Folder Arrangement in EMAN2.1 projects
When using e2projectmanager.py and following canonical EMAN2.1 procedures, your data will be contained within a "project" with a very specific organization. For things to work properly you must not break this organization. If you are just running EMAN2 command-line programs yourself, and are not using the projectmanager or other GUI tools, you can do what you like, of course, but regardless we strongly suggest following the canonical structure.
Note: It is critical when running command-line programs within a project that you run them from the project folder, not from subfolders. For example, if you are in the particles folder, then try to build a set by referencing ../sets you can create all sorts of havoc.
A project directory will normally contain these folders, and some other (unlisted) files:
info/ particles/ micrographs/ (optional) sets/ multi_xx r2d_xx refine_xx
The particles/ folder will contain files like:
01252014_AE_100__ctf_flip.hdf 01252014_AE_100__ctf_flip_hp.hdf 01252014_AE_100__ctf_wiener.hdf 01252014_AE_100_ptcls.hdf 01252014_AE_101__ctf_flip.hdf 01252014_AE_101__ctf_flip_hp.hdf 01252014_AE_101__ctf_wiener.hdf 01252014_AE_101_ptcls.hdf
where the (double underscore) denotes modifications of the same set of particles. Sets/ will contain files like: and the contents of one of these .lst files will look like: Note that the references to individual particles are from the project folder. my_combine__ctf_flip_hp.lst
my_combine__ctf_flip.lst
my_combine__ctf_wiener.lst
my_combine_ptcls.lst
#LSX
# This file is in fast LST format. All lines after the next line have exactly the number of characters shown on the next line. This MUST be preserved if editing.
# 47
0 particles/01252014_AE_100_ptcls.hdf
1 particles/01252014_AE_100_ptcls.hdf
2 particles/01252014_AE_100_ptcls.hdf
3 particles/01252014_AE_100_ptcls.hdf
4 particles/01252014_AE_100_ptcls.hdf
5 particles/01252014_AE_100_ptcls.hdf