|
⇤ ← Revision 1 as of 2019-03-16 18:04:21
Size: 2060
Comment:
|
Size: 2566
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = Important Facts = | = Important Information = |
| Line 4: | Line 4: |
| * When doing single particle reconstruction, tomography or subtomogram averaging, 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. * EMAN2 can read/write just about any [[Eman2DataStorage|image file format]], but for internal use [[Eman2HDF|HDF5 files]] are used for image data, and [[Eman2InfoMetadata|JSON files]] are used for metadata. Do not try to force EMAN2 to use some other file format when going through a reconstruction workflow. Other file formats are for import/export only. JSON files are primarily in the info/ folder, and are human readable, but also try ''e2procjson.py''. * HDF5 files may contain a variety of [[Eman2Metadata|header information]], which can be easily accessed using the "Info" button in ''e2display.py'' or using ''e2iminfo.py''. |
* 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". * EMAN2 can read/write just about any [[Eman2DataStorage|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 [[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. |
| Line 11: | Line 14: |
| * Choosing the correct particle [[EMAN2/BoxSize|box-size]] is critical for getting optimal results! | * There are special considerations if working in [[EMAN2/NegativeStain|Negative Stain]] * Choosing the correct particle [[EMAN2/BoxSize|box-size]] is critical for getting optimal results |
| Line 16: | Line 20: |
| * 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. |
Important Information
For Everyone
EMAN2 makes use of a 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".
EMAN2 can read/write just about any image file format, but for projects, HDF5 files are used for image data, and 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 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 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
EMAN2 has many 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.
Single Particle Reconstruction
There are special considerations if working in Negative Stain
Choosing the correct particle box-size is critical for getting optimal results
EMAN2 supports all of the possible symmetries for biomolecules: cN,dN,tet,oct,icos,hA:B:C:D:E
.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.
Tomography
The 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 processing pipeline, starting with the raw tilt series, be completed in EMAN2.