxsize=0.05 --peaktype=centerofmass --maxthresh=0.8 --thresh=0.35 --median=2 --lowpass=15 --highpass=0 --planereg --bin=4 --diam=190 --pixlimit=2.0 --template-list=22,21 --range-list=0,180,10x0,180,10 --thread-findem --use-mirrors --expId=10743 -m 12dec03f_Prj377_Keap1-50ug-ml-thincarbon_i001_00054sq_v01_00002hl_v01_00002en.mrc
Otherwise, just make another jobfile and run the template correlator as usual.