|
Size: 1178
Comment:
|
Size: 2843
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 2: | Line 2: |
| '''''Under Construction''''' | |
| Line 4: | Line 3: |
| proc2d == This program performs various processing operations on images and sets of images (WARNING: auto normalization removed) == == Usage: == proc2d 3244.img start.hed invert apix=5 lp=18 |
''There are over 200 command-line programs in EMAN, this list contains more detailed documentation for the most commonly used programs. See the fixed documentation for a full list.'' |
| Line 9: | Line 5: |
| proc2d start.hed start.hed invert inplace | '''GUI Programs''' ||[wiki:/Eman eman]||Image browser and tutorial interface|| ||[wiki:/Boxer boxer]||Manual particle picking|| ||[wiki:/CTFit ctfit]||CTF parameter determination and simulation|| ||[wiki:/V4 v4]||Viewing 3-D models in projection|| ||[wiki:/QSegment qsegment]||Interactive slice-by-slice 3D model segmentation|| ||[wiki:/QIndex qindex]||2D crystal preprocessing and evaluation|| ||[wiki:/HelixBoxer helixboxer]||Program for picking and evaluating non-square 'boxes'|| |
| Line 11: | Line 14: |
| == Description == IMPORTANT NOTE: proc2d no longer automatically normalizes output images. Use the 'norm' or 'edgenorm' flag to re-enable this. |
'''Refinement Programs''' ||[wiki:/Refine2D refine2d.py]||Make high-quality 2-D class-averages from stacks of raw particle images|| ||[wiki:/Refine refine]||3-D model refinement|| ||[wiki:EoTest eotest]||Even/odd data split for resolution evaluation after refinement|| ||[wiki:/MultiRefine multirefine]||Simultaneous multiple model 3-D refinement|| |
| Line 14: | Line 20: |
| This program is used to perform a variety of generic 2D image processing tasks. Like all of the EMAN programs, it will read any supported file format. By default it outputs to an Imagic file although there are options to change this. Note that, by default, images are appended to the end of the output file if it already exists. All images in one file MUST have the same size. ie - if you try to copy 50x50 images to the end of a file that already contains 100x100 images, an error will result. Note the 'first=' and 'last=' options allow a subset of the input file to be processed. The 'inplace' keyword may be used to cause output images to overwrite the input images rather than being appended to the end of the file. | '''Utility Programs''' ||[wiki:/Proc2D proc2d]||Generic 2-D image processing|| ||[wiki:/Proc3D proc3d]||Generic 3-D image processing|| ||[wiki:/ProcPDB procpdb.py]||Simple PDB file manipulation|| ||[wiki:/ImInfo iminfo]||Dump information about image files|| ||[wiki:/SpeedTest speedtest]||Simple application-specific computer benchmarking program|| ||[wiki:LstCat lstcat.py]||Generate pseudoimage text files|| ||[wiki:LstFast lstfast.py]||Optimize pseudoimage files for rapid access|| ||[wiki:PdbToMrc pdbtomrc]||Convert PDB files to MRC density maps|| '''Refinement-related Processing''' ||[wiki:/BatchBoxer batchboxer]||Command-line automatic particle picking and box manipulation|| ||[wiki:/FitCtf fitctf]||Automatic CTF parameter determination|| ||[wiki:/ApplyCtf applyctf]||Perform phase flipping and other CTF-correction operations|| ||[wiki:MakeInitialModel makeinitialmodel.py]||Interactive script for generating initial models out of Gaussian blobs|| ||[wiki:StartCSym startcsym]||Generate initial models from data with Cn and Dn symmetries|| ||[wiki:StartIcos starticos]||Generate initial models from data with icosahedral (532) symmetry|| ||[wiki:StartOct startoct||Generate an initial model from data with octahedral (432) symmetry|| ||[wiki:StartAny startAny]||Initial model generation using common-lines. Usually a bad idea...|| '''AIRS Tools (Analysis of Intermediate Resolution Structures)''' ||[wiki:/FoldHunter foldhunter.py]||Dock a PDB file or density segment in a 3-D reconstruction|| ||[wiki:/SseHunter ssehunter.py]||Identify/locate secondary structural elements in subnanometer resolution reconstructions|| ||[wiki:/HelixHunter helixhunter.py]||Program to locate alpha-helices in subnanometer resolution reconstructions|| |
EMAN1 Individual Programs
There are over 200 command-line programs in EMAN, this list contains more detailed documentation for the most commonly used programs. See the fixed documentation for a full list.
GUI Programs
[wiki:/Eman eman] |
Image browser and tutorial interface |
[wiki:/Boxer boxer] |
Manual particle picking |
[wiki:/CTFit ctfit] |
CTF parameter determination and simulation |
[wiki:/V4 v4] |
Viewing 3-D models in projection |
[wiki:/QSegment qsegment] |
Interactive slice-by-slice 3D model segmentation |
[wiki:/QIndex qindex] |
2D crystal preprocessing and evaluation |
[wiki:/HelixBoxer helixboxer] |
Program for picking and evaluating non-square 'boxes' |
Refinement Programs
[wiki:/Refine2D refine2d.py] |
Make high-quality 2-D class-averages from stacks of raw particle images |
[wiki:/Refine refine] |
3-D model refinement |
[wiki:EoTest eotest] |
Even/odd data split for resolution evaluation after refinement |
[wiki:/MultiRefine multirefine] |
Simultaneous multiple model 3-D refinement |
Utility Programs
[wiki:/Proc2D proc2d] |
Generic 2-D image processing |
[wiki:/Proc3D proc3d] |
Generic 3-D image processing |
[wiki:/ProcPDB procpdb.py] |
Simple PDB file manipulation |
[wiki:/ImInfo iminfo] |
Dump information about image files |
[wiki:/SpeedTest speedtest] |
Simple application-specific computer benchmarking program |
[wiki:LstCat lstcat.py] |
Generate pseudoimage text files |
[wiki:LstFast lstfast.py] |
Optimize pseudoimage files for rapid access |
[wiki:PdbToMrc pdbtomrc] |
Convert PDB files to MRC density maps |
Refinement-related Processing
[wiki:/BatchBoxer batchboxer] |
Command-line automatic particle picking and box manipulation |
[wiki:/FitCtf fitctf] |
Automatic CTF parameter determination |
[wiki:/ApplyCtf applyctf] |
Perform phase flipping and other CTF-correction operations |
[wiki:MakeInitialModel makeinitialmodel.py] |
Interactive script for generating initial models out of Gaussian blobs |
[wiki:StartCSym startcsym] |
Generate initial models from data with Cn and Dn symmetries |
[wiki:StartIcos starticos] |
Generate initial models from data with icosahedral (532) symmetry |
[wiki:StartOct startoct |
Generate an initial model from data with octahedral (432) symmetry |
[wiki:StartAny startAny] |
Initial model generation using common-lines. Usually a bad idea... |
AIRS Tools (Analysis of Intermediate Resolution Structures)
[wiki:/FoldHunter foldhunter.py] |
Dock a PDB file or density segment in a 3-D reconstruction |
[wiki:/SseHunter ssehunter.py] |
Identify/locate secondary structural elements in subnanometer resolution reconstructions |
[wiki:/HelixHunter helixhunter.py] |
Program to locate alpha-helices in subnanometer resolution reconstructions |