= Important Information =

== For Everyone ==
 * '''Working with Images''' - EMAN2 has '''many''' [[EMAN2/Modular/Overview|general image processing methods]], and the list is continuously expanding. Use ''e2help.py'' to get lists of the different operations, then use them with ''e2proc2d.py'', ''e2proc3d.py'' or ''e2filtertool.py''.
 * '''Help''' - You can give any program the ''--help'' option for general usage information and a list of command-line options.
 * '''EMAN2 Folders''' - EMAN2 makes use of a [[EMAN2/DirectoryStructure|project folder system]]. You create a folder for a particular project and run ALL EMAN2 commands from that folder. EMAN2 will make and manage subfolders for you, but you should NOT 'cd' into those subfolders when running commands.
  * This does not apply to running utility programs like e2proc* programs outside the context of a "project".
 * '''File Formats''' - EMAN2 can read/write just about any [[EMAN2/ImageFormats|image file format]], but for projects, [[Eman2HDF|HDF5 files]] are used for image data, and [[Eman2InfoMetadata|JSON files]] are used for metadata. 
  * JSON files are primarily in the info/ folder, and are human readable, but also try ''e2procjson.py''.
  * HDF5 files may contain a variety of [[EMAN2/Eman2Metadata|header information]], which can be easily accessed using the "Info" button in ''e2display.py'' or using ''e2iminfo.py''.
  * Do not try to force EMAN2 to use some other file format when going through a reconstruction workflow. When going through a standard workflow, other file formats are for import/export only. 
 * '''LST files''' - [[Eman2OtherFiles|.lst]] files are normally found only in sets/ folders. These are text files containing links to actual image data, somewhat similar to the STAR files used in other packages. However, EMAN2 will treat .lst files as actual image files for most purposes. Try ''e2proclst.py --help''

== Single Particle Reconstruction ==
 * '''Symmetry''' - EMAN2 supports all of the possible [[EMAN2/Symmetry|symmetries for biomolecules]]: cN,dN,tet,oct,icos,hA:B:C:D:E
 * '''Box Size''' - Choosing the correct particle [[EMAN2/BoxSize|box-size]] is critical for getting optimal results
 * '''Box Files''' - [[Eman2OtherFiles|.box]] files are not used internally by EMAN2. They may be imported or exported, but particle locations for EMAN2 use are stored in info/*.json files.
 * '''Negative Stain''' - There are special considerations if working in [[EMAN2/NegativeStain|Negative Stain]]
 * '''Simulated Data''' - For testing purposes, and to better understand how the programs work, it is possible to make [[EMAN2/SimulatedData|simulated single particle data]]

== Tomography ==
 * The [[EMAN2/Programs/tomoseg|semi-automated tomogram annotation tool]] can be used on tomograms from any source
 * The new tomography workflow can achieve subnanometer resolution subtomogram averaging, but requires that the full [[EMAN2/e2tomo|processing pipeline]], starting with the raw tilt series, be completed in EMAN2.