Appion

This feature needs workaround while in Appion 2.2. This will not be necessary once 3.0 is released

Appion 2.2 assumes the use of default installation of CentOS 5 with python 2.4 and EMAN 1.
DDprocess needs python 2.6 included in CentOS 6. However, EMAN 1 suffers a library problem found in CentOS 6.2 (current release) so that it creates corrupted particle stacks.

Th workaround is the following:
1. Run makestack2.py from command line on a computer with python 2.6 and associated libraries (tifffile) with --commit and --saveall to commit the particles in the database while leave the *.down.mrc that are gain-corrected frame integrated dd images.

For example:
makestack2.py --single=start.hed --selectionid=23 --no-invert --boxsize=400 --description="example" --projectid=333 --preset=ed --session=12mar26c --runname=stack10 --rundir=/data/appion/12mar26c/stacks/stack10 --no-rejects --no-wait --commit --ddstartframe=5 --ddnframe=10 --continue --expId=9731 --jobtype=makestack2 --saveall

2. Change to a computer where EMAN 1 works properly (CentOS 5) and go to the directory of the run,
3. Remove the files of the following wild card: "*.donedict" and "start.*" This way you can rerun the same command without adding extra particles into the database and stack file.
4. Rerun the same makestack2.py command (You may find a log of it in makestack2.log) with these modifications:

• change --commit to --no-commit
• add option --usedownmrc

For example:
makestack2.py --single=start.hed --selectionid=23 --no-invert --boxsize=400 --description="example" --projectid=333 --preset=ed --session=12mar26c --runname=stack10 --rundir=/data/appion/12mar26c/stacks/stack10 --no-rejects --no-wait --no-commit --ddstartframe=5 --ddnframe=10 --continue --expId=9731 --jobtype=makestack2 --saveall --usedownmrc

Code changes required for this workaround is committed as r16537 in trunk and merged to 2.2 branch as r16541